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TitleSupramolecular assembly of the LdcI upon acid stress.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 118, Issue 2, Year 2021
Publish dateJan 12, 2021
AuthorsMatthew Jessop / Clarissa Liesche / Jan Felix / Ambroise Desfosses / Megghane Baulard / Virgile Adam / Angélique Fraudeau / Karine Huard / Grégory Effantin / Jean-Philippe Kleman / Maria Bacia-Verloop / Dominique Bourgeois / Irina Gutsche /
PubMed AbstractPathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ...Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ensure enterobacterial survival at low pH. Here, we investigate the acid stress-response regulation of LdcI by combining biochemical and biophysical characterization with negative stain and cryoelectron microscopy (cryo-EM) and wide-field and superresolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localization of nanobody-labeled endogenous wild-type LdcI in acid-stressed cells and show that it organizes into distinct patches at the cell periphery. Consistent with recent hypotheses that in vivo clustering of metabolic enzymes often reflects their polymerization as a means of stimulus-induced regulation, we show that LdcI assembles into filaments in vitro at physiologically relevant low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-EM and reveal the molecular determinants of LdcI polymerization, confirmed by mutational analysis. Finally, we propose a model for LdcI function inside the enterobacterial cell, providing a structural and mechanistic basis for further investigation of the role of its supramolecular organization in the acid stress response.
External linksProc Natl Acad Sci U S A / PubMed:33372137 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.28 Å
Structure data

10849

6yn5

EMDB-10849, PDB-6yn5:
Inducible lysine decarboxylase LdcI decamer, pH 7.0
Method: EM (single particle) / Resolution: 2.7 Å

10850

6yn6

EMDB-10850, PDB-6yn6:
Inducible lysine decarboxylase LdcI stacks, pH 5.7
Method: EM (single particle) / Resolution: 3.28 Å

Source
  • Escherichia coli K-12 (bacteria)
  • escherichia coli (strain k12) (bacteria)
KeywordsLYASE / Acid stress-inducible / decarboxylase / LAOdc

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