Summary: A cellulolytic fiber‐degrading bacterium, R uminococcus champanellensis , was isolated from human faecal samples, and its genome was recently sequenced. Bioinformatic analysis of the R . champanellensis genome revealed numerous cohesin and dockerin modules, the basic elements of the cellulosome, and manual sequencing of partially sequenced genomic segments revealed two large tandem scaffoldin‐coding genes that form part of a gene cluster. Representative R . champanellensis dockerins were tested against putative cohesins, and the results revealed three different cohesin–dockerin binding profiles which implied two major types of cellulosome architectures: (i) an intricate cell‐bound system and (ii) a simplistic cell‐free system composed of a single cohesin‐containing scaffoldin. The cell‐bound system can adopt various enzymatic architectures, ranging from a single enzyme to a large enzymatic complex comprising up to 11 enzymes. The variety of cellulosomal components together with adaptor proteins may infer a very tight regulation of its components. The cellulosome system of the human gut bacterium R . champanellensis closely resembles that of the bovine rumen bacterium R uminococcus flavefaciens . The two species contain orthologous gene clusters comprising fundamental components of cellulosome architecture. Since R . champanellensis is the only human colonic bacterium known to degrade crystalline cellulose, it may thus represent a keystone species in the human gut.

In this report we describe the cloning, organization, and promoter analysis of the Staphylococcus aureus thioredoxin ( trxA ) and thioredoxin reductase ( trxB ) genes and their transcription in response to changes in oxygen concentration and to oxidative stress compounds. Northern analysis showed that the S. aureus trxA and trxB genes were transcribed equally well in aerobic and anaerobic conditions. Several oxidative stress compounds were found to rapidly induce transcription of the trxA and trxB genes. The most pronounced effects were seen with diamide, a thiol-specific oxidant that promotes disulfide bond formation; menadione, a redox cycling agent; and τ-butyl hydroperoxide, an organic peroxide. In each case the induction was independent of the general stress sigma factor σ ^B . These studies show that the S. aureus trxA and trxB genes are upregulated following exposure to these oxidative stress agents, resulting in increased disulfide bond formation. In contrast, no effect of hydrogen peroxide on induction of the trxA and trxB genes was seen. We also show that the S. aureus thioredoxin reductase appears to be essential for growth. This observation, coupled with structural differences between the bacterial and mammalian thioredoxin reductases, suggests that it may serve as a target for the development of new antimicrobials.

The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade >10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment. A segment of the global marine carbon cycle that has been poorly characterized is the mineralization of complex polysaccharides to carbon dioxide, a greenhouse gas. It also remained a mystery whether prokaryotes mineralize plant/algal cell walls and woody material in the oceans via carbohydrase systems and, if so, which organisms are involved. We have analyzed the complete genome sequence of the marine bacterium Saccharophagus degradans to better ascertain the potential role of prokaryotes in marine carbon transformation. We discovered that S. degradans, which is related to a number of other newly discovered marine strains, has an unprecedented quantity and diversity of carbohydrases, including the first characterized marine cellulose system. In fact, extensive analysis of the S. degradans genome sequence and functional followup experiments identified an extensive collection of complete enzyme systems that degrade more than 10 complex polysaccharides. These include agar, alginate, and chitin, altogether representing an extraordinary range of catabolic capability. Genomic analyses further demonstrated that the carbohydrases are unusually modular; sequence comparisons revealed that many of the functional modules were acquired by lateral transfer. These results suggest that the prokaryotic contribution to marine carbon fluxes is substantial and cannot be ignored in predictions of climate change.

Clostridium thermocellum produces a highly efficient cellulolytic extracellular complex, termed the cellulosome, for hydrolyzing plant cell wall biomass. The composition of the cellulosome is affected by the presence of extracellular polysaccharides; however, the regulatory mechanism is unknown. Recently, we have identified in C. thermocellum a set of putative σ and anti-σ factors that include extracellular polysaccharide-sensing components [Kahel-Raifer et al. (2010) FEMS Microbiol Lett 308:84–93]. These factor-encoding genes are homologous to the Bacillus subtilis bicistronic operon sigI-rsgI , which encodes for an alternative σ ^I factor and its cognate anti-σ ^I regulator RsgI that is functionally regulated by an extracytoplasmic signal. In this study, the binding of C. thermocellum putative anti-σ ^I factors to their corresponding σ factors was measured, demonstrating binding specificity and dissociation constants in the range of 0.02 to 1 μM. Quantitative real-time RT-PCR measurements revealed three- to 30-fold up-expression of the alternative σ factor genes in the presence of cellulose and xylan, thus connecting their expression to direct detection of their extracellular polysaccharide substrates. Cellulosomal genes that are putatively regulated by two of these σ factors, σ ^I1 or σ ^I6 , were identified based on the sequence similarity of their promoters. The ability of σ ^I1 to direct transcription from the sigI1 promoter and from the promoter of celS (encodes the family 48 cellulase) was demonstrated in vitro by runoff transcription assays. Taken together, the results reveal a regulatory mechanism in which alternative σ factors are involved in regulating the cellulosomal genes via an external carbohydrate-sensing mechanism.