Chen Xiao-Huang, Yang Ming-Kun, Li Yuan-Yuan, Xie Zhang-Xian, Zhang Shu-Feng, Töpel Mats, Amin Shady A, Lin Lin, Ge Feng, Wang Da-Zhi
State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, 361005 China.
Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Zhuhai, 519082 China.
Mar Life Sci Technol. 2023 Feb 3;5(1):102-115. doi: 10.1007/s42995-022-00161-y. eCollection 2023 Feb.
Diatoms are unicellular eukaryotic phytoplankton that account for approximately 20% of global carbon fixation and 40% of marine primary productivity; thus, they are essential for global carbon biogeochemical cycling and climate. The availability of ten diatom genome sequences has facilitated evolutionary, biological and ecological research over the past decade; however, a complimentary map of the diatom proteome with direct measurements of proteins and peptides is still lacking. Here, we present a proteome map of the model marine diatom using high-resolution mass spectrometry combined with a proteogenomic strategy. In-depth proteomic profiling of three different growth phases and three nutrient-deficient samples identified 9526 proteins, accounting for ~ 81% of the predicted protein-coding genes. Proteogenomic analysis identified 1235 novel genes, 975 revised genes, 104 splice variants and 234 single amino acid variants. Furthermore, our quantitative proteomic analysis experimentally demonstrated that a considerable number of novel genes were differentially translated under different nutrient conditions. These findings substantially improve the genome annotation of and provide insights into new biological functions of diatoms. This relatively comprehensive diatom proteome catalog will complement available diatom genome and transcriptome data to advance biological and ecological research of marine diatoms.
The online version contains supplementary material available at 10.1007/s42995-022-00161-y.
硅藻是单细胞真核浮游植物，约占全球碳固定量的20%和海洋初级生产力的40%；因此，它们对全球碳生物地球化学循环和气候至关重要。在过去十年中，十个硅藻基因组序列的可得性促进了进化、生物学和生态学研究；然而，仍然缺乏一个能直接测量蛋白质和肽的硅藻蛋白质组补充图谱。在这里，我们结合蛋白质基因组学策略，利用高分辨率质谱法展示了模式海洋硅藻的蛋白质组图谱。对三个不同生长阶段和三个营养缺乏样本的深度蛋白质组分析鉴定出9526种蛋白质，约占预测蛋白质编码基因的81%。蛋白质基因组分析鉴定出1235个新基因、975个修订基因、104个剪接变体和234个单氨基酸变体。此外，我们的定量蛋白质组分析通过实验证明，相当数量的新基因在不同营养条件下差异翻译。这些发现极大地改进了[具体硅藻名称未给出]的基因组注释，并为硅藻的新生物学功能提供了见解。这个相对全面的硅藻蛋白质组目录将补充现有的硅藻基因组和转录组数据，以推进海洋硅藻的生物学和生态学研究。
在线版本包含可在10.1007/s42995-022-00161-y获取的补充材料。
