Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system

Bareket Dassa,Raphael Lamed,Bernard Henrissat,Ilya Borovok,Edward A Bayer,Yue Huang,Pedro Coutinho,Jizhong Zhou,Christopher L Hemme

doi:10.1186/1471-2164-13-210

Abstract

BackgroundMicrobial degradation of plant cell walls and its conversion to sugars and other byproducts is a key step in the carbon cycle on Earth. In order to process heterogeneous plant-derived biomass, specialized anaerobic bacteria use an elaborate multi-enzyme cellulosome complex to synergistically deconstruct cellulosic substrates. The cellulosome was first discovered in the cellulolytic thermophile, Clostridium thermocellum, and much of our knowledge of this intriguing type of protein composite is based on the cellulosome of this environmentally and biotechnologically important bacterium. The recently sequenced genome of the cellulolytic mesophile, Acetivibrio cellulolyticus, allows detailed comparison of the cellulosomes of these two select cellulosome-producing bacteria.ResultsComprehensive analysis of the A. cellulolyticus draft genome sequence revealed a very sophisticated cellulosome system. Compared to C. thermocellum, the cellulosomal architecture of A. cellulolyticus is much more extensive, whereby the genome encodes for twice the number of cohesin- and dockerin-containing proteins. The A. cellulolyticus genome has thus evolved an inflated number of 143 dockerin-containing genes, coding for multimodular proteins with distinctive catalytic and carbohydrate-binding modules that play critical roles in biomass degradation. Additionally, 41 putative cohesin modules distributed in 16 different scaffoldin proteins were identified in the genome, representing a broader diversity and modularity than those of Clostridium thermocellum. Although many of the A. cellulolyticus scaffoldins appear in unconventional modular combinations, elements of the basic structural scaffoldins are maintained in both species. In addition, both species exhibit similarly elaborate cell-anchoring and cellulosome-related gene- regulatory elements.ConclusionsThis work portrays a particularly intricate, cell-surface cellulosome system in A. cellulolyticus and provides a blueprint for examining the specific roles of the various cellulosomal components in the degradation of complex carbohydrate substrates of the plant cell wall by the bacterium.

Highlights

IntroductionPlant cell walls are composed of different types of recalcitrant polysaccharides, notably cellulose, which together with lignin form a rigid, stable composite material
Microbial degradation of plant cell walls and its conversion to sugars and other byproducts is a key step in the carbon cycle on Earth
The previous publications have indicated that this mesophilic bacterium harbors an intricate cellulosome system, which is characterized by several unique properties that distinguish A. cellulolyticus from the archetypical C. thermocellum cellulosome: The progression of the ScaA primary scaffoldin, the ScaB adaptor scaffoldin and the ScaC anchoring scaffoldin, with their resident cohesins (7, 4 and 3, respectively), suggests that the resultant fully occupied cellulosome complex would include up to 84 dockerin- containing proteins in addition to the intrinsic ScaA cellulase

Summary

Introduction

Plant cell walls are composed of different types of recalcitrant polysaccharides, notably cellulose, which together with lignin form a rigid, stable composite material. Microbial degradation of these polysaccharides and its conversion to sugars is a key step in the carbon cycle, and its subsequent conversion to ethanol is a vital objective for of the free enzyme systems of other bacteria and fungi, except that the cellulosomal enzymes contain a dockerin module in place of a carbohydrate-binding module (CBM), which would target the individual enzymes to the substrate. Acetivibrio cellulolyticus is a mesophilic, anaerobic, gram-positive bacterium, known both for its efficient degradation of crystalline cellulose [12,13,14,15] and for its distinct protuberant cell surface ultrastructure [16]. Only four scaffoldin proteins of the bacterium have been recognized and analyzed prior to sequencing of its genome [22]

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