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Supramolecular assembly of the Escherichia coli LdcI upon acid stress.


ABSTRACT: 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 Escherichia coli 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 E. coli 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.

SUBMITTER: Jessop M 

PROVIDER: S-EPMC7812809 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Supramolecular assembly of the <i>Escherichia coli</i> LdcI upon acid stress.

Jessop Matthew M   Liesche Clarissa C   Felix Jan J   Desfosses Ambroise A   Baulard Megghane M   Adam Virgile V   Fraudeau Angélique A   Huard Karine K   Effantin Grégory G   Kleman Jean-Philippe JP   Bacia-Verloop Maria M   Bourgeois Dominique D   Gutsche Irina I  

Proceedings of the National Academy of Sciences of the United States of America 20210101 2


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 <i>Escherichia coli</i> LdcI by combining biochemical and biophysical characterization with negative stain and cryoelectron microscopy (cryo-EM) and wide-field and superresolution fluorescence imaging  ...[more]

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