Omics in Chlamydomonas for Biofuel Production

Aucoin, Hanna R.; Gardner, Joseph J.; Boyle, Nanette R.

doi:10.1007/978-3-319-25979-6_18

Cited by 14 publications

(6 citation statements)

References 89 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To investigate the interactions between transcriptomes and proteomes, the common approach is point-topoint comparative analysis: i.e., the transcriptome is compared to the proteome at the same time point [19,85]. However, Abraham's paper revealed a temporal delay in the expression of proteins related to transcription, and proposed a "shift" method to investigate the relationship between them [40].…”

Section: Comparison Of Transcriptome and Proteome Using K-shape Approachmentioning

confidence: 99%

Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica

You

Wei

Gong

et al. 2020

Biotechnol Biofuels

View full text Add to dashboard Cite

Background: Under nitrogen deficiency situation, Nannochloropsis spp. accumulate large amounts of lipids in the form of triacylglycerides (TAG). Mechanisms of this process from the perspective of transcriptome and metabolome have been obtained previously, yet proteome analysis is still sparse which hinders the analysis of dynamic adaption to nitrogen deficiency. Here, proteomes for 3 h, 6 h, 12 h, 24 h, 48 h and 10th day of nitrogen deplete (N−) and replete (N+) conditions were obtained and integrated with previous transcriptome data for N. oceanica. Results: Physiological adaptations to N− not apparent from transcriptome data were unveiled: (a) abundance of proteins related to photosynthesis only slightly decreased in the first 48 h, indicating that photosynthesis is still working efficiently, and protein amounts adjust gradually with reduction in chloroplast size. (b) Most proteins related to the TCA cycle were strongly upregulated after 48 h under N−, suggesting that respiration is enhanced after 48 h and that TCA cycle efflux supports the carbon required for lipid synthesis. (c) Proteins related to lipid accumulation via the Kennedy pathway increased their abundance at 48 h, synchronous with the previously reported diversification of fatty acids after 48 h. Conclusions: This study adds a proteome perspective on the major pathways for TAG accumulation in Nannochloropsis spp. Temporal changes of proteome exhibited distinct adaptation phases that are usually delayed relative to transcriptomic responses. Notably, proteome data revealed that photosynthesis and carbon fixation are still ongoing even after 48 h of N−. Moreover, sometimes completely opposite trends in proteome and transcriptome demonstrate the relevance of underexplored post-transcriptional regulation for N− adaptation.

show abstract

Section: Comparison Of Transcriptome and Proteome Using K-shape Approachmentioning

confidence: 99%

Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica

You

Wei

Gong

et al. 2020

Biotechnol Biofuels

View full text Add to dashboard Cite

show abstract

“…Chlamydomonas has two polar flagella (10 μm body), a much bigger genome than Ostreococcus (120 Mb; Merchant et al, 2007) and lives in sweet water environments. Omics are currently intensely used to explore Chlamydomonas potential in biotechnological applications (Aucoin et al, 2016). As a representative Spermatophyte or seed plant, Arabidopsis has several characteristics that make it especially useful for Systems Biology studies in general and circadian experiments in particular, as well as a bigger genome and a complex physiology in comparison to microalgae (Van Norman and Benfey, 2009; Koornneef and Meinke, 2010).…”

Section: Introductionmentioning

confidence: 99%

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

et al. 2017

View full text Add to dashboard Cite

Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions.

show abstract

“…To investigate the interactions between transcriptomes and proteomes, the common approach is point-topoint comparative analysis: i.e. the transcriptome is compared to the proteome at the same time point [19,83]. However, Abraham's paper revealed a temporal delay in the expression of proteins related to transcription, and proposed a "shift" method to investigate the relationship between them [38].…”

Section: Comparison Of Transcriptome and Proteome Using K-shape Approachmentioning

confidence: 99%

Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica

You

Wei

Gong

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Under nitrogen deficiency situation, Nannochloropsis spp. accumulate large amounts of lipid in the form of triacylglycerides (TAG). Several researches have studied the mechanism of this process from the perspective of transcriptome and metabolome, yet proteome analysis on this process is still sparse and lacking the analysis of the dynamic adaption to nitrogen deficiency. Here, proteomes for 03h, 06h, 12h, 24h, 48h and 10th day of nitrogen deplete and replete conditions were compared. New proteome results were integrated with existing transcriptome and other data. Results: Obtained results illuminated physiological adaptations not deduced from previous transcriptome data: (a) Abundance of proteins related to photosynthesis only slightly decreased in the first 48h, indicating that photosynthesis is still working efficiently, and protein amounts adjust gradually with reduction in chloroplast size. (b) Most proteins related to the TCA cycle were strongly upregulated after 48h under nitrogen deficiency, suggesting that respiration is enhanced after 48h and that TCA cycle efflux supports the carbon required for lipid synthesis. (c) Proteins related to lipid accumulation via the Kennedy pathway increased their abundance at 48h, synchronous with the previously reported diversification of fatty acids after 48h. Conclusions: This study adds a proteome perspective on the major pathways for TAG accumulation by Nannochloropsis due to absence of nitrogen: photosynthesis, membrane lipid conversion, protein degradation, TCA cycle. By integrating existing transcriptome and other data, our research provided for Nannochloropsis oceanica a multi-layered description of adaptation to nitrogen limitation and lipid accumulation. Cluster analysis of this integrated dataset allowed inference of post-transcriptional regulation events.

show abstract

Omics in Chlamydomonas for Biofuel Production

Cited by 14 publications

References 89 publications

Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica

Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

Integration of proteome and transcriptome refines key molecular processes underlying oil production in Nannochloropsis oceanica

Contact Info

Product

Resources

About