The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T

Abstract

Here we report the draft genome of Yersinia entomophaga type strain MH96T. The genome shows 93.8% nucleotide sequence identity to that of Yersinia nurmii type strain APN3a-cT, and comprises a single chromosome of approximately 4,275,531 bp. In silico analysis identified that, in addition to the previously documented Y. entomophaga Yen-TC gene cluster, the genome encodes a diverse array of toxins, including two type III secretion systems, and five rhs-associated gene clusters. As well as these multicomponent systems, several orthologs of known insect toxins, such as VIP2 toxin and the binary toxin PirAB, and distant orthologs of some mammalian toxins, including repeats-in-toxin, a cytolethal distending toxin, hemolysin-like genes and an adenylate cyclase were identified. The genome also contains a large number of hypothetical proteins and orthologs of known effector proteins, such as LopT, as well as genes encoding a wide range of proteolytic determinants, including metalloproteases and pathogen fitness determinants, such as genes involved in iron metabolism. The bioinformatic data derived from the current in silico analysis, along with previous information on the pathobiology of Y. entomophaga against its insect hosts, suggests that a number of these virulence systems are required for survival in the hemocoel and incapacitation of the insect host.

Keywords: Rhs; Yersinia entomophaga; Yersinia nurmii; Yersinia ruckeri; entomopathogen; genome sequence.

Figure 1

Genome Atlas diagram of the Y. entomophaga genome compared with those of Y. enterocolitica 8081 and Y. ruckeri ATCC 29473. The image represents a circular view of the complete genome sequence. Innermost circle 1: GC-Skew. Circle 2: COG classification: 1. information storage and processing; 2. cellular processes and signaling; 3. metabolism; 4. poorly characterized; and 5. ORFs with uncharacterized COGs or no COG assignment. Circle 3: Prediction of membrane-bound and cell surface proteins. White: no transmembrane helices (TMH) were identified. Black: ORFs with at least one TMH. Red: ORFs predicted to encompass a signal peptide sequence. Blue: ORFs predicted to incorporate both TMH and a signal peptide sequence. Circle 4: ORF orientation. ORFs in the sense orientation (ORF+) are shown in blue; ORFs oriented in the anti-sense direction (ORF−) are in red. Circle 5: G+C content deviation. Deviations from the average G+C content are shown in either green (low G+C spike) or orange (high G+C spike). Circles 6–8: BlastP comparison of the Y. entomophaga ORFeome with custom Y. enterocolitica 8081, Y. ruckeri ATCC 29473 Blast databases. Regions in blue represent unique proteins in Y. entomophaga, while highly conserved features are shown in red. The degree of color saturation corresponds with the level of similarity. Circle 9: Order of the numbered contigs comprising the draft genome. Contig names are shown in red, refer to Section 4.3 for contig information. Regions and ORFs of specific interest are shown at their respective genome location, bars are drawn to scale.

Figure 2

Schematic of virulence-associated Regions 1 (A) and 2 (B), which encode a range of toxin components, iron acquisition systems, and adhesin-encoding genes. The positions of Regions 1 and 2 relative to the draft Y. entomophaga genome sequence are shown in Figure 1. Arrows denote: speckled: putative virulence determinant; grey fill: characterized ortholog; horizontal waves: proteolytic/substrate binding protein; no fill: hypothetical protein; checkered: regulator protein; cross-hatched: fimbrial/pili-associated protein. Selected loci are labeled, refer to Table 1 for locus annotation.

Figure 3

Schematic of Y. entomophaga Rhs-associated regions Rhs2–Rhs5. The positions of Rhs-associated regions relative to the draft Y. entomophaga genome sequence are shown in Figure 1. Arrows denote: speckled: putative virulence determinant; black fill: IS or transposon element; forward diagonal: Rhs element; grey fill: characterized ortholog; no fill: hypothetical protein; checkered: regulator. Dashed horizontal line denotes region of ~70% DNA identity of the Rhs-associated Region 3 to the S. fonticola strain DSM 4576 genome sequence (gb|CP011254.1). Box foward diagonals located within Rhs-associated Region 3, denotes BlastX non functional translated Rhs similarty. tRNA loci are indicated, selected loci are labeled, refer to Table S2 for locus annotation.

Figure 4

Schematic of the Y. entomophaga type II (T2SS) and III (T3SS) secretion systems. (A) the Y. entomophaga T3SSs T3SSYE1 and T3SSYE2. Orthologs shared between T3SSYE1 and T3SSYE2 are similarly shaded. (B) Y. entomophaga type II (T2SS). Arrows denote: black fill: IS or transposon element; grey fill: characterized ortholog; no fill: hypothetical protein; checkered: regulator protein; verticle dashes: cellular transport protein. tRNA loci are indicated, selected loci are labeled, refer to Table S3, for locus annotation. The positions of these protein secretion regions relative to the draft Y. entomophaga genome sequence are shown in Figure 1.

Figure 5

Schematic of putative Y. entomophaga accessory virulence determinants. The positions of these virulence determinants relative to the draft Y. entomophaga genome sequence are shown in Figure 1. Arrows denote: speckled: putative virulence determinant; grey fill: characterized ortholog; no fill: hypothetical protein; checkered: regulator protein; cross-hatched: fimbrial/pili-associated protein; horizontal waves: proteolytic/substrate binding protein; verticle dashes: cellular transport protein. Selected loci are labeled, refer to Table S4 for locus annotation.

Figure 6

Amino acid sequence alignment of the Y. entomophaga serralysins PL78_03960; PL78_03965; PL78_03970. The Zn-endopeptidase metal-binding motif (HexxHxxGxxH) is indicated. Refer to Figure 2A for relative position of the serralysin-associated gene cluster within Region 1.

Figure 7

Schematic of selected Y. entomophaga cell surface appendage-encoding genes. Fimbrial-associated island (FAI_YE96)-, cellulose gene cluster (CEL)-, and the lipopolysaccharide (LPS)-encoding regions. The positions of these regions relative to the draft Y. entomophaga genome sequence are shown in Figure 1. Arrows denote: checkered: regulator; cross-hatched: fimbrial/pili-associated protein; verticle dashes: cellular transport; grey fill: characterized ortholog; no fill: hypothetical protein; tRNA loci are indicated, selected loci are labeled, refer to Table S5 for locus annotation.