Regulation of biomass degradation by alternative σ factors in cellulolytic clostridia

Abstract

Bacteria can adjust their genetic programs via alternative σ factors to face new environmental pressures. Here, we analyzed a unique set of paralogous alternative σ factors, termed σIs, which fine-tune the regulation of one of the most intricate cellulolytic systems in nature, the bacterial cellulosome, that is involved in degradation of environmental polysaccharides. We combined bioinformatics with experiments to decipher the regulatory networks of five σIs in Clostridium thermocellum, the epitome of cellulolytic microorganisms, and one σI in Pseudobacteroides cellulosolvens which produces the cellulosomal system with the greatest known complexity. Despite high homology between different σIs, our data suggest limited cross-talk among them. Remarkably, the major cross-talk occurs within the main cellulosomal genes which harbor the same σI-dependent promoter elements, suggesting a promoter-based mechanism to guarantee the expression of relevant genes. Our findings provide insights into the mechanisms used by σIs to differentiate among their corresponding regulons, representing a comprehensive overview of the regulation of the cellulosome to date. Finally, we show the advantage of using a heterologous host system for analysis of multiple σIs, since information generated by their analysis in their natural host can be misinterpreted owing to a cascade of interactions among the different σIs.

Distinctive ligand‐binding specificities of tandem PA14 biomass‐sensory elements from Clostridium thermocellum and Clostridium clariflavum

“…Previous work indicated that C. thermocellum σ I3 and σ I11 from B. cellulosolvens use highly conserved promoter sequences to regulate genes encoding pectin‐degrading enzymes …”

“…In order to identify the conserved promoter motif for genes encoding xylan‐degrading enzymes, we performed bioinformatics analysis to identify the putative regulon of C. clariflavum σ I4 . We first compared the promoter regions of C. clariflavum sigI4 and A. cellulolyticus sigI4 to the previously predicted σ I ‐dependent promoter of B. cellulosolvens sigI1 . As shown in Figure A, the predicted −35 region of the putative σ I promoter of C. clariflavum sigI4 has a conserved AAAA tetrad, and a conserved CGA triad three nucleotides upstream of the latter tetrad.…”

“…The spacer between the −35 and −10 region is 13 nucleotides (Figure A). Assuming that C. clariflavum sigI4 is autoregulated, as has already been shown in other alternative σ I factor genes, we searched for putative σ I4 ‐dependent promoters in the genome of C. clariflavum by using the conserved motifs of the predicted σ I ‐dependent promoter of C. clariflavum sigI4 (Figure A). During the search, we allowed a distance of 12‐14 nucleotides between the AAAA tetrad and the CGAAT pentad.…”

“…Their CBL2s comprise residues NNTGN and NNTGY respectively, which are very similar to CBL2 from PA14 A of C. clariflavum (NNTGN; Figure , black square). Three of them were predicted to bind xylan according to the promoter sequences of their respective genes and were verified experimentally . The supporting observation that the sequence of CBL2 is conserved within the group of pectin‐binding bacteria was also detected in the sequences of CBL2 from C. straminisolvens and C. sp ., that comprise residues QHVRA and QHVRD, respectively, which are very similar to CBL2 from PA14 A of C. thermocellum (QHVRA) (Figure , black square).…”

An Extracytoplasmic Function Sigma Factor Controls Cellulose Utilization by Regulating the Expression of an Outer Membrane Protein in Cytophaga hutchinsonii

“…Activation of ECF factors therefore depends on release from the constraint inflicted by anti-factors. This method of factor activation has been well documented in another cellulolytic bacterium, C. thermocellum, in which a set of unique alternative and anti-factors with extracellular polysaccharide-sensing modules regulate the composition of the cellulosome in response to the presence of extracellular polysaccharides (30,31,36,37).…”