title: De novo transcriptome profiling uncovers a drastic downregulation of photosynthesis upon nitrogen deprivation in the nonmodel green alga Botryosphaerella sudeticus.
abstract: BACKGROUND
  Neutral lipid storage is enhanced by nitrogen deprivation (ND) in numbers of green microalgal species. However, little is known about the metabolic pathways whose transcription levels are most significantly altered following ND in green microalgae, especially the nonmodel species.
  
  
  RESULTS
  To start gaining knowledge on this, we performed transcriptome profiling of the nonmodel green microalga Botryosphaerella sudeticus cells in response to ND. Transcriptome of B. sudeticus is de novo assembled based on millions of HiSEQ short sequence reads using CLC Genomics Workbench software. The resulting non-redundant ESTs are annotated based on the best hits generated from the BLASTX homology comparison against the "best" proteins in the model microalgae Chlamydomonas reinhardtii and Chlorella variabilis. By using a pathway-based approach according to KEGG databases, we show that ESTs encoding ribosomal proteins and photosynthetic functions are the most abundantly expressed ESTs in the rapidly growing B. sudeticus cells. We find that ESTs encoding photosynthetic function but not the ribosomal proteins are most drastically downregulated upon ND. Notably, ESTs encoding lipid metabolic pathways are not significantly upregulated. Further analyses indicate that chlorophyll content is markedly decreased by 3-fold and total lipid content is only slightly increased by 50%, consistent with the transcriptional profiling. On the other hand, carbon content and photosynthesis efficiency are only marginally decreased by 7% and 20%, respectively, indicating that photosynthesis is only slightly reduced upon drastic downregulation of photosynthetic ESTs and chlorophyll content upon ND. In addition, TAG content is found to be greatly increased by 50-fold, though total lipid content is only slightly increased by 1.5-fold.
  
  
  CONCLUSIONS
  Taken together, our results suggest that light-harvesting proteins and chlorophylls are in excess in B. sudeticus. Degradation of excess photosynthesis proteins is most likely a mechanism for recycling of nitrogen-rich molecules to synthesize new proteins for preparation of gametogenesis and zygospore formation in adaptation and survival upon ND. Furthermore, our analyses indicate that TAG accumulation is largely attributed to the modification of other pre-existing lipid molecules, rather than de novo synthesis. We propose that this is likely an evolutionarily conserved mechanism in many green microalgae species.
authors.forename: Deying
authors.initials: D
authors.lastname: Sun
authors.forename: Jiaqi
authors.initials: J
authors.lastname: Zhu
authors.forename: Lei
authors.initials: L
authors.lastname: Fang
authors.forename: Xin
authors.initials: X
authors.lastname: Zhang
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Chow
authors.affiliation: Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, #02-01, Singapore 138672, Singapore. liujh@gis.a-star.edu.sg.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Liu
mesh_terms: D000460:Chlorophyta / Q000235:genetics* / Q000378:metabolism*; D016000:Cluster Analysis; D004734:Energy Metabolism / Q000235:genetics; D020224:Expressed Sequence Tags; D005718:Gametogenesis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D050356:Lipid Metabolism; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D009584:Nitrogen / Q000378:metabolism*; D010788:Photosynthesis / Q000235:genetics*; D012269:Ribosomal Proteins / Q000235:genetics; D059467:Transcriptome
chemical_list: D012269:Ribosomal Proteins; D009584:Nitrogen