Time-resolved transcriptomics reveals mechanisms of acute and sustained low-pH adaptation in <i>Corynebacterium glutamicum</i>.
Corynebacterium glutamicum shows a rapid loss of viability under acute low-pH shock, while sustained stress leads to a more gradual decline, highlighting the need for different strategies in strain engineering.
Where it sits
this study against the rest of the bofanglutide corpusSummary and findings
This study investigated low-pH adaptation mechanisms in Corynebacterium glutamicum under acute and sustained acid stress. Acute shock at pH 4.0 resulted in a 93% loss of viability within 2 hours, while sustained stress at pH 5.5 led to a 4.1-log10 decline over 18 hours. The research identified differentially expressed genes and metabolic responses associated with these stress conditions.
Abstract
<i>Corynebacterium glutamicum</i> is a major industrial cell factory for amino acid production. Acidic byproduct accumulation can lower broth pH, disrupt cytoplasmic pH homeostasis, induce oxidative stress, and ultimately compromise productivity. As low-pH stress is dynamic and process-dependent, distinguishing responses to acute acid shock versus sustained acidification is important for improving strain robustness. Here, we investigated low-pH adaptation under two regimes: acute, unbuffered pH 4.0 shock and sustained pH 5.5 stress with pH control, by integrating viability assays, time-series RNA-seq, and genetic validation. Acute shock caused 93% viability loss within 2 h, followed by broth neutralisation and regrowth, whereas sustained stress led to a 4.1-log<sub>10</sub> decline over 18 h. Transcriptomics identified 905/847 differentially expressed genes at 1/4 h under acute shock and 643/608/1857 genes at 1/8/18 h under sustained stress. Shared responses included repression of central metabolism and induction of β-ketoadipate catabolism, potassium uptake, sodium/proton antiport, urease-mediated ammonium release, amino acid biosynthesis, and oxidative and membrane-stress defences. Acute shock showed rapid global reprogramming dominated by oxidative protection, chaperone induction, and ion-flux control, whereas sustained stress induced progressive metabolic rewiring, cell envelope reinforcement, and redox buffering. Functional validation using both overexpression and knockout mutants confirmed the contribution of ion transport, iron regulation, β-ketoadipate metabolism, urease, and respiratory modules to low-pH tolerance in a regime-dependent manner. This study provides the first time-resolved, regime-specific transcriptomic dissection of low-pH adaptation in <i>C. glutamicum</i> and identifies key modules for engineering acid-resilient strains.
Background
This paper addresses the mechanisms of low-pH adaptation in Corynebacterium glutamicum, a key organism in amino acid production. Previous research has indicated that acidic byproduct accumulation can disrupt cellular functions, but the specific responses to different pH stress conditions were not fully understood. This study is significant as it provides insights into the dynamic responses of C. glutamicum to acute and sustained low-pH stress, which could inform strain engineering for improved productivity.
Methods
The study utilized a combination of viability assays, time-series RNA sequencing, and genetic validation to investigate low-pH adaptation. Two regimes were tested: acute, unbuffered pH 4.0 shock and sustained pH 5.5 stress with pH control. The primary outcome measures included the assessment of viability loss and the identification of differentially expressed genes over specified time points.
Results
Under acute shock at pH 4.0, there was a 93% loss of viability within 2 hours. In contrast, sustained stress at pH 5.5 resulted in a 4.1-log10 decline in viability over 18 hours. Transcriptomic analysis revealed 905 differentially expressed genes at 1 hour and 847 at 4 hours for acute shock, while sustained stress showed 643 genes at 1 hour, 608 at 8 hours, and 1857 at 18 hours.
Interpretation
The findings indicate significant differences in the transcriptional response of C. glutamicum to acute versus sustained low-pH stress, with implications for metabolic engineering. While the statistical significance of the findings is clear, the clinical relevance in terms of practical applications for strain robustness remains to be fully established. Limitations include potential confounding factors such as the specific growth conditions and the absence of long-term viability assessments.
Key findings
- 93% viability loss within 2 h under acute shock.
- 4.1-log10 decline in viability over 18 h under sustained stress.
- 905 differentially expressed genes at 1 h and 847 at 4 h under acute shock.
- 643 differentially expressed genes at 1 h, 608 at 8 h, and 1857 at 18 h under sustained stress.
Limitations
- Not reported in abstract.