Fig 1.
The circular genome maps of the P. agglomerans KM1 draft genome.
Genome map showing the features of P. agglomerans KM1 chromosome and plasmids pKM1_1, pKM1_2, and pKM1_3. Circles illustrate the following from outermost to innermost rings: (1) forward CDS, (2) reverse CDS, (3) GC content, and (4) GC skew. All the annotated open reading frames (ORFs) are colored differently according to the COG assignments. Stacked bar chart shows the relative abundance (%) of COG categories calculated based on the total number of predicted ORFs present in the annotated genome.
Fig 2.
Phylogenetic analysis of P. agglomerans KM1.
A: Neighbor-joining phylogenetic tree showing the phylogenetic relationship between P. agglomerans KM1 and selected Pantoea strains. The neighbor-joining tree was constructed from an alignment of concatenated fusA, gyrB, leuS, pyrG, rplB, and rpoB gene sequences. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. Superscript “T” indicates a type strain. The scale bar represents the number of substitutions per site. Escherichia coli strain K12 substr. MG1655 was used as an outgroup. B: Heatmap showing the OrthoANI values between P. agglomerans KM1 genome and its closely related species. Values greater than 97% indicate that strains belong to the same species.
Fig 3.
Genome alignments showing synteny blocks among P. agglomerans strains obtained using progressive Mauve.
P. agglomerans KM1 were compared with other closely related strains namely C410P1, UAEU18, TH81 and L15. Each genome is laid out horizontally with homologous segment outlined as colored rectangles. Each same color block represents a locally collinear block (LCB) or homologous region shared among genomes. Rearrangement of genomic regions was observed between the two genomes in terms of collinearity. Inverted regions relative to KM1 are localized in the negative strand indicated by genomic position below the black horizontal centerline in the Mauve alignment.
Fig 4.
Genomic islands (GIs) in P. agglomerans strain KM1 predicted using IslandViewer4.
The predicted genomic islands are colored based on the prediction methods. Red indicates an integrated analysis, blue represents IslandPath-DIMOB prediction, orange represents SIGI-HMM prediction, and green indicates IslandPick analysis. The circular plots show the genomic islands in P. agglomerans KM1 chromosome, and plasmids pKM1_1, pKM1_2 and pKM1_3. GIs are labelled in blue. Prophage regions predicted by PHASTER were indicated in red boxes for prophage region 1 (P1) and region 2 (P2).
Table 1.
Antibiotic susceptibility profile of P. agglomerans KM1.
Table 2.
Genes associated with resistance to environmental stress in P. agglomerans KM1.
Table 3.
Virulence factors of P. agglomerans KM1.
Fig 5.
Pan-genome analysis of P. agglomerans strains obtained using Gview server.
The innermost circle shows the pan-genome (purple), and outer circlers indicate the genomes of Pantoea agglomerans strains L15 (orange), TH81 (brown), UAEU18 (red), C410P1 (blue), and KM1 (green). Genes with specialized functions were labelled with different colors: virulence-related genes (blue), antibiotic resistance genes (red), and strain-specific regions (black).
Fig 6.
Roary matrix-based pan-genome analysis of P. agglomerans strains.
The core-genome tree generated was compared with a matrix where the core and accessory genes were either present (blue) or absent (white).
Fig 7.
Cytokine and nitrite production by RAW 264.7 macrophages stimulated with a heat inactivated whole-cell P. agglomerans.
Panels A, D, G and J show TNF-α, IL-6, Nitrite and IL-10 secretion by the simulated RAW 264.7 cells (RAW), TLR4 knock-out RAW 264.7 cells (TLR4KO), RAW 264.7 cells (RAW) in combination with TLR2 inhibitor (RAW+ TLR2 inhib), TLR4 knock-out RAW 264.7 cells in combination with TLR2 inhibitor (TLR4KO + TLR2 inhib.). Additionally stimulations were performed using RAW 264.7 cells in combination with NFκB inhibitor (RAW+NFκB inhib.), TLR4 knock-out RAW 264.7 cells in combination with NFκB inhibitor (TLR4KO + NFκB inhib.) and RAW 264.7 cells in combination with MEK1/2 inhibitor (RAW + MEK inhib.). Panels B, E, H, and K, include control conditions: RAW 264.7 cells stimulated with TLR4 agonist ultrapure LPS (RAW + LPS), TLR4 knock-out RAW 264.7 cells stimulated with TLR4 agonist ultrapure LPS (TLR4KO + LPS), non-stimulated RAW 264.7 cells (RAW control), non-stimulated TLR4 knock-out RAW 264.7 cells (TLR4 control). Panels C, F, I and L include control stimulations: RAW 264.7 cells and TLR4 knock-out RAW 264.7 cells in the presence of inhibitors alone, RAW + TLR2 inhibitor, TLR4KO + TLR2 inhibitor, RAW + NFκB inhibitor, TLR4KO + NFκB inhibitor, and RAW + MEK inhibitor. Values with P < 0.001 were considered as significantly different (****).