Genomic diversity and organization of complex polysaccharide biosynthesis clusters in the genus Dickeya

Abstract

The pectinolytic genus Dickeya (formerly Erwinia chrysanthemi) comprises numerous pathogenic species which cause diseases in various crops and ornamental plants across the globe. Their pathogenicity is governed by complex multi-factorial processes of adaptive virulence gene regulation. Extracellular polysaccharides and lipopolysaccharides present on bacterial envelope surface play a significant role in the virulence of phytopathogenic bacteria. However, very little is known about the genomic location, diversity, and organization of the polysaccharide and lipopolysaccharide biosynthetic gene clusters in Dickeya. In the present study, we report the diversity and structural organization of the group 4 capsule (G4C)/O-antigen capsule, putative O-antigen lipopolysaccharide, enterobacterial common antigen, and core lipopolysaccharide biosynthesis clusters from 54 Dickeya strains. The presence of these clusters suggests that Dickeya has both capsule and lipopolysaccharide carrying O-antigen to their external surface. These gene clusters are key regulatory components in the composition and structure of the outer surface of Dickeya. The O-antigen capsule/group 4 capsule (G4C) coding region shows a variation in gene content and organization. Based on nucleotide sequence homology in these Dickeya strains, two distinct groups, G4C group I and G4C group II, exist. However, comparatively less variation is observed in the putative O-antigen lipopolysaccharide cluster in Dickeya spp. except for in Dickeya zeae. Also, enterobacterial common antigen and core lipopolysaccharide biosynthesis clusters are present mostly as conserved genomic regions. The variation in the O-antigen capsule and putative O-antigen lipopolysaccharide coding region in relation to their phylogeny suggests a role of multiple horizontal gene transfer (HGT) events. These multiple HGT processes might have been manifested into the current heterogeneity of O-antigen capsules and O-antigen lipopolysaccharides in Dickeya strains during its evolution.

Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage vB_Dsol_D5 (ΦD5) results in fitness tradeoffs for the bacterium during infection

“…Two operons of D. solani strain IPO 2222 involved in the interaction of the bacterium m with lytic bacteriophage ΦD5. (A) Operon associated with rfa gene cluster involved in thee biosynthesis of the core region of LPS in Gram-negative bacteria and (B) Putative O-antigen LPS biosynthesis cluster (Ranjan et al, 2021). The D. solani IPO 2222 ORFs affectctedby the Tn5 insertion are marked in blue.…”

“…The role of WbeA has not been assessed in detail in plant pathogenic bacteria yet. Likewise, the knowledge of the function of WbeA in the ecology and pathogenicity of SRP bacteria is limited (Ranjan et al, 2021). wbeA gene is a conserved member of the putative O-antigen LPS gene cluster present in members of the genus Dickeya spp.…”

“…Specifically, these operons are participating in the biosynthesis of the core region of LPS together with the biosynthesis of O-antigen of LPS in Gram-negative bacteria (Fig. 1) (Schnaitman and Klena, 1993; Ranjan et al, 2021). As no phage resistant mutants analyzed in this study had Tn5 insertions in other D. solani genes and operons, we believe bacterial envelope components ( viz .…”

“…wbeA gene is a conserved member of the putative O-antigen LPS gene cluster present in members of the genus Dickeya spp. (Ranjan et al, 2021). Its glycosyltransferase activity and genomic location suggest that its involvement in LPS synthesis, together with another glycosyltransferase WbeB, present in the same operon (Ranjan et al, 2021).…”

Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae

“…[ 97 , 98 , 99 , 100 , 101 , 102 ] and Dickeya sp. [ 80 , 95 , 103 , 104 ] have been revealed by NMR, and they were found to be very diverse. It is reasonable to propose that additional tailspikes should provide recognition of OPS with different structures.…”