Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Abstract

We have determined the complete genome sequences of a host-promiscuous Salmonella enterica serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis. Significantly, the genome of S. Gallinarum has undergone extensive degradation through deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those identified previously in other host-adapted bacteria reveals the loss of many common functional traits and provides insights into possible mechanisms of host and tissue adaptation. We propose that experimental analysis in chickens and mice of S. Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica.

Figure 1.

Global comparison between S. Typhimurium, S. Enteritidis, and S. Gallinarum. ACT comparison (http://www.sanger.ac.uk/Software/ACT) of amino acid matches between the complete six-frame translations (computed using TBLASTX) of the whole-genome sequences of S. Typhimurium LT2 (LT2), S. Enteritidis PT4 (PT4), and S. Gallinarum 287/91 (GAL). Forward and reverse strands of DNA are shown for each genome (light gray horizontal bars). The red bars between the DNA lines represent individual TBLASTX matches, with inverted matches colored blue. The position of all the fimbrial operons in these three genomes are marked as colored boxes positioned on the forward and reverse strands of DNA. Analogous fimbrial operons are colored the same. The boxes of fimbrial operons that include pseudogenes are crossed with a white line. Other genomic features are only shown if they constitute breaks in synteny between genomes. The position of the origin and terminus are marked (solid black arrows).

Figure 2.

Circular representation of the S. Enteritidis PT4 chromosome. From the outside in, the outer circle 1 marks the position of regions of difference (mentioned in the text) and is detailed in Table 2. Circle 2 shows the size in base pairs. Circles 3 and 4 show the position of CDS transcribed in a clockwise and anti-clockwise direction, respectively (for color codes see below); circle 5 shows the position of S. Enteritidis PT4 pseudogenes. Circles 6 and 8 show the position of S. Enteritidis PT4 genes that have orthologs (by reciprocal FASTA analysis) in S. Typhimurium strain LT2 (all CDS colored green) and S. Gallinarum strain 287/91 (all CDS colored blue), respectively. Circles 7 and 9 show the position of S. Enteritidis PT4 genes that lack orthologs in (by reciprocal FASTA analysis) in S. Typhimurium strain LT2 (all CDS colored pink) and S. Gallinarum strain 287/91 (all CDS colored gray), respectively. Circle 10 shows the position of S. Enteritidis PT4 rRNA operons (red). Circle 11 shows a plot of G + C content (in a 10-kb window). Circle 12 shows a plot of GC skew ([G − C]/[G + C]; in a 10-kb window). Genes in circles 3 and 4 are color-coded according to the function of their gene products: dark green, membrane or surface structures; yellow, central or intermediary metabolism; cyan, degradation of macromolecules; red, information transfer/cell division; cerise, degradation of small molecules; pale blue, regulators; salmon pink, pathogenicity or adaptation; black, energy metabolism; orange, conserved hypothetical; pale green, unknown; and brown, pseudogenes.

Figure 3.

Distribution of orthologous CDS in S. Enteritidis PT4, S. Typhimurium LT2, and S. Gallinarum 287/91. The Venn diagram shows the number of genes unique or shared between two other S. enterica serovars (see Methods). The associated pie charts show the breakdown of the functional groups assigned for CDS in relevant sections of the Venn diagram. Color code for the pie charts is as follows: (1) hypothetical proteins, (2) conserved hypothetical proteins, (3) chemotaxis and motility, (4) chromosomal replication, (5) chaperones, (6) protective responses, (7) transport and binding proteins, (8) adaptations to atypical conditions, (9) cell division, (10) macromolecule degradation, (11) synthesis and modification of macromolecules, (12) amino acid biosynthesis, (13) biosynthesis of cofactors, prosthetic groups and carriers, (14) central intermediary metabolism, (15) small-molecule degradation, (16) energy metabolism, (17) fatty acid biosynthesis, (18) nucleosides and nucleotide biosynthesis and metabolism, (19) periplasmic/exported/lipoproteins, (20) ribosomal proteins, (21) laterally acquired (including prophage CDS), (22) pathogenicity and virulence, (23) general regulation, and (24) miscellaneous function. PT4 indicates S. Enteritidis PT4; LT2, S. Typhimurium LT2; and GAL, S. Gallinarum 287/91

Figure 4.

Comparison of the ROD21 locus of S. Enteritidis with related genomic islands. ACT comparison (http://www.sanger.ac.uk/Software/ACT) of amino acid matches between the complete six-frame translations (computed using TBLASTX) of ROD21 compared with related loci uropathogenic E. coli strain CFT073 (UPEC), Erwinia carotovora sbsp. atroseptica strain SCRI1043 (two loci: ECA1 and ECA2), and Photorhabidus luminescens,sbsp. laumondii TT01 (PHL; see Methods). The red bars spanning between the genomes represent individual TBLASTX matches. CDS are marked as colored boxes positioned on the horizontal gray DNA bars: (orange) genes conserved in two or more of the genomic islands; (light green) variable genes of unknown function; (dark pink) hnsB; (dark blue) hnsT; (light pink) integrase; (dark green) type IV pilin-associated genes; (red) plasmid-related mobility functions; (salmon pink) transposase-related genes; (yellow) tRNA genes; (light blue)repeats. The G + C profile for the UPEC loci is shown above. The scale is marked in base pairs.

Figure 5.

Circular representation of the S. Gallinarum 287/91 chromosome. For a full description of this figure, see legend to Figure 2. The exception is that circle 5 shows the position of S. Gallinarum 287/91 pseudogenes. Circles 6 and 8 show the position of S. Gallinarum 287/91 genes which have orthologs (by reciprocal FASTA analysis) in S. Typhimurium LT2 (all CDS colored green) or S. Enteritidis PT4 (all CDS colored blue), respectively. Circles 7 and 9 show the position of S. Gallinarum 287/91 genes that lack orthologs in (by reciprocal FASTA analysis) in S. Typhimurium strain LT2 (all CDS colored pink) and S. Enteritidis PT4 (all CDS colored gray), respectively. Circle 10 shows the position of the S. Gallinarum 287/91 rRNA operons (red).

Figure 6.

Line diagram to represent the whole-genome differences of S. Enteritidis PT4, S. Typhimurium strain LT2, and S. Gallinarum strain 287/91. A summary of the observed loss and gain of RODs described in Table 2. The diagram is based on the assumption that following the divergence of PT4 and LT2 from a common ancestor PT4 and GAL have subsequently diverged. Branches are not intended to infer phylogenetic distance. Evidence that a locus was once present in LT2, PT4, or GAL (see legend to Figure 1) but has subsequently been deleted from that genome is marked by the suffix *, $, or £, respectively. Brackets indicate the name for locus in GAL. Parentheses indicate the name for locus in PT4. Dotted arrows mark the position in the pseudo-tree at which that ROD(s) appears