Revisiting the regulation of the primary scaffoldin gene in Clostridium thermocellum

Lizett Ortiz de Ora, Iván Muñoz-Gutiérrez, Edward A. Bayer, Yuval Shoham, Raphael Lamed, Ilya Borovok*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Cellulosomes are considered to be one of the most efficient systems for the degradation of plant cell wall polysaccharides. The central cellulosome component comprises a large, noncatalytic protein subunit called scaffoldin. Multiple saccharolytic enzymes are incorporated into the scaffoldins via specific high-affinity cohesin-dockerin interactions. Recently, the regulation of genes encoding certain cellulosomal components by multiple RNA polymerase alternative σI factors has been demonstrated in Clostridium (Ruminiclostridium) thermocellum. In the present report, we provide experimental evidence demonstrating that the C. thermocellum cipA gene, which encodes the primary cellulosomal scaffoldin, is regulated by several alternative σI factors and by the vegetative σA factor. Furthermore, we show that previously suggested transcriptional start sites (TSSs) of C. thermocellum cipA are actually posttranscriptional processed sites. By using comparative bioinformatic analysis, we have also identified highly conserved σIand σA-dependent promoters upstream of the primary scaffoldin-encoding genes of other clostridia, namely, Clostridium straminisolvens, Clostridium clariflavum, Acetivibrio cellulolyticus, and Clostridium sp. strain Bc-iso-3. Interestingly, a previously identified TSS of the primary scaffoldin CbpA gene of Clostridium cellulovorans matches the predicted σI-dependent promoter identified in the present work rather than the previously proposed σA promoter. With the exception of C. cellulovorans, both σI and σA promoters of primary scaffoldin genes are located more than 600 nucleotides upstream of the start codon, yielding long 5'- untranslated regions (5'-UTRs). Furthermore, these 5'-UTRs have highly conserved stem-loop structures located near the start codon. We propose that these large 5'-UTRs may be involved in the regulation of both the primary scaffoldin and other cellulosomal components.

Original languageEnglish
Article numbere03088-16
JournalApplied and Environmental Microbiology
Issue number8
StatePublished - 1 Apr 2017


FundersFunder number
Sidney E. Frank Foundation
Weizmann Institute of Science
United States-Israel Binational Science Foundation2011049
Consejo Nacional de Ciencia y Tecnología238334, 440354
Israel Science Foundation1349/13, 24/11, 177/14
Tel Aviv University
Technion-Israel Institute of Technology


    • 5'-UTR
    • Cellulosome
    • CipA
    • Clostridium thermocellum
    • Gene regulation
    • Promoters
    • Scaffoldin
    • Sigma factors


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