Welcome to Escherichia coli str. K-12 substr. MG1655

Introduction

Neutrophilic bacteria are exposed to acidic environments, for example, in digestive tracts, acidic soils, fermented foods, or phagosomes in macrophages (1). Escherichia coli is equipped with a high number of defense mechanisms to survive the low pH (pH 2-3) in the stomach and accordingly its infectious dose is lower (below 50 cells) in comparison to other enteropathogens (2). Protective mechanisms that counteract acid stress and ensure survival in low pH habitats include proton pumps, membrane remodeling, acid-dependent chemotaxis, amino acid decarboxylase antiporter systems, chaperones and acid shock proteins (3-4).

E. coli has four H+-consuming amino acid decarboxylase systems, the glutamate decarboxylase (Gad), arginine decarboxylase (Adi), lysine decarboxylase (Cad) and ornithine decarboxylase (Orn) systems (also known as acid resistance (AR) systems AR2 - AR5) (5-6). Each of these systems consists of an amino acid decarboxylase (GadA/GadB, AdiA, CadA, SpeF) and a cognate antiporter (GadC, AdiC, CadB, PotE) to take up the amino acid and export the more alkaline reaction product into the medium. This strategy ensures a simultaneous increase in both, extracellular and intracellular pH (6-8). Each system is activated at different external pH values and growth phases. We have previously found that individual E. coli cells exposed to consecutively increasing acid stress activate the Gad, Adi and Cad systems in a heterogeneous manner, resulting in a functional diversification and increased fitness of the population (9-10).

We used Ribo-Seq and RNA-Seq to determine the response of E. coli K-12 to pH 7.6, 5.8, and 4.4 with the goal of identifying the fine-tuned response of E. coli under each condition and the interconnectivity of the ARs systems. We uncovered several transcriptional regulators involved in the response to acid stress, discovered examples of acid-dependent differential transcriptional and translational regulation and potential novel small open reading frames. These results expand the acid resistance network and provide new insights into the fine-tuned response of E. coli.

Here we present a JBrowse2 instance to browse Ribo-Seq and RNA-Seq data generated at pH 7.6, 5.8 and 4.4 in Escherichia coli MG1655.

Publication

The publication describing this project can be accessed via the following DOI: https://doi.org/10.1101/2023.06.02.543275

Data availability

The raw sequencing data used in this study can be accessed via the GEO accession number GSE219022.

The processed files used in this JBrowse2 genome browser can be downloaded here.

JBrowse2

Access Area

Default session
Access JBrowse

Annotation tracks

We provide multiple annotation tracks for the Escherichia coli str. K-12 substr. MG1655 genome.
All annotation files can be loaded and unloaded using their respective check box in the track selector.
Annotation files are indexed and specific genes can be searched by gene name, locus tag or gene id using the search box in the top center of the JBrowse2 instance.
This JBrowse2 instance includes:

Track Description
The Reference Annotation The reference annotation for Escherichia coli str. K-12 substr. MG1655
DeepRibo Predictions A list of ORF predictions created using the tool DeepRibo.
Reparation Predictions A list of ORF predictions created using the tool Reparation.
Start Codon Motifs All ATG motifs for the reference genome.
Alternative Start Codon Motifs All GTG and TTG motifs for the reference genome.
Stop Codon Motifs All TAA, TAG and TGA motifs for the reference genome.
RBS Motif All AAGG motifs for the reference genome.

Coverage tracks

Coverage tracks show the normalized read counts per nucleotide position. There are multiple mapping types used (threeprime/fiveprime/global). The mapping method of each file is marked in their description.

Shareable Links

JBrowse2 allows you to easily share observations with your colleagues and collaborators.
Using the "share"-button next to the session name, you can automatically generate a link. Anyone that uses this link will see the exact session you are currently looking at. This includes colors, zoom level, scale, loaded tracks etc...
This is a very powerful tool for sharing potential discoveries.

JBrowse2 user guide

For more information on how to use JBrowse2, please have a look at the comprehensive user guide provided by the JBrowse team. The chapter on basic usage is highly recommended to get familiar with the JBrowse2 interface.

Contributors

This project is a collaboration between the universities of Munich, Freiburg and Würzburg.

AG Jung
  • Prof. Dr. Kirsten Jung
  • Kilian Schumacher
University Munich Logo
AG Barquist
  • Dr. Willow Kion-Crosby
  • Lars Barquist
Helmholtz HIRI Logo
AG Backofen
  • Prof. Rolf Backofen
  • Rick Gelhausen
University Freiburg Logo

References

  1. Schwarz, J., Schumacher, K., Brameyer, S., and Jung, K. (2022). Bacterial battle against acidity. FEMS Microbiol. Rev.
    https://doi.org/10.1093/femsre/fuac037
  2. Tilden, J., Young, W., McNamara, A.M., Custer, C., Boesel, B., Lambert-Fair, M.A., Majkowski, J., Vugia, D., Werner, S.B., Hollingsworth, J., et al. (1996). A new route of transmission for Escherichia coli: Infection from dry fermented salami. Am. J. Public Health 86, 1142-1145.
    https://doi.org/10.2105/ajph.86.8_pt_1.1142
  3. Arcari, T., Feger, M.-L., Guerreiro, D.N., Wu, J., and O'Byrne, C.P. (2020). Comparative Review of the Responses of Listeria monocytogenes and Escherichia coli to Low pH Stress. Genes (Basel). 11.
    https://doi.org/10.3390/genes11111330
  4. Foster, J.W. (2004). Escherichia coli acid resistance: Tales of an amateur acidophile. Nat. Rev. Microbiol. 2, 898-907.
    https://doi.org/10.1038/nrmicro1021
  5. Castanie-Cornet, M.P., and Foster, J.W. (2001). Escherichia coli acid resistance: CAMP receptor protein and a 20 bp cis-acting sequence control pH and stationary phase expression of the gadA and gadBC glutamate decarboxylase genes. Microbiology 147, 709-715.
    https://doi.org/10.1099/00221287-147-3-709
  6. Kanjee, U., and Houry, W.A. (2013). Mechanisms of acid resistance in escherichia coli. Annu. Rev. Microbiol. 67, 65-81.
    https://doi.org/10.1146/annurev-micro-092412-155708
  7. De Biase, D., and Lund, P.A. (2015). The Escherichia coli Acid Stress Response and Its Significance for Pathogenesis (Elsevier).
    https://doi.org/10.1016/bs.aambs.2015.03.002
  8. Lund, P., Tramonti, A., and De Biase, D. (2014). Coping with low pH: Molecular strategies in neutralophilic bacteria. FEMS Microbiol. Rev. 38, 1091-1125.
    https://doi.org/10.1111/1574-6976.12076
  9. Brameyer, S., Hoyer, E., Bibinger, S., Burdack, K., Lassak, J., and Jung, K. (2020). Molecular design of a signaling system influences noise in protein abundance under acid stress in different gammaproteobacteria. J. Bacteriol. 202.
    https://doi.org/10.1128/JB.00121-20
  10. Brameyer, S., Schumacher, K., Kuppermann, S., and Jung, K. (2022). Division of labor and collective functionality in Escherichia coli under acid stress. Commun. Biol. 5, 1-14.
    https://doi.org/10.1038/s42003-022-03281-4