Genome-wide identification of genes important for growth of dickeya dadantii and dickeya dianthicola in potato (solanum tuberosum) tubers

Authors: Helmann, Tyler; Filiatrault, Melanie; Stodghill, Paul

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2022
Publication Date: 1/25/2022
Citation: Helmann, T.C., Filiatrault, M.J., Stodghill, P. 2022. Genome-wide identification of genes important for growth of dickeya dadantii and dickeya dianthicola in potato (solanum tuberosum) tubers. Frontiers in Microbiology. 13:778927. https://doi.org/10.3389/fmicb.2022.778927.
DOI: https://doi.org/10.3389/fmicb.2022.778927

Interpretive Summary: Soft rot bacteria such as Dickeya cause disease in various important crops including potato. There are still considerable gaps in our knowledge of the bacterial factors that allow specific Dickeya species to be successful plant colonizers and what genes are critical for survival in various hosts. In this study we constructed and mapped barcoded transposon libraries in Dickeya dadantii and D. dianthicola to identify genes that contributed to host colonization and survival. Bacteria with barcoded transposon insertions were inoculated into potato tubers to identify genes that contributed to bacterial fitness during the development of potato soft rot. We identified shared and unique Dickeya genes essential for survival in potato tubers. This study also revealed the importance during growth in tubers of five novel transcriptional regulators. This research provides insight into the mechanisms soft rot pathogens use to cause disease.

Technical Abstract: Dickeya species are causal agents of soft rot diseases in many economically important crops, including soft rot disease of potato (Solanum tuberosum). Using random barcode transposon-site sequencing (RB-TnSeq), we generated genome-wide mutant fitness profiles of D. dadantii 3937, D. dianthicola ME23, and D. dianthicola 67-19 isolates collected after passage through in vitro (LB, Potato Dextrose Broth, and M9 minimal medium) and in vivo (tubers) conditions. The potato cultivars “Atlantic”, “Dark Red Norland”, and “Upstate Abundance” provided highly similar local conditions for bacterial growth. Using the homolog detection software PyParanoid, we matched fitness values for orthologous genes in the three strains. Direct comparison of fitness among the strains highlighted shared and variable traits important for growth. Bacterial growth in minimal medium required many metabolic traits that were also essential for competitive growth in planta, such as amino acid, carbohydrate, and nucleotide biosynthesis. Growth in tubers specifically required the pectin degradation gene kduD. Disruption in three putative DNA-binding proteins had strain-specific effects on competitive fitness in tubers. Though the Soft Rot Pectobacteriaceae can cause disease with little host specificity, it remains to be seen the extent to which strain-level variation impacts virulence.