Functional assignment of multiple catabolic pathways for d-apiose

Abstract

Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind D-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for D-apiose with eleven previously unknown reactions. The new enzymes include D-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible ( http://efi.igb.illinois.edu/efi-est/ ), so similar 'genomic enzymology' strategies for discovering novel pathways can be used by the community.

Revisiting the methionine salvage pathway and its paralogues

“…The RuBisCO-like enzymes (RLPs) involved in the catabolic pathway for D-apiose, a branched pentose present in rhamnogalacturonan-II-containing cell walls of higher plants and in apigalacturonan containing the cell walls of aquatic monocotshave activities reminiscent to those postulated here. As cases in point, the RLPs from Agrobacterium radiobacter K84 and Xanthobacter autotrophicus ATCC BAA-1158 catalyse decarboxylation and transcarboxylation/hydrolation of 3-oxo-isoapionate-4-phosphate (Carter et al, 2018). These newly identified pathways may thus be related to the fate of AdoMet after its involvement in the many pathways where it is an essential substrate before dioxygen was widespread.…”

‘Democratized’ genomic enzymology web tools for functional assignment

“…The descriptions of the Pfam families for the proteins encoded by the neighboring genes then can be used to infer a pathway for experimental testing. Examples of this strategy are available [32–34], the most recent describing the discovery of four catabolic pathways for D-apiose, a constituent of the rhamnogalacturonan- of plant cell walls [35]. …”

“…The bioinformatic community has developed a multitude of software platforms, e.g., Pythoscape [14] and ShortBRED [38] ( vide supra ), but these often are not easily accessible by experimentalists. EFI-EST and EFI-GNT described in this article have been developed and disseminated with resources provided by a Program Project (P01GM118303) focused on using SBPs for transport systems to discover novel enzymes in novel catabolic pathways [32–35]. his project benefits from the web tools—we recognized that they also would synergize other projects.…”

Ecogenomics of key prokaryotes in the arctic ocean

“…RuBisco Form IV and IV-like RuBisCo (or RuBisCo like proteins, RLP) do not perform CO2 fixation and may be involved in methionine salvage, sulfur metabolism and D-apiose catabolism 56,57 . RLPs were found in two Gammaproteobacteria MAGs (novel BACL14 sp.…”