Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria
Open Access
- 18 June 2012
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 7 (6), e39331
- https://doi.org/10.1371/journal.pone.0039331
Abstract
Cellulose degrading enzymes have important functions in the biotechnology industry, including the production of biofuels from lignocellulosic biomass. Anaerobes including Clostridium species organize cellulases and other glycosyl hydrolases into large complexes known as cellulosomes. In contrast, aerobic actinobacteria utilize systems comprised of independently acting enzymes, often with carbohydrate binding domains. Numerous actinobacterial genomes have become available through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. We identified putative cellulose-degrading enzymes belonging to families GH5, GH6, GH8, GH9, GH12, GH48, and GH51 in the genomes of eleven members of the actinobacteria. The eleven organisms were tested in several assays for cellulose degradation, and eight of the organisms showed evidence of cellulase activity. The three with the highest cellulase activity were Actinosynnema mirum, Cellulomonas flavigena, and Xylanimonas cellulosilytica. Cellobiose is known to induce cellulolytic enzymes in the model organism Thermobifida fusca, but only Nocardiopsis dassonvillei showed higher cellulolytic activity in the presence of cellobiose. In T. fusca, cellulases and a putative cellobiose ABC transporter are regulated by the transcriptional regulator CelR. Nine organisms appear to use the CelR site or a closely related binding site to regulate an ABC transporter. In some, CelR also regulates cellulases, while cellulases are controlled by different regulatory sites in three organisms. Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms.Keywords
This publication has 39 references indexed in Scilit:
- A phylogeny-driven genomic encyclopaedia of Bacteria and ArchaeaNature, 2009
- Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T)Standards in Genomic Sciences, 2009
- CebR as a Master Regulator for Cellulose/Cellooligosaccharide Catabolism Affects Morphological Development in Streptomyces griseusJournal of Bacteriology, 2009
- IMG ER: a system for microbial genome annotation expert review and curationBioinformatics, 2009
- Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptationsGenome Research, 2009
- The Carbohydrate-Active EnZymes database (CAZy): an expert resource for GlycogenomicsNucleic Acids Research, 2008
- Dendroscope: An interactive viewer for large phylogenetic treesBMC Bioinformatics, 2007
- Locating proteins in the cell using TargetP, SignalP and related toolsNature Protocols, 2007
- Genome Sequence and Analysis of the Soil Cellulolytic ActinomyceteThermobifida fuscaYXJournal of Bacteriology, 2007
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994