Supramolecular assembly of the E. coli LdcI upon acid stress

Matthew 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

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Received Date: 2nd May 20

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 E. coli LdcI by combining biochemical and biophysical characterisation with negative stain and cryo-electron microscopy, and wide-field and super-resolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localisation of endogenous wild-type LdcI in acid-stressed E. coli cells, and show that it organises into patches following an apparent long-range pseudo-helical order. Consistent with recent hypotheses that in vivo clustering of metabolic enzymes often reflects their polymerisation as a means of stimulus-induced regulation, we show that LdcI assembles into filaments in vitro at low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-electron microscopy, and reveal the molecular determinants of LdcI polymerisation, 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 organisation in the acid stress response.

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This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

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