Comparative genomics of cultured and uncultured strains suggests genes essential for free-living growth of Liberibacter

Abstract

The full genomes of two uncultured plant pathogenic Liberibacter, Ca. Liberibacter asiaticus and Ca. Liberibacter solanacearum, are publicly available. Recently, the larger genome of a closely related cultured strain, Liberibacter crescens BT-1, was described. To gain insights into our current inability to culture most Liberibacter, a comparative genomics analysis was done based on the RAST, KEGG, and manual annotations of these three organisms. In addition, pathogenicity genes were examined in all three bacteria. Key deficiencies were identified in Ca. L. asiaticus and Ca. L. solanacearum that might suggest why these organisms have not yet been cultured. Over 100 genes involved in amino acid and vitamin synthesis were annotated exclusively in L. crescens BT-1. However, none of these deficiencies are limiting in the rich media used to date. Other genes exclusive to L. crescens BT-1 include those involved in cell division, the stringent response regulatory pathway, and multiple two component regulatory systems. These results indicate that L. crescens is capable of growth under a much wider range of conditions than the uncultured Liberibacter strains. No outstanding differences were noted in pathogenicity-associated systems, suggesting that L. crescens BT-1 may be a plant pathogen on an as yet unidentified host.

Figure 1. Liberibacter genome alignment.

Microsynteny was observed across all three sequenced Liberibacter genomes, using L. crescens as a reference. From outer to inner circle: L. crescens (blue), CLso (yellow), CLas (green). Additionally, prophage regions (black) and rRNA operons (red) are denoted for L. crescens.

Figure 2. Venn Diagram showing genes shared between all three Liberibacter genomes.

A total of 2005 separate genes were identified based on RAST orf predictions. A sequence-based comparison showed that 822 of these are shared between all Liberibacter species studied. Liberibacter crescens (Lcres); Ca. Liberibacter asiaticus (CLas); and Ca. Liberibacter solanacearum (CLso).

Figure 3. KEGG pathway indicating the extent of Folate Biosynthesis in Liberibacter species.

All genomes lack alkaline phosphatase (EC 3.1.3.1.). This pathway is further incomplete in Ca. Liberibacter asiaticus, which has lost several enzymes for the production of Dihydrofolate (DHF).