Part:BBa_K5404001
Downregulated DEGs in Synechocystis sp. Under pH11 Conditions
The 67 downregulated differentially expressed genes (DEGs) under pH 11 conditions were identified through RNA sequencing (RNA-seq) analysis, comparing the transcriptomes of Synechocystis sp. grown at pH 7.5 and pH 11. Using statistical analysis, including fold change and p-value thresholds (|fold change| ≥ 2 and p-value < 0.05), we identified genes significantly downregulated in response to the high pH environment. These downregulated genes include key components of photosynthesis, such as Phycobilisome proteins and Photosystem I and II subunits, indicating a reduced photosynthetic activity under alkaline stress. Additionally, genes related to translation, such as 16S ribosomal RNA and various tRNAs, were suppressed, suggesting a shift away from protein synthesis and cellular growth towards resource conservation. The downregulation of these pathways highlights how Synechocystis adapts to high pH by reallocating energy and carbon resources away from growth and photosynthesis, instead promoting stress survival mechanisms and enhancing PHB production. Understanding these downregulated genes provides insights for optimizing metabolic pathways in cyanobacteria under stress, allowing for more efficient PHB biosynthesis in synthetic biology applications.
Specifically, our team utilized downregulated genes to find optimal strategies to produce PHB under modified Synechocystis growth techniques. Differentially Expressed Genes (DEG) are genes that show dramatically different expressions under lab conditions [1]. The downregulated genes refer to those that have decreased receptor sites, having decreased responsiveness and less transcription abilities.
Our team utilized RNA sequencing to evaluate the effectiveness of pH level modifications because of the distinctive advantage it has. Compared to DNA sequencing, RNA sequencing allows to visually indicate the full catalog of transcripts, define specific structures of genes, and measure gene expression levels [2]. The downregulation of these genes convey how Synechocystis responds to modified pH levels and improve PHB production through revealing stress levels received by genes according to fond change in Table 2.
Accordingly, the results of RNA sequencing for downregulated genes are shown in Table 2. The Fold Change column signifies how much each gene's productivity decreased, quantifying the degree of impact of the modified pH level conditions. The gene that performed highest fold change demonstrated -24.62, and the gene that performed lowest fold change demonstrated -4.02. Overall, the data that our team collected should be considered accurate, since the p-value indicates the probability that the result obtained is due to a random occurrence. Having a range of [0,0.045], the values designate that the fold change values are only attributable from the pH modifications.
Table 2. List of 67 downregulated 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. How to employ statistical approaches to identify differentially expressed genes (DEG). (2023). Novogene. https://www.novogene.com/us-en/resources/blog/how-to-employ-statistical-approaches-to-identify-differentially-expressed-genes-deg/#:~:text=DEGs%20are%20genes%20that%20show
2. Lê, N. (2023, June 13). Explaining DNA vs. RNA sequencing. Dispendix.com; DISPENDIX GmbH. https://dispendix.com/blog/explaining-dna-vs-rna-sequencing#:~:text=RNA%20sequencing%20(RNA%2DSeq)
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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