Phylogenetic position of strain S32 and J9 based on the gapA sequences. This analysis was performed using the gapA sequences of strains belonging to well-characterized Serratia species, and of Serratia sp. strains whose genome encodes a PL1 pectate lyase. The gene gapA of Chania multitudinisentens was used as an outgroup. The evolutionary history was inferred using the neighbour-joining method . The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the branches . The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site (718 positions). Evolutionary analyses were conducted in MEGA7 .

Phylogenetic tree of the PL1 protein Pel1 of strain S32. The evolutionary history was inferred using the neighbour-joining method . The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches . The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site (430 positions). Evolutionary analyses were conducted in MEGA7 . This analysis was performed using the sequences of the different Serratia strains encoding a PL1 protein. A homologous protein of Cellulosimicrobium cellulans was used as an outgroup.

Genes and proteins of strain S32 potentially involved in pectin catabolism. A: Genetic organization. Genes are symbolized by arrows; their name and ID number are given. B: Proposed metabolic pathway deduced from the predicted protein localization and from the function of homologous proteins. The extracellularly pectate lyase Pel1 generates unsaturated oligogalacturonides (u-oligoGalA) up to dimers (u-diGalA, unsaturated digalacturonide). The activity of outer membrane anchored polygalacturonases, PehA and PehB, generates saturated oligomers up to dimers (oligoGalA, oligogalacturonides; diGalA, digalacturonide). Extracellular oligomers enter the periplasm using the specific outer-membrane porin, KdgM. Short oligomers enter the cytoplasm using two specific transporters, TogMNAB and TogT. In the cytoplasm, they are further cleaved up monomers by the action of the exopolygalacturonase PehX and the oligogalacturonate lyase, Ogl. The two pathways involved in the catabolism of galacturonate (GalA) and unsaturated galacturonate (uGalA) converge to produce a common intermediate, KDG (2-keto-3-deoxygluconate) which is converted to pyruvate and glyceraldehyde 3-phosphate.