Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria

Abstract

Background: ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact.

Results: Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants.

Conclusions: Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria.

Keywords: Genome evolution; Horizontal gene transfer; Mobile genetic elements (MGE); Phytopathology.

Fig. 1

Distribution of ICEs among bacterial strains. Solar explosion chart indicating the elements found in all strains. Bacterial species were arranged from the species with the largest number of elements to the species with the least number of elements and separated by color: Lilac: P. syringae; Dark blue: D. solani; Light blue: R. pseudosolanacearum; Green (from the darkest to the lightest, respectively): P. atrosepticum, X. fastidiosa, A. tumefaciens, X. campestris; Yellow: R. syzigii; Light orange: P. carotovorum; Dark orange: D. dadantii. From the inside out of the chart: The bacterial species, name of the strains, and the identified elements present in each strain. b Hierarchical organization of ICEs distribution around bacterial species, with color-coding in species as shown in the legend. The scale beside the plot shows the number of ICEs found for each species

Fig. 2

General ICES identification results. a Bar chart of ICEs number distribution by groups of bacteria (dark blue: total elements, light blue: different elements); b Distribution chart of genome size, in bases pair, compared to the size of ICEs; c The type of Integrases found in the ICEs. d The type of Relaxase family found in the ICEs. e Bar chart of ICEs size by species f) Bar chart of GC content of the ICEs by species

Fig. 3

Putative functions of ICEs genes. a Bar chart of putative roles codified by ICEs genes separated by categories (Unsure category comprises Hypothetical protein, Domain of unknown function (DUF genes), and genes with undetermined function). b Bar chart of Cargo genes divided by putative roles. c Pie chart representing putative roles of Virulence factors carried by ICEs

Fig. 4

Different Expression Analyses—RPKM Heatmaps: Significant genes of P. atrosapticum elements ICEPa1 and ICEPa2 (SCRI1043 isolate) in tobacco plants. a Coronafacic acid biosynthesis gene cluster carried by ICEPca1. b Cargo gene of ICEPca2 with putative Virulence role – Phospholipase D. c Relaxases of ICEPca1 and ICEPca2. Scaled expression values are color-coded, and the red color represents high expression. Abbreviation: Z1: Asymptomatic zone, Z2: Symptomatic zone

Fig. 5

P. syringae ICEs. a P. syringae ICEs co-occurrence and in-tandem configuration. (White rectangles: bacterial chromosomes – small colored rectangles: ICEs, the colors represent different elements); b P. syringae ICEs identity matrix heatmap: red—high identity, purple -intermediate white—low identity

Fig. 6

ICEs core-gene conservation and evolutionary history. a Plot of eight core genes found in ICEs dataset with the number of components of T4SS grouped by species. Blue colored square indicates the presence of the gene in the element and the colorless square indicates the absence. Abbreviation for Rec, Recombinase; T4CP, type-IV coupling proteins; topo III, topoisomerase III; Single-strand DNA-binding protein (SSB). b Maximum Likelihood tree based on the eight backbone gene alignments. The General Time Reversible model and a bootstrap confidence value of 1,000 were applied to the tree. The alignment and phylogenetic analysis were done using MEGA X. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site