Regulation of biomass degradation by alternative \u03c3 factors in cellulolytic clostridia

Qiu Cui,Yingang Feng,Jian Xu,Edward A Bayer,Yuval Shoham,Raphael Lamed,Ya-Jun Liu,Iván Muñoz-Gutiérrez,Lizett Ortiz De Ora

doi:10.1038/s41598-018-29245-5

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.

Highlights

Bacteria can sense the extracellular environment and transmit information intracellularly by using different types of signal transduction mechanisms[1]
In the cellulosome-producing bacteria Clostridium (Ruminiclostridium) thermocellum, the enzymatic composition of the cellulosome is probably regulated by a group of at least 6 paralogous alternative σI factors that are related to the Bacillus subtilis σI factor[8,9,10,11,12]
To overcome the lack of convenient genetic tools to work directly in C. thermocellum[24], we analyzed the recognition of the predicted promoters by C. thermocellum σI3 and σI6 in a heterologous B. subtilis host system[10]

Summary

Introduction

Bacteria can sense the extracellular environment and transmit information intracellularly by using different types of signal transduction mechanisms[1]. One type of response is regulation of genes at the level of transcription initiation by alternative sigma (σ) factors allowing bacteria to adjust their transcriptional programs to environmental changes. All bacteria harbor one primary σ factor (known as the housekeeping σ factor, σ70 or σA) that is responsible for basal expression level of most genes. When the environmental conditions change, the housekeeping σ factor is substituted by the alternative σ factors, thereby redirecting the RNA polymerase to alternative promoters of genes that will help the bacterium deal with the new environmental conditions[4]. The features of the σIs are consistent with almost all of the characteristics of the ECF (extracytoplasmic function) σ factors[2]. (ii) They are usually located in an operon with an anti-σ factor gene. The above-mentioned characteristics render σI factors unique members of the σ70 family

Methods

Results

Conclusion