Abstract

BackgroundEscherichia coli C forms more robust biofilms than other laboratory strains. Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced.ResultsHere we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43, waaSBOJYZUL for lipopolysaccharide (LPS) synthesis, and cpsB for curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulator csrA gene. This insertion is located 86 bp upstream of the csrA start codon inside the − 35 region of P4 promoter and blocks the transcription from the sigma32 and sigma70 promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of the csgD gene. And finally, E. coli C encodes an additional sigma70 subunit driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions provided insights into understanding this regulatory pathway in E. coli.ConclusionsBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains of E. coli grown for decades in vitro have evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain of E. coli C produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence of this classic strain, which provides for a base level of characterization and makes it useful for many biofilm-based applications.

Highlights

  • Escherichia coli C forms more robust biofilms than other laboratory strains

  • We found that the E. coli C strain formed robust biofilms on both microscope slides and in

  • In minimal M9 with glycerol medium, the strain C produced 1.5- to 3-fold more biofilm than the other laboratory strains; and in Luria-Bertani (LB) rich medium, the strain C biofilm formation was as much as 7.4-fold higher (Fig. 1b)

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Summary

Introduction

Biofilm formation and cell aggregation under a high shear force depend on temperature and salt concentrations. It is the last of five E. coli strains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. E. coli strain C was isolated at the Lister Institute and deposited into the National Collection of Type Cultures, London, in 1920 (Strain No 122). It was characterized as more spherical than other E. coli strains and its nuclear matter was shown to be peripherally distributed in the cell [1]. Some research on genes involved in biofilm formation in this strain has been attempted but hasn’t been continued (Federica Briani, Università degli Studi di Milano, personal communication) [6]

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