Abstract
Chaperone-usher (CU) fimbriae are adhesive surface organelles common to many Gram-negative bacteria. Escherichia coli genomes contain a large variety of characterised and putative CU fimbrial operons, however, the classification and annotation of individual loci remains problematic. Here we describe a classification model based on usher phylogeny and genomic locus position to categorise the CU fimbrial types of E. coli. Using the BLASTp algorithm, an iterative usher protein search was performed to identify CU fimbrial operons from 35 E. coli (and one Escherichia fergusonnii) genomes representing different pathogenic and phylogenic lineages, as well as 132 Escherichia spp. plasmids. A total of 458 CU fimbrial operons were identified, which represent 38 distinct fimbrial types based on genomic locus position and usher phylogeny. The majority of fimbrial operon types occupied a specific locus position on the E. coli chromosome; exceptions were associated with mobile genetic elements. A group of core-associated E. coli CU fimbriae were defined and include the Type 1, Yad, Yeh, Yfc, Mat, F9 and Ybg fimbriae. These genes were present as intact or disrupted operons at the same genetic locus in almost all genomes examined. Evaluation of the distribution and prevalence of CU fimbrial types among different pathogenic and phylogenic groups provides an overview of group specific fimbrial profiles and insight into the ancestry and evolution of CU fimbriae in E. coli.
Highlights
Fimbriae are long proteinaceous organelles that extend from the surface of many bacteria and mediate diverse functions, including adherence and biofilm formation
Fimbrial operons were identified using an iterative usher BLASTp search against a selection of 36 Escherichia complete genomes and 132 Escherichia spp. plasmids (Table 1 and S1)
CU fimbriae are cell surface-located organelles produced by many Gram-negative bacteria
Summary
Fimbriae are long proteinaceous organelles that extend from the surface of many bacteria and mediate diverse functions, including adherence and biofilm formation. Many different types of fimbriae have been described in Grampositive and Gram-negative bacteria [1]. In Gram-negative bacteria, fimbriae are assembled via a range of different protein translocation systems, including the chaperone-usher (CU) pathway, the type IV secretion pathway and the extracellular nucleation precipitation pathway [2]. The chaperone facilitates several essential steps in the pathway; it mediates the folding of fimbrial subunit proteins, prevents their polymerization in the periplasm and directs their passage to the usher. The usher in turn acts as an assembly platform; it forms a binding scaffold for fimbrial subunit protein-chaperone complexes from the periplasm and facilitates the assembly of the fimbrial structural organelle [5,6,7,8,9,10,11]
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