Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus

Abstract

Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications.

Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification

“…Using a combination of biochemical and physiological approaches, we have determined that the four GH3 members of Cellvibrio japonicus play unique roles in targeting different glucosidic linkages in diverse polysaccharides. Our work further illuminates the mechanism by which this model saprophyte, which has served as a treasure trove for CAZyme discovery for decades (Hazlewood and Gilbert, 1998;Gardner, 2016), utilizes the ubiquitous plant cell wall matrix glycans MLG, XyG and callose. As such, the use of truly systems biology approaches is XyG hydrolysis is initiated outside of the cell by endoxyloglucanases (e.g., CjGH74 (Attia et al, 2016)), followed by XyGO transport into the periplasm by a TonB-dependent transporter (TBDT).…”

“…Of these, the Gram-negative bacterium Cellvibrio japonicus (formerly Pseudomonas fluorescens subsp. cellulosa) has emerged as a powerful system for biomass enzyme discovery, due to its ability to degrade nearly all plant cell wall polysaccharides via the production of more than 150 Carbohydrate-Active enZymes (CAZymes) from 59 glycoside hydrolase (GH), polysaccharide lyase (PL), carbohydrate esterase (CE) and auxiliary activity (AA) families (Deboy et al, 2008;Lombard et al, 2014;Gardner, 2016). Moreover, robust reversegenetic and transcriptomic tools for C. japonicus have been developed, which significantly enable systems biology and metabolic engineering for industrial applications (Gardner and Keating, 2010a;Larsbrink et al, 2014a;Nelson et al, 2015;Forsberg et al, 2016;Gardner et al, 2014).…”

The complex physiology of Cellvibrio japonicus xylan degradation relies on a single cytoplasmic β‐xylosidase for xylo‐oligosaccharide utilization

“…do not appear to organize CAZyme genes in operons, which is in contrast to Bacteroides sp. where CAZyme genes are often clustered into large Polysaccharide Utilization Loci (PULs) (DeBoy et al, 2008;Dodd et al, 2011;Gardner, 2016). Therefore, the study of xylanase CAZyme coregulation and synergy is not trivial for Cellvibrio sp.…”

Systems analysis of the glycoside hydrolase family 18 enzymes from Cellvibrio japonicus characterizes essential chitin degradation functions

“…One reason for this lack of knowledge is the multiplicity of chitinolytic enzymes in many, but not all, chitindegrading bacteria, which makes functional analysis of the individual enzymes challenging. While several model organisms have been used to study chitin degradation (16)(17)(18), one that is emerging as a powerful model, due to the available systems biology tools, is the saprophytic Gram-negative bacterium Cellvibrio japonicus (19,20). This bacterium is a potent chitin degrader (13), and has a suite of nine genes encoding enzymes with predicted functions in chitin degradation (21).…”