Figure 6. Quantitative changes in Clostridium thermocellum cellulosome composition in response to carbon substrate – Part II.

Quantitative data shown is combined from two biological and two technical replicates and expressed as Log₂Ratio (LowerCI, UpperCI) of cellulosomal component X during growth on substrate Y over that in ¹⁵N-labeled Cellulose cellulosome sample. Substrate key: C = Crystalline Cellulose (with ¹⁴N or ¹⁵N labeled nitrogen source), C-X = Cellulose-Xylan (5 g/L total in 3∶2 weight ratio), C-P = Cellulose-Pectin (3∶2), C-P-X = Cellulose-Pectin-Xylan (3∶1∶1), SWG = Pretreated Switchgrass (50% glucan, 8% xylan, 24% lignin), Cb = Cellobiose, Z-T = Z-Trim® (60% amorphous cellulose, 16% hemicellulose). Data was normalized to the scaffoldin CipA protein. Locus entries highlighted in Blue have not been observed experimentally prior to this study. Quantitation data highlighted in Yellow (increased expression in Substrate Y) and Orange (decreased expression in Substrate Y) satisfy the cut-off criteria. Criteria for differential expression was based on control comparison of ¹⁴N- and ¹⁵N-labeled cellulose cellulosome samples and were, (1) Log₂Ratio should be >+0.4 or <−0.4 and (2) Upper/Lower Confidence Intervals should exclude Log₂Ratio = 0. Structural, catalytic and/or binding module information was obtained from the following sources: http://pfam.sanger.ac.uk/; http://www.cazy.org/; http://genome.ornl.gov/microbial/cthe/. Domain key: GH = Glycoside Hydrolase, CE = Carbohydrate Esterase, PL = Polysaccharide Lyase, CBM = Carbohydrate Binding Module. Legend key: MW = Molecular Weight, Log₂Ratio (LowerCI, UpperCI) - protein was quantified in both biological replicates (BR), with overlapping confidence intervals; Blank - protein not identified or quantified; d - protein quantified in only one BR, but result indicates down-regulation (UpperCI<0, Log₂ratio<−0.4); D - protein quantified in both BR, but confidence intervals don't overlap. Both confidence intervals indicate down-regulation (UpperCI<0, Log₂ratio<−0.4); i - identified in one BR, but no quantification result; I - identified in both BR, but no quantification result; n - protein quantified in only one BR, with result indicating no change in expression (−0.4<Log₂ratio<+0.4); N - protein quantified in both BR, but confidence intervals don't overlap. Both confidence intervals indicate no change in expression (−0.4<Log₂ratio<+0.4); u - protein quantified in only one BR, but result indicates up-regulation (LowerCI>0, Log₂ratio>+0.4); U - protein quantified in both BR, but confidence intervals don't overlap. Both confidence intervals indicate up-regulation (LowerCI>0, Log₂ratio>+0.4); A indicates that the protein was identified in both ¹⁴N and ¹⁵N forms in both BR; A single underscore indicates that the protein was identified in both ¹⁴N and ¹⁵N forms in only one BR; No underscore indicates that we did not identify both ¹⁴N and ¹⁵N forms in either BR.