Analysis of cellulosomal proteins of C. thermocellum wild-type and mutant strains. Cellulosome proteins were isolated by using a modified cellulose-affinity procedure  (see Materials and methods) and analyzed by (A) sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) with Coomassie blue staining and (B) immunoblotting using an antibody directed against a C-terminal XDocII peptide to detect the full-length CipA protein. Six bands corresponding to known cellulosomal proteins are identified to the right of the Coomassie blue-stained gel [9, 27]. Intact CipA protein was not detected in any of the CipA-truncated mutants either by staining or immunoblotting, indicating successful gene disruption. Both cellulosomal and extracellular proteins (Additional file 9) of CipA-ΔXDocII contain a band that was slightly smaller than wild-type CipA (indicated by an asterisk) and was identified by mass spectroscopy as a truncated CipA lacking an XDocII module (Additional file 6 and Additional file 7). Secondary scaffoldins are not detectable in Coomassie blue-stained SDS-polyacrylamide gels of purified cellulosomes because they are expressed at low levels, and the affinity purification enriches for proteins that bind directly to cellulose [27, 29, 30]. M, protein markers.