Regulation of biomass degradation by alternative σ factors in cellulolytic clostridia

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number11036
JournalScientific Reports
Issue number1
StatePublished - 1 Dec 2018


FundersFunder number
Israel-China ISF-NSFC2566/160
Sidney E. Frank Foundation
National Natural Science Foundation of China31661143023
Consejo Nacional de Ciencia y Tecnología440354
Israel Science Foundation1349/13, 24/11, 177/14


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