The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist

Abstract

Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.

Functional Screening and In Vitro Analysis Reveal Thioesterases with Enhanced Substrate Specificity Profiles That Improve Short-Chain Fatty Acid Production in Escherichia coli

“…The second source of thioesterases, Pseudomonas putida KT2440 (GenBank accession number NC_002947.3), was chosen for its phylogenetic similarity to E. coli and because it is a known producer of polyhydroxyalkanoates, which may indicate the presence of thioesterases with specificity to 3-hydroxy acyl-CoAs (31). The remaining three organisms, Prevotella ruminicola 23 (GenBank accession number NC_014033.1), Fibrobacter succinogenes S85 (GenBank accession number NC_017448.1), and Ruminococcus albus 7 (GenBank accession number NC_014833.1), were chosen because they are prevalent in the cow rumen microbiome and contribute to the high concentrations of SCFAs found there (3,4,32). Each of the 62 putative thioesterases was individually overexpressed in E. coli containing all the necessary genes for CoA-dependent biosynthesis of valerate (Fig.…”

“…The resulting profusion of metabolic diversity provides a wealth of potential enzymes with known genetic sequences for improving biosynthetic pathways. For example, recent genomic sequencing has unveiled the metabolic diversity of important members from the cow rumen microbiome, an environment rich in SCFAs (3,4). These genome sequences provide an opportunity to find enzymes that improve production and specificity in SCFA biosynthesis pathways.…”

Rumen microbial (meta)genomics and its application to ruminant production

“…Data from the two bovine metagenome studies (Brulc et al, 2009;Hess et al, 2011), the muskoxen microbial eukaryotic metatranscriptomic study (Qi et al, 2011), and the completed genome sequences of four representative fibrolytic rumen bacteria. These are Butyrivibrio proteoclasticus B316 (Kelly et al, 2010), Fibrobacter succinogenes S85 (Suen et al, 2011), Prevotella ruminicola 23 (Purushe et al, 2010) and Ruminococcus albus 7. Information on their GH profiles was obtained from the CAZy database (http://www.cazy.org/).…”

Caldicellulosiruptor Core and Pangenomes Reveal Determinants for Noncellulosomal Thermophilic Deconstruction of Plant Biomass

“…Crystalline cellulose deconstruction via cell membrane-bound cellulosomes was first described in the thermophile Clostridium thermocellum and has since been described in other mesophilic Firmicutes, such as Clostridium cellulolyticum, Acetivibrio cellulolyticus, and Ruminococcus flavefaciens (3). Analysis of genome sequence data from biomass-degrading microorganisms has helped to identify noncellulosomal bacteria that also lack identifiable cellobiohydrolases, such as Cytophaga hutchinsonii (96) and Fibrobacter succinogenes (77), both of which require close attachment to cellulose for efficient hydrolysis, and Sacharophagus degradans (95), which uses processive endocellulases (94), indicating that there is great diversity in strategies used for crystalline cellulose hydrolysis. As members of the phylum Firmicutes, Caldicellulosiruptor species are distinct from the thermophilic, anaerobic clostridia in that they secrete free and S-layer-bound cellulases and hemicellulases (9,23,24,43,44,58,60,63,75,84,89,90) that are not assembled into cellulosomes (85,89).…”