Flashy flagella : flagellin modification is relatively common and highly versatile among the Enterobacteriaceae

De Maayer, Pieter; Cowan, Don A.

Flashy flagella : flagellin modification is relatively common and highly versatile among the Enterobacteriaceae

De Maayer, Pieter; Cowan, Don A.

Date: 2016-05-20

Abstract:

BACKGROUND : Post-translational glycosylation of the flagellin protein is relatively common among Gram-negative bacteria, and has been linked to several phenotypes, including flagellar biosynthesis and motility, biofilm formation, host immune evasion and manipulation and virulence. However to date, despite extensive physiological and genetic characterization, it has never been reported for the peritrichously flagellate Enterobacteriaceae. RESULTS : Using comparative genomic approaches we analyzed 2,000 representative genomes of Enterobacteriaceae, and show that flagellin glycosylation islands are relatively common and extremely versatile among members of this family. Differences in the G + C content of the FGIs and the rest of the genome and the presence of mobile genetic elements provide evidence of horizontal gene transfer occurring within the FGI loci. These loci therefore encode highly variable flagellin glycan structures, with distinct sugar backbones, heavily substituted with formyl, methyl, acetyl, lipoyl and amino groups. Additionally, an N-lysine methylase, FliB, previously identified only in the enterobacterial pathogen Salmonella enterica, is relatively common among several distinct taxa within the family. These flagellin methylase island loci (FMIs), in contrast to the FGI loci, appear to be stably maintained within these diverse lineages. CONCLUSIONS : The prevalence and versatility of flagellin modification loci, both glycosylation and methylation loci, suggests they play important biological roles among the Enterobacteriaceae.

Description:

All genome sequences incorporated in this study are publically available in the NCBI Genome database. The NCBI accession numbers for the contigs/ chromosomes on which the target loci are found are indicated in Additional file 1: Table S1.

Table S1. Enterobacteriaceae strains analysed in this study. The deep-branching clade to which they belong (Fig. 1), the presence/ absence of fliDCAZ loci, the NCBI accession numbers of the contigs on which these loci occur, and presence/absence of FGI and FMI loci are indicated. Table S2. Characteristics of FGI+ Enterobacteriaceae and their flagellin glycosylation islands. The isolation sources and deep-branching clade to which they belong in the Enterobacteriaceae phylogeny (Fig. 1) are indicated for each of the FGI+ enterobacterial strains. The sizes, G + C contents, G + C deviation from the rest of the genome and number of proteins encoded on each FGI are shown. Table S3. Characteristics of FMI+ Enterobacteriaceae and their flagellin methylation islands. The isolation sources and deep-branching clade to which they belong in the Enterobacteriaceae phylogeny (Fig. 1) are indicated for each of the FMI+ enterobacterial strains. The sizes, G + C contents, G + C deviation from the rest of the genome and number of proteins encoded on each FMI are shown. Table S4. Annotations of the proteins encoded on the enterobacterial FGIs. The number of strains and genera in which orthologs of each distinct protein are encoded within the FGIs are indicated, as well as the closest non-enterobacterial Blast hit, obtained by BlastP analysis against the NCBI non-redundant protein database. Orthologs were only considered among the top 500 BLAST hits and for those orthologs with > 30 % amino acid identity to the query protein. The putative function and conserved domains observed after BLAST analyses against the NCBI protein and conserved domain databases are shown. Table S5. Genomics inserts in the fliDCAZ loci of FGI−/FMI− Enterobacteriaceae. The insert size, G + C content, G + C deviation from the rest of the genome, number of proteins encoded and putative functions of the encoded proteins in each insert are shown. (XLSX 234 kb)

Figure S1. Schematic diagrams of inserts within the fliDCAZ loci of FGI−/FMI− Enterobacteriaceae. Flanking genes are indicated by yellow arrows, predicted phage genes by blue arrows, fimbrial biogenesis genes by grey arrows and sugar/amino acid transporter genes by orange arrows. Black arrows indicate predicted transposase or endonuclease genes, while the red arrows indicate genes with disrupted reading frames. The flagellin glycan biosynthetic genes in the FGI+ strains E. tracheiphila Buff/ PSU-1 are indicated by green arrows, upstream of the predicted phage integration site. (TIF 471 kb)

Figure S2. Schematic diagrams of stereotypical flagellin glycosylation islands of the forty-two distinct FGI types. Glycosyltransferase and sugar biosynthetic genes are indicated by dark and light green arrows, respectively. Formyltransferases, methyltransferases, acetyltransferases and aminotransferases are encoded by genes represented by dark blue, purple, light blue and yellow arrows, respectively. Pink arrows indicates genes involved in fatty acid biosynthesis. Flanking genes are indicated by grey arrows, genes coding for hypothetical proteins or involved in functions with no relative known function in flagellin glycosylation by white arrows and black arrows indicate transposes and endonuclease genes. (TIF 3168 kb)

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