The Floating (Pathogenicity) Island: A Genomic Dessert

Abstract

Among the prokaryotic genomic islands (GIs) involved in horizontal gene transfer (HGT) are the classical pathogenicity islands, including the integrative and conjugative elements (ICEs), the gene-transfer agents (GTAs), and the staphylococcal pathogenicity islands (SaPIs), the primary focus of this review. While the ICEs and GTAs mediate HGT autonomously, the SaPIs are dependent on specific phages. The ICEs transfer primarily their own DNA, the GTAs exclusively transfer unlinked host DNA, and the SaPIs combine the capabilities of both. Thus the SaPIs derive their importance from the genes they carry (their genetic cargo) and the genes they move. They act not only as versatile high-frequency mobilizers but also as mediators of phage interference and consequently are major benefactors of their host bacteria.

Keywords: Staphylococcus; horizontal gene transfer; mobile genetic element; pathogenicity island; phage interference; transduction.

Fig. 1. SaPI1 genome

Scheme: orange – flanking chromosomal genes; yellow – int/xis; blue – regulatory genes; purple – replication module; red – interference module; aqua – terS; pink –accessory genes; gray – hypothetical proteins; black – att sites. Tick marks represent nucleotide scale with a spacing of 1 kb. Abbreviations: int – integrase; HP – hypothetical protein; ent –enterotoxin; reg – regulation; xis – excision function; - pri-rep – primase-replication initiation; ori –replication origin; ppi – phage packaging inhibition; pti – phage transcription inhibition; terS –terminase small subunit; tst – toxic shock syndrome toxin 1 (TSST-1); ear – extracellular β-lactamase (ampicillin resistance) homolog. The region including operon 1 and the interference module is amplified for clarity. Most of the gene assignments are based on experimental data [16] [6]; a few on GenBank annotations.

Fig. 2. Electron micrographs of SaPI and GTA particles

A. Electron micrograph of a mixed helper phage-SaPI lysate (Kindly provided by Dr. Terje Dokland, U. Alabama) B. Electron micrograph of infectious GTA particles, (reproduced from reference with the kind permission of Nature Publishing Group)

Fig. 3. SaPI-helper phage interactions

Key interacting genes and proteins for typical prophages (top) and SaPIs (bottom), with lighter colors for phage elements, darker for SaPI. See Table 2 for explanation of the interactions involving the interference genes.

Fig. 4. S. aureus strain NCTC8325 chromosome showing SaPI pseudo-pac (ppac) sites

Chromosomal replication origin is at 0 kbp (RO). The 3 prophage genomes are omitted and several of the well-characterized SaPIs are indicated. Numbers represent ppac sites, with those on the outside oriented clockwise, on the inside, counterclockwise. Tabulation in the center lists the types of genes within 16 kb of each ppac site, on either side. Note that those downstream of any ppac site will be transduced by the SaPI at much higher frequency than those upstream (reprinted from [40] with the kind permission of Elsevier).

Fig. 5. Ortholog analysis of SaPI ORFs

An ortholog list [43] was prepared for each of the 22 ORFs of SaPI-Mu50(V) listed along the abscissa. Each vertical bar represents all orthologs with ≥50% nucleotide sequence identity to the index ORF. The type of insert corresponding to each ortholog was determined by inspecting the KEGG genome pattern in the regions flanking the ORF. The data on which this chart is based are listed in online supplementary material, Table S1. Typical KEGG genome patterns for SaPIs and prophages are shown in online supplementary material Figs. 5A and B, respectively. Gray – NI - no insert; pink – prophage; blue – SaPI. Below the graph is a diagram of the genome of SaPI-Mu50(V) showing the genes corresponding to those in the graph.

Fig. 6. A. Genomes of lactococcal PICIs

Gene coloring is the same as in Fig. 1 with the addition of green for procapsid and light red-orange for the transposon in the NZ9000(0.03) element. Numbers after the strain names represent approximate genome locations. B. Genomes of phage-related elements from lactobacilli. Color coding is as in Fig. 1, with the addition of green for capsid morphogenesis. Annotations are from GenBank. Abbreviations in addition to those in Fig. 1: LsvCI-UC1118 – L. salivarius UCC118; PSrp – ribosome-associated protein; reg (c1) –λc1-like repressor; reg (cro) - λcro-like regulator; mFC – comF protein 3; LrCI-GG – L. rhamnosus GG; pep – phosphomonomutase-like protein; reg – regulation; HNH – HNH nuclease; terL – terminase large subunit; portal – portal protein; php – prohead protease; htj – head-tail joining protein. C. Hypothetical origins of proto-SaPI and GTA. At top is shown the genome of a generic prophage that could be from either a Gram+ or a Gram- organism. Below is shown a possible “proto-SaPI” consisting of the 5′ region of the prophage from int to terS. Below the “proto-SaPI” is shown the RcGTA, consisting of most of the 3′ region of the prophage from terS to the tape measure gene, but lacking the extreme 3′ end. Gene annotations are from the KEGG orthology lists [43] or from GenBank. Colors: yellow – int/xis; blue – regulatory; purple – replication; aqua – terS; green – capsid morphogenesis; - brown – tail morphogenesis; pink – lysis; orange –flanking genes; red box – replication origin.

Fig. 6. A. Genomes of lactococcal PICIs

Gene coloring is the same as in Fig. 1 with the addition of green for procapsid and light red-orange for the transposon in the NZ9000(0.03) element. Numbers after the strain names represent approximate genome locations. B. Genomes of phage-related elements from lactobacilli. Color coding is as in Fig. 1, with the addition of green for capsid morphogenesis. Annotations are from GenBank. Abbreviations in addition to those in Fig. 1: LsvCI-UC1118 – L. salivarius UCC118; PSrp – ribosome-associated protein; reg (c1) –λc1-like repressor; reg (cro) - λcro-like regulator; mFC – comF protein 3; LrCI-GG – L. rhamnosus GG; pep – phosphomonomutase-like protein; reg – regulation; HNH – HNH nuclease; terL – terminase large subunit; portal – portal protein; php – prohead protease; htj – head-tail joining protein. C. Hypothetical origins of proto-SaPI and GTA. At top is shown the genome of a generic prophage that could be from either a Gram+ or a Gram- organism. Below is shown a possible “proto-SaPI” consisting of the 5′ region of the prophage from int to terS. Below the “proto-SaPI” is shown the RcGTA, consisting of most of the 3′ region of the prophage from terS to the tape measure gene, but lacking the extreme 3′ end. Gene annotations are from the KEGG orthology lists [43] or from GenBank. Colors: yellow – int/xis; blue – regulatory; purple – replication; aqua – terS; green – capsid morphogenesis; - brown – tail morphogenesis; pink – lysis; orange –flanking genes; red box – replication origin.

Fig. 6. A. Genomes of lactococcal PICIs

Gene coloring is the same as in Fig. 1 with the addition of green for procapsid and light red-orange for the transposon in the NZ9000(0.03) element. Numbers after the strain names represent approximate genome locations. B. Genomes of phage-related elements from lactobacilli. Color coding is as in Fig. 1, with the addition of green for capsid morphogenesis. Annotations are from GenBank. Abbreviations in addition to those in Fig. 1: LsvCI-UC1118 – L. salivarius UCC118; PSrp – ribosome-associated protein; reg (c1) –λc1-like repressor; reg (cro) - λcro-like regulator; mFC – comF protein 3; LrCI-GG – L. rhamnosus GG; pep – phosphomonomutase-like protein; reg – regulation; HNH – HNH nuclease; terL – terminase large subunit; portal – portal protein; php – prohead protease; htj – head-tail joining protein. C. Hypothetical origins of proto-SaPI and GTA. At top is shown the genome of a generic prophage that could be from either a Gram+ or a Gram- organism. Below is shown a possible “proto-SaPI” consisting of the 5′ region of the prophage from int to terS. Below the “proto-SaPI” is shown the RcGTA, consisting of most of the 3′ region of the prophage from terS to the tape measure gene, but lacking the extreme 3′ end. Gene annotations are from the KEGG orthology lists [43] or from GenBank. Colors: yellow – int/xis; blue – regulatory; purple – replication; aqua – terS; green – capsid morphogenesis; - brown – tail morphogenesis; pink – lysis; orange –flanking genes; red box – replication origin.