Table 1.
Escherichia genomes analysed and CU fimbrial operons identified per strain.
Figure 1.
Unrooted phylogram of fimbrial usher proteins identified in Escherichia.
A total of 1075 amino acid positions were used to infer the evolutionary relationship of 383 aligned usher proteins. These consist of 379 usher amino acid sequences belonging to intact fimbrial gene clusters and an additional four usher amino acid sequences of disrupted fimbrial gene clusters (Yhc and AAF/II), which lack intact representatives in the genome sequenced strains examined in this dataset. The corresponding 383 fimbrial gene clusters can be classified as 38 types based on the evolutionary phylogeny of usher amino acid sequence and genetic locus position. Fimbrial gene clusters were grouped according to the Nuccio clade system (α, β, γ, π, κ, σ, open circles represent cladistic nodes) [3], and highlighted in colour. The text of fimbrial types located on PAI's or plasmids is highlighted in blue and red, respectively. Bootstrap values (1000) are displayed as percentage on major nodes. The scale represents the number of amino acid substitutions per site.
Figure 2.
Locus positions of chromosome-borne CU fimbrial operons relative to the genome of E.coli MG1655.
The E. coli K-12 MG1655 chromosome (outer black ring) was used as a reference map to visualise the locus position of 30 chromosome-borne CU fimbrial types. Types highlighted in blue are present in E. coli K-12 MG1655, types in red are absent in this strain. Fimbrial types associated with PAIs are indicated by an asterisk. A number of PAI associated fimbrial gene clusters occupy different locus positions relative to the MG1655 genome. tRNA sites that flank CU-containing PAIs are indicated on the inner blue ring.
Figure 3.
Prevalence and genetic organisation of CU fimbrial types identified in Escherichia.
The genetic organisation of the different fimbrial types is depicted diagrammatically. Fimbriae are grouped according to the Nuccio clading scheme [3]. Fimbrial prevalence is represented as a percentage of all the strains in the genome dataset. Plasmid-borne fimbriae not part of a genome are highlighted as ‘Plasmid DB’. Genes are colour coded according to predicted function of the corresponding protein product, with associated Pfam and COG domains indicated. The scale represents DNA length in kilo base pair. Reference operon locus tags for individual fimbrial types are displayed on the right. 1PAI and plasmid-borne operons are highlighted in blue and red, respectively.
Figure 4.
Distribution of CU fimbrial gene clusters among E. coli pathotypes.
The inner ring represents the concatenated nucleotide sequences of the 38 fimbrial operons. Each segment is labelled in the outer ring according to the name and clade [3] of the corresponding fimbrial usher type with the intervening 36 rings displaying the presence of intact CU fimbrial gene clusters in each of the strains analysed. The legend on the right lists the colour of each strain that we included in our study, grouped according to pathogenicity class. Circular comparison was generated using BLAST ring image generator (BRIG) [69]. 1CFT073 contains two copies of the P fimbriae operon.
Figure 5.
Distribution of E. coli fimbrial gene clusters in an evolutionary context.
Left: The phylogeny of the Escherichia strains is displayed as inferred using the Neighbour Joining method on the concatenated nucleotide sequence of 7 housekeeping genes (∼9 kb). E. coli strains are colour-coded according to phylogroup (A, B1, B2, D and E). To determine CU fimbrial gene cluster ancestry, the Salmonella pan-genome was investigated for the presence of Escherichia fimbrial types. The scale indicates the number of substitutions per nucleotide. Right: The names of fimbrial types are displayed along the top of a fimbrial gene cluster matrix, with the names of PAI or plasmid-born CU fimbrial gene clusters highlighted in blue and red, respectively. Dark blue and light blue cells represent intact and disrupted CU fimbrial gene clusters, respectively. The heterogenous distribution of CU fimbrial types identified in our dataset suggests substantial acquisition and loss of CU fimbrial gene clusters during the evolution of the Escherichia genus. Depending on their distribution, CU fimbrial types can be classified as core-associated, clade-specific, or sporadic. 1CFT073 possesses two copies of the P fimbriae operon.