Faculty of Chemistry and Biology, University of Santiago of Chile, Av. Libertador Bernardo O'Higgins, 3363, Santiago, Chile.
Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.
BMC Genomics. 2018 Nov 20;19(1):829. doi: 10.1186/s12864-018-5226-4.
The marine alga Ulva compressa is the dominant species in coastal areas receiving effluents from copper mines. The alga can accumulate high amounts of copper and possesses a strong antioxidant system. Here, we performed short-term transcriptomic analyses using total RNA of the alga cultivated with 10 μM of copper for 0, 3, 6, 12 and 24 h by RNA-seq.
De novo transcriptomes were assembled using the Trinity software, putative proteins were annotated and classified using Blast2GO. Differentially expressed transcripts were identified using edgeR. Transcript levels were compared by paired times 0 vs 3, 0 vs 6, 0 vs 12 and 0 vs 24 h at an FDR < 0.01 and Log2 Fold Change > 2. Up-regulated transcripts encode proteins belonging to photosystem II (PSII), Light Harvesting II Complex (LHCII), PSI and LHCI, proteins involved in assembly and repair of PSII, and assembly and protection of PSI. In addition, transcripts encoding enzymes leading to β-carotene synthesis and enzymes belonging to the Calvin-Benson cycle were also increased. We further analyzed photosynthesis and carotenoid levels in the alga cultivated with 10 μM of copper for 0 to 24 h. Photosynthesis was increased from 3 to 24 h as well as the level of total carotenoids. The increase in transcripts encoding enzymes of the Calvin-Benson cycle suggests that C assimilation may also be increased.
Thus, U. compressa displays a short-term response to copper stress enhancing the expression of genes encoding proteins involved in photosynthesis, enzymes involved carotenoids synthesis, as well as those belonging to the Calvin-Benson cycle, which may result in an increase in C assimilation.
海洋藻类 U. compressa 是沿海地区的优势物种，这些地区的污水来自铜矿。该藻类可以积累大量的铜，并且具有强大的抗氧化系统。在这里，我们通过 RNA-seq 对用 10 μM 铜培养的藻类进行了为期 0、3、6、12 和 24 h 的短期转录组分析。
使用 Trinity 软件组装从头转录组，使用 Blast2GO 对推定蛋白进行注释和分类。使用 edgeR 鉴定差异表达的转录本。通过将配对时间 0 与 3、0 与 6、0 与 12 和 0 与 24 h 进行比较，确定转录本水平在 FDR<0.01 和 Log2 Fold Change >2 时存在差异。上调的转录本编码属于光系统 II（PSII）、光收集 II 复合物（LHCII）、PSI 和 LHCI 的蛋白质，参与 PSII 组装和修复以及 PSI 组装和保护的蛋白质。此外，编码导致β-胡萝卜素合成的酶和属于卡尔文-本森循环的酶的转录本也增加了。我们进一步分析了用 10 μM 铜培养的藻类在 0 至 24 h 内的光合作用和类胡萝卜素水平。从 3 小时到 24 小时，光合作用以及总类胡萝卜素水平都增加了。编码卡尔文-本森循环酶的转录本增加表明 C 同化也可能增加。
因此，U. compressa 对铜胁迫表现出短期响应，增强了参与光合作用、类胡萝卜素合成以及卡尔文-本森循环的蛋白质编码基因的表达，这可能导致 C 同化的增加。
