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.

Figure 1. Taxonomic distribution analysis of the F. succinogenes proteome.

The wide range of phyla/groups that F. succinogenes proteins are mapped to indicates it is not similar to other bacterial genomes, thereby confirming its placement into its own phylum.

Figure 2. An overview of metabolism and transport in Fibrobacte succinogenes S85.

Enzymes missing from metabolic pathways are indicated with a red cross. The major fermentative products succinate, acetate, and formate are shown with gray arrows indicating their export out of the cell. Predicted transporters are also shown, including sodium ion channel protein transporters in purple, ABC transporters in red, sec-dependent protein export in green, and other substrates in blue. Export or import of solutes is shown through the direction of the arrow through the transporter. Energy coupling mechanisms are also shown, including solutes transported by channel proteins; secondary transporters with two arrows into the cell indicating the solute and coupling ion; ATP-driven transporters with an ATP hydrolysis reaction; and transporters with an unknown energy-coupling mechanism, shown with a single arrow. Some multi-step pathways are not fully-represented, and are denoted with orange arrowheads. Abbreviations: AA, amino acids; Ala, alanine; Met, methionine; Pro, proline; PRPP, 5′-phospho-α-D-ribose 1-diphosphate; PEP, phosphoenolpyruvate; Meso 2,6 DAP, meso-2,6- diaminopimelic acid.