Unraveling the pectinolytic function of Bacteroides xylanisolvens using a RNA-seq approach and mutagenesis.

Jordane Despres,Grégory Jubelin,Bryan A White,Sophie Comtet-Marre,Evelyne Forano,Margret E Berg Miller,Bernard Henrissat,Christopher J Fields,Catherine M.G.C Renard,Carine Le Bourvellec,Nicolas Terrapon,Pascale Mosoni,Carl J Yeoman,Pascale Lepercq

doi:10.1186/s12864-016-2472-1

Abstract

BackgroundDiet and particularly dietary fibres have an impact on the gut microbiome and play an important role in human health and disease. Pectin is a highly consumed dietary fibre found in fruits and vegetables and is also a widely used additive in the food industry. Yet there is no information on the effect of pectin on the human gut microbiome. Likewise, little is known on gut pectinolytic bacteria and their enzyme systems. This study was undertaken to investigate the mechanisms of pectin degradation by the prominent human gut symbiont Bacteroides xylanisolvens.ResultsTranscriptomic analyses of B. xylanisolvens XB1A grown on citrus and apple pectins at mid- and late-log phases highlighted six polysaccharide utilization loci (PUL) that were overexpressed on pectin relative to glucose. The PUL numbers used in this report are those given by Terrapon et al. (Bioinformatics 31(5):647-55, 2015) and found in the PUL database: http://www.cazy.org/PULDB/. Based on their CAZyme composition, we propose that PUL 49 and 50, the most overexpressed PULs on both pectins and at both growth phases, are involved in homogalacturonan (HG) and type I rhamnogalacturonan (RGI) degradation, respectively. PUL 13 and PUL 2 could be involved in the degradation of arabinose-containing side chains and of type II rhamnogalacturonan (RGII), respectively. Considering that HG is the most abundant moiety (>70 %) within pectin, the importance of PUL 49 was further investigated by insertion mutagenesis into the susC-like gene. The insertion blocked transcription of the susC-like and the two downstream genes (susD-like/FnIII). The mutant showed strong growth reduction, thus confirming that PUL 49 plays a major role in pectin degradation.ConclusionThis study shows the existence of six PULs devoted to pectin degradation by B. xylanisolvens, one of them being particularly important in this function. Hence, this species deploys a very complex enzymatic machinery that probably reflects the structural complexity of pectin. Our findings also highlight the metabolic plasticity of B. xylanisolvens towards dietary fibres that contributes to its competitive fitness within the human gut ecosystem. Wider functional and ecological studies are needed to understand how dietary fibers and especially plant cell wall polysaccharides drive the composition and metabolism of the fibrolytic and non-fibrolytic community within the gut microbial ecosystem.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2472-1) contains supplementary material, which is available to authorized users.

Highlights

Diet and dietary fibres have an impact on the gut microbiome and play an important role in human health and disease
The third polysaccharide bears the confusing name of rhamnogalacturonan II (RGII), it is a backbone of HG rather than RG, with complex side chains of rare sugars attached to the galacturonic acid (GalA) residues
Upregulation of potential Pectin Utilization Loci in B. xylanisolvens XB1A B. xylanisolvens XB1A grows at a rate comparable to that seen with glucose, when commercial citrus and carbohydrate active enzyme (CAZyme) family Enzyme function

Summary

Introduction

Diet and dietary fibres have an impact on the gut microbiome and play an important role in human health and disease. Symbiotic microorganisms that reside in the human large intestine have the capacity to utilize and convert dietary fibres into simple molecules such as the short chain fatty acids acetate, propionate and butyrate that provide an important energy source to the host and additional health benefits [3,4,5,6,7]. Plant cell wall (PCW) polysaccharide components are much more difficult to study because of their molecular complexity and the difficulty preparing homogenous and pure fractions. This is true for pectin, which is composed of as many as 17 different monosaccharides and more than 20 different linkages [10]. RGI is the most heterogeneous of these three pectic polysaccharides because of its diverse sugar composition and the variation in length of sugar side chains whereas RGII is thought to have a highly conserved structure [11]

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