In the human gastrointestinal tract, bacteria have survival strategies in response to acidic environments. Escherichia coli, known for its high level of acid resistance, employs multiple acid defense mechanisms to ensure its survival under these harsh conditions. The main acid resistance mechanism involves three proton-consuming protection strategies, each consisting of an amino acid decarboxylase and an antiporter to take up the amino acid and release the more alkaline polyamine into the surrounding medium (Brameyer et al. 2022).

In recent years, due to the advances in detection techniques, a significant number of previously uncharacterized small proteins have been identified in bacteria (Fuchs and Engelmann 2023). These small proteins encoded by small open reading frames (sORFs) are often overlooked during annotation and are difficult to characterize using conventional biochemical techniques.

In 2023, ribosome profiling revealed 18 novel stress-induced sORFs in E. coli, found particularly under severe (pH 4.4) acid stress conditions (Schumacher et al. 2023). The current project aims to gain further insights into the subcellular location, properties, potential interactions, and the role in the acid resistance mechanism of the newly identified sORF candidates. sORF15 is located between gadW, encoding one of the major transcriptional regulators of the Gad acid resistance system, and mdtF, encoding a multidrug resistance protein. Interestingly, the last 64 bp of sORF15 overlaps with 3′ of mdtF. We found that E. coli MG1655 was more tolerant to stress imposed by organic acids and antibiotics than E. coli MG1655 ∆sORF15.

References:

Brameyer, Sophie, Kilian Schumacher, Sonja Kuppermann, and Kirsten Jung. 2022. "Division of Labor and Collective Functionality in Escherichia Coli under Acid Stress." Communications Biology 5 (1): 1–14. https://doi.org/10.1038/s42003-022-03281-4.

Fuchs, Stephan, and Susanne Engelmann. 2023. "Small Proteins in Bacteria - Big Challenges in Prediction and Identification." Proteomics 23 (23–24): e2200421. https://doi.org/10.1002/pmic.202200421.

Schumacher, Kilian, Rick Gelhausen, Willow Kion-Crosby, Lars Barquist, Rolf Backofen, and Kirsten Jung. 2023. "Ribosome Profiling Reveals the Fine-Tuned Response of Escherichia Coli to Mild and Severe Acid Stress." mSystems 8 (6): e0103723. https://doi.org/10.1128/msystems.01037-23.