Fig. 3.
Pectin degradation by the honey bee gut microbiota. (A) Proteins involved in pectin catabolism, for which respective genes were identified, are indicated in red. The illustrated pectin molecule shows the homo- and rhamnogalacturonate backbone with side chains (50) and cleavage sites for identified GHs and PLs. PaeY indicates a pectin acetyl esterase removing ester residues. Except for proteins marked with an asterisk, the encoding genes were present in the Gamma bin. Genes encoding the oligogalacturonide-specific porin KdgM, the inner-membrane transporters TogT, ExuT, and KdgT, and a pathway for galacturonide conversion were also identified. (B) Four different loci assigned to the Gamma bin encoding key proteins for pectin breakdown (scaffold numbers are indicated). The first two loci encode proteins involved in metabolism of PGA. The latter two might be involved in breakdown and metabolism of xylose side chains. Blue, green, magenta, and yellow indicate functions associated with glycoside cleavage, transport, cellular catabolism, and regulation, respectively. (C) PGA degradation is detected by the formation of clearance zones around bacterial lawns. The species to which each bacterial isolate belongs is indicated. γ, Gilliamella; β, Snodgrassella; α1, Alpha-1; and B, Bifido. (D) Maximum-likelihood protein phylogeny of metagenomic pectate lyases of the PL1 family and their closest homologs found in other bacteria as well as outgroups Aspergillus niger and Arabidopsis thaliana. Bootstrap values >80 and ecological niche of bacteria are indicated.