Tomato root-associated
Sphingobium
harbors genes for catabolizing toxic steroidal glycoalkaloids
Authors: Nakayasu Masaru , Takamatsu Kyoko , Kanai Keiko , Masuda Sachiko , Yamazaki Shinichi , Aoki Yuichi , Shibata Arisa , Suda Wataru , Shirasu Ken , Yazaki Kazufumi , Sugiyama Akifumi 
Published: September 2023

Plant roots exude various organic compounds, including plant specialized metabolites (PSMs), into the rhizosphere. The secreted PSMs enrich specific microbial taxa to shape the rhizosphere microbiome, which is crucial for the healthy growth of the host plants. PSMs often exhibit biological activities; in turn, some microorganisms possess the capability to either resist or detoxify them. Saponins are structurally diverse triterpene-type PSMs that are mainly produced by angiosperms. They are generally considered as plant defense compounds. We have revealed that α-tomatine, a steroid-type saponin secreted from tomato (
Solanum lycopersicum
) roots, increases the abundance of
Sphingobium
bacteria. To elucidate the mechanisms underlying the α-tomatine-mediated enrichment of
Sphingobium
, we isolated
Sphingobium
spp. from tomato roots and characterized their saponin-catabolizing abilities. We obtained the whole-genome sequence of
Sphingobium
sp. RC1, which degrades steroid-type saponins but not oleanane-type ones, and performed a gene cluster analysis together with a transcriptome analysis of α-tomatine degradation. The
in vitro
characterization of candidate genes identified six enzymes that hydrolyzed the different sugar moieties of steroid-type saponins at different positions. In addition, the enzymes involved in the early steps of the degradation of sapogenins (i.e., aglycones of saponins) were identified, suggesting that orthologs of the known bacterial steroid catabolic enzymes can metabolize sapogenins. Furthermore, a comparative genomic analysis revealed that the saponin-degrading enzymes were present exclusively in certain strains of
Sphingobium
spp., most of which were isolated from tomato roots or α-tomatine-treated soil. Taken together, these results suggest a catabolic pathway for highly bioactive steroid-type saponins in the rhizosphere.

IMPORTANCE

Saponins are a group of plant specialized metabolites with various bioactive properties, both for human health and soil microorganisms. Our previous works demonstrated that
Sphingobium
is enriched in both soils treated with a steroid-type saponin, such as tomatine, and in the tomato rhizosphere. Despite the importance of saponins in plant–microbe interactions in the rhizosphere, the genes involved in the catabolism of saponins and their aglycones (sapogenins) remain largely unknown. Here we identified several enzymes that catalyzed the degradation of steroid-type saponins in a
Sphingobium
isolate from tomato roots, RC1. A comparative genomic analysis of
Sphingobium
revealed the limited distribution of genes for saponin degradation in our saponin-degrading isolates and several other isolates, suggesting the possible involvement of the saponin degradation pathway in the root colonization of
Sphingobium
spp. The genes that participate in the catabolism of sapogenins could be applied to the development of new industrially valuable sapogenin molecules.