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

Abstract

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.

Genome engineering of Nannochloropsis with hundred‐kilobase fragment deletions by Cas9 cleavages

“…also feature extensive omics resources for functional assessment of chromosomal regions genome‐wide. For example, in Nannochloropsis oceanica IMET1, which is an industrial strain for both TAG and EPA, rich resources are available for genomic (Gong et al ., 2020; Wang et al ., 2014a; Wei et al ., 2013), transcriptomic (Hu et al ., 2014; Jia et al ., 2015; Li et al ., 2014; Wei et al ., 2019a; You et al ., 2020), proteomic (Chen et al ., 2019; Dong et al ., 2013; Wei et al ., 2019a; You et al ., 2020), lipidomic (Jia et al ., 2015; Li et al ., 2014) as well as physiological data (Han et al ., 2017; He et al ., 2017; Lu et al ., 2014; Wang et al ., 2014b; Xiao et al ., 2015). Taking advantage of these resources, we employed this strain to establish a method to precisely and serially delete large genome fragments of ~100 kb from its 30.01 Mb nuclear genome.…”

The NanDeSyn database for Nannochloropsis systems and synthetic biology

“…Moreover, complete plastid and mitochondrial genomes have been reported for several Nannochloropsis species (Wei et al ., 2013). Additional functional resources have also been recently developed, such as transcriptomic data for N. oceanica , including IMET1 (Li et al ., 2014; Wei et al ., 2019a, 2020; You et al ., 2020) and CCMP1779 (Vieler et al ., 2012; Poliner et al ., 2015; Mühlroth et al ., 2017), N. gaditana B‐31 (Corteggiani Carpinelli et al ., 2014) and CCMP526 (Radakovits et al ., 2012), N. salina CCMP1776 (Jeong et al ., 2017) and proteomic data for N. oceanica IMET1 (Chen et al ., 2019; Wei et al ., 2019a) and N. gaditana (Fernández‐Acero et al ., 2019). These resources are of value in dissecting metabolic pathways and identifying targets for genetic engineering.…”