Part:BBa_K5404000
Upregulated DEGs in Synechocystis sp. Under pH11 Conditions
The 40 overexpressed differentially expressed genes (DEGs) under pH 11 conditions were identified through RNA sequencing (RNA-seq) analysis, which allowed us to compare the transcriptomes of Synechocystis sp. grown at pH 7.5 and pH 11. By applying statistical analysis, including fold change and p-value thresholds (|fold change| ≥ 2 and p-value < 0.05), we isolated genes that showed significant upregulation in response to the high pH environment. These overexpressed genes include those involved in critical metabolic pathways, such as Mannose-1-phosphate guanyltransferase and Polyphosphate kinase, which enhance carbon flux towards polyhydroxybutyrate (PHB) production, as well as stress response elements like Alkaline phosphatase. Identifying these genes is essential because it reveals the molecular mechanisms that enable Synechocystis to adapt to alkaline conditions, rerouting metabolic resources to optimize survival and bioplastic synthesis. Understanding these upregulated pathways opens the door for future engineering strategies aimed at improving PHB production and CO₂ fixation in cyanobacteria under stress conditions, contributing to more sustainable biomanufacturing approaches.
Differentially expressed genes (DEGs) are genes that show statistically significant differences in expression levels between various experimental conditions. Upregulated DEGs specifically involve genes that reveal increased expression from the original condition [1]. This increased expression can be attributed to various responses, including metabolic adjustments and post-transcriptional modifications. Understanding how organisms influence their gene expression in response to environmental changes is crucial for creating potential biotechnological applications.
In our project, we utilized RNA-sequencing to compare the gene expressions of Synechocystis sp. grown at pH 7.5 and pH 11. We chose this approach over DNA sequencing because RNA sequencing can capture the dynamic state of the transcriptome, which helps reveal which genes are actively expressed under different conditions. By focusing on RNA, we were able to identify specific genes that were upregulated in response to high pH conditions, thus giving information on how Synechocystis adapts to alkaline environments. This information is extremely valuable for developing strategies to enhance PHB production and CO2 uptake in cyanobacteria under stressful conditions.
The RNA sequencing revealed that there were up to 40 upregulated DEGs in Synechocystis under pH 11 conditions when compared to pH 7.5 [Table 1]. The fold changes had a wide range, with fold change values varying from 3.87 (gene-MYO_3720) to 19.09 (gene-MYO_14210). More importantly, all of these changes were statistically significant, as they had an associated p-value of less than 0.05. The top five most upregulated genes were all hypothetical proteins, with fold changes ranging from 9.48 to 19.09, but functional genes, such as alkaline phosphatase and isochorismate synthase showed comparatively lower upregulation. Additionally, transposase genes were typically less upregulated, with fold changes between 4.78 and 6.06. Overall, the data highlighted the diverse range of gene expression when placed in high pH environments, with the hypothetical proteins having the largest increases in expression.
Table 1. List of 40 upregulated differentially expressed genes (DEGs) identified through RNA-seq analysis of Synechocystis sp. grown under pH 11 conditions compared to pH 7.5. The fold change (pH11_5/pH7) and corresponding p-value indicate the magnitude of expression difference and statistical significance.
References:
1. McDermaid, A., Monier, B., Zhao, J., Liu, B., & Ma, Q. (2018). Interpretation of differential gene expression results of RNA-seq data: review and integration. Briefings in Bioinformatics, 20(6), 2044–2054. https://doi.org/10.1093/bib/bby067
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