Table S3: Ranked Abundance for Selected Cellulosome and Cellulase Genes

Table S3: Ranked abundance for selected cellulosome and cellulase genes.

Locus Tag / Protein name / Protein Function / DS3 rank abundance
(Δhpt) / DS11 rank abundance
(Δhpt, ΔcipA) / CTN4 rank abundance(Δhpt, ΔcipA, ΔolpB, Δorf2A, ΔolpA, ΔsdbA) / CTN5 rank abundance(Δhpt, ΔolpB, Δorf2A, ΔolpA, ΔsdbA) / CTN7 rank abundance(Δhpt, ΔcipA, ΔolpB, Δorf2A, ΔolpA, ΔsdbA, ΔolpC)
Non-catalytic cellulosomal proteins
Clo1313_0627 / CipA / Cellulosome anchoring protein cohesinregion / 94.9 / del. / del. / 100.0 / del.
Clo1313_0628 / OlpB / Cellulosome anchoring protein cohesinregion / 65.3 / 92.4 / del. / del. / del.
Clo1313_0629 / Orf2p / Cellulosome anchoring protein cohesinregion / 91.6 / 98.5 / del. / del. / del.
Clo1313_0630 / OlpA / Cellulosome anchoring protein cohesinregion / 83.1 / 95.9 / del. / del. / del.
Clo1313_0950 / SdbA / Cellulosome anchoring protein cohesinregion / 66.1 / 60.5 / del. / del. / del.
Clo1313_1487 / ScaE / Cellulosome anchoring protein cohesinregion / 72.0 / 64.8 / 76.4 / 98.2 / 82.9
Clo1313_1488 / Cellulosome anchoring protein cohesinregion / 51.7 / 45.8 / 57.8 / 75.8 / 61.5
Clo1313_1768 / OlpC / Cellulosome anchoring protein cohesinregion / 94.4 / 70.9 / 72.3 / 97.5 / del.
Cellulosomalcellulase genes
Clo1313_0135 / Dockerin type 1 / 14.7 / 11.6 / 14.2 / 19.8 / 10.7
Clo1313_0177 / XynD / Glycoside hydrolase family 10 / 28.5 / 89.4 / 93.4 / 41.9 / 96.3
Clo1313_0349 / CelV / Glycoside hydrolase family 9 / 38.3 / 85.0 / 88.4 / 55.6 / 89.6
Clo1313_0350 / LecA / Glycoside hydrolase family 9 / 32.9 / 77.6 / 79.1 / 35.0 / 83.5
Clo1313_0399 / ManA / Dockerin type 1 / 70.0 / 87.0 / 85.3 / 98.0 / 94.5
Clo1313_0400 / CelT / Glycoside hydrolase family 9 / 87.2 / 94.2 / 97.0 / 97.0 / 98.7
Clo1313_0413 / CelG / Glycoside hydrolase family 5 / 92.0 / 96.7 / 97.4 / 99.0 / 98.5
Clo1313_0420 / Dockerin type 1 / 21.4 / 30.7 / 29.7 / 14.0 / 34.0
Clo1313_0500 / Pectinesterase / 4.7 / 20.9 / 23.9 / 10.1 / 21.5
Clo1313_0501 / Pectatelyase/Amballergen / 14.8 / 43.4 / 49.9 / 46.2 / 52.9
Clo1313_0521 / XynA / Glycoside hydrolase family 11 / 61.5 / 93.8 / 98.0 / 89.9 / 98.4
Clo1313_0563 / Carbohydrate binding family 6 / 40.8 / 54.9 / 65.0 / 93.0 / 68.1
Clo1313_0685 / Dockerin type 1 / 29.9 / 26.3 / 27.5 / 54.4 / 35.6
Clo1313_0689 / Peptidase S8 and S53 subtilisinkexinsedolisin / 65.8 / 50.3 / 52.3 / 24.3 / 60.7
Clo1313_0693 / Carbohydrate binding family 6 / 16.1 / 56.8 / 69.1 / 19.0 / 77.4
Clo1313_0849 / glycosyl hydrolase 53 domain protein / 38.3 / 46.5 / 54.1 / 81.9 / 59.6
Clo1313_0851 / Xgh74A / Dockerin type 1 / 67.3 / 80.8 / 88.4 / 98.3 / 91.7
Clo1313_0985 / Alpha-L-arabinofuranosidaseB / 47.4 / 72.4 / 84.1 / 58.5 / 92.5
Clo1313_0987 / Carbohydrate binding family 6 / 38.1 / 32.5 / 36.6 / 47.6 / 40.5
Clo1313_1305 / XynY / Glycoside hydrolase family 10 / 85.6 / 91.4 / 91.0 / 91.4 / 96.8
Clo1313_1396 / CelD / Glycoside hydrolase family 9 / 71.9 / 70.8 / 60.8 / 72.1 / 54.7
Clo1313_1398 / ManA / Coagulation factor 41767 type domain protein / 72.2 / 90.1 / 80.6 / 89.5 / 88.9
Clo1313_1424 / Lipolytic protein G-D-S-L family / 28.6 / 83.8 / 67.9 / 39.4 / 76.7
Clo1313_1425 / CelE / Glycoside hydrolase family 5 / 29.5 / 52.4 / 64.7 / 31.5 / 67.6
Clo1313_1477 / CelW / Glycoside hydrolase family 9 / 39.6 / 92.3 / 93.0 / 84.5 / 96.0
Clo1313_1494 / Dockerin type 1 / 17.7 / 35.8 / 47.9 / 17.0 / 69.6
Clo1313_1563 / Ricin B lectin / 62.7 / 81.3 / 79.6 / 86.7 / 86.6
Clo1313_1564 / Glycoside hydrolase family 81 / 27.0 / 49.1 / 47.7 / 57.2 / 56.5
Clo1313_1587 / Dockerin type 1 / 48.0 / 45.2 / 49.7 / 83.6 / 55.7
Clo1313_1603 / CelQ / Glycoside hydrolase family 9 / 91.9 / 98.2 / 99.7 / 98.4 / 99.8
Clo1313_1604 / CelJ / Glycoside hydrolase family 9 / 66.9 / 99.1 / 98.8 / 93.2 / 99.7
Clo1313_1659 / CelR / Glycoside hydrolase family 9 / 89.3 / 99.0 / 99.5 / 94.9 / 99.6
Clo1313_1694 / CelF / Glycoside hydrolase family 9 / 82.1 / 96.4 / 97.9 / 97.8 / 99.2
Clo1313_1701 / CelB / Glycoside hydrolase family 5 / 91.4 / 92.1 / 93.7 / 98.0 / 97.2
Clo1313_1786 / Dockerin type 1 / 37.5 / 58.5 / 57.7 / 37.8 / 71.2
Clo1313_1788 / Glycoside hydrolase family 9 / 86.4 / 95.4 / 97.5 / 95.4 / 98.9
Clo1313_1808 / CbhA / Glycoside hydrolase family 9 / 92.9 / 99.4 / 99.1 / 98.9 / 98.6
Clo1313_1809 / CelK / Glycoside hydrolase family 9 / 99.5 / 100.0 / 99.5 / 99.1 / 99.5
Clo1313_1816 / CelL / Glycoside hydrolase family 5 / 79.4 / 91.9 / 95.3 / 87.9 / 95.7
Clo1313_1955 / CelP / Glycoside hydrolase family 9 / 61.1 / 84.9 / 81.9 / 90.6 / 88.1
Clo1313_1959 / ChiA / Glycoside hydrolase family 18 / 74.8 / 95.8 / 90.7 / 92.8 / 94.7
Clo1313_1960 / CelA / Glycoside hydrolase family 8 / 93.3 / 98.6 / 98.5 / 97.2 / 99.7
Clo1313_1971 / Dockerin type 1 / 74.3 / 77.3 / 89.9 / 81.4 / 88.8
Clo1313_1983 / Carbohydrate binding family 6 / 26.2 / 58.6 / 66.4 / 61.7 / 76.3
Clo1313_1990 / Spore coat protein CotH / 61.1 / 81.9 / 84.6 / 68.9 / 84.3
Clo1313_2022 / LicB / Glycoside hydrolase family 16 / 34.5 / 49.0 / 44.7 / 53.2 / 50.0
Clo1313_2042 / Proteinase inhibitor I4 serpin / 36.7 / 85.1 / 80.5 / 85.3 / 84.2
Clo1313_2043 / Proteinase inhibitor I4 serpin / 32.5 / 63.8 / 74.7 / 85.4 / 89.9
Clo1313_2188 / CseP / Spore coat protein CotH / 12.3 / 43.7 / 44.3 / 13.7 / 59.2
Clo1313_2189 / CelN / Glycoside hydrolase family 9 / 76.2 / 93.0 / 93.3 / 98.9 / 98.5
Clo1313_2202 / Dockerin type 1 / 58.1 / 66.6 / 85.4 / 99.6 / 92.2
Clo1313_2216 / Alpha-L-arabinofuranosidaseB / 22.0 / 41.4 / 41.4 / 31.3 / 34.6
Clo1313_2234 / CelH / Glycoside hydrolase family 5 / 38.9 / 44.3 / 46.1 / 88.3 / 51.6
Clo1313_2479 / Ig domain protein group 2 domain protein / 54.5 / 76.0 / 83.3 / 75.0 / 82.1
Clo1313_2530 / XynC / Glycoside hydrolase family 10 / 95.1 / 89.9 / 93.6 / 96.6 / 97.4
Clo1313_2564 / Dockerin type 1 / 48.1 / 79.4 / 44.4 / 71.8 / 54.4
Clo1313_2635 / XynZ / Glycoside hydrolase family 10 / 84.8 / 97.0 / 95.0 / 62.7 / 94.0
Clo1313_2693 / Dockerin type 1 / 58.7 / 62.4 / 70.3 / 90.8 / 83.4
Clo1313_2747 / CelS / Glycoside hydrolase family 48 / 98.0 / 100.0 / 99.3 / 99.7 / 99.6
Clo1313_2793 / Carbohydrate binding family 6 / 33.7 / 39.5 / 43.3 / 61.0 / 46.5
Clo1313_2794 / Glycoside hydrolase family 43 / 10.1 / 51.2 / 68.5 / 19.5 / 79.7
Clo1313_2795 / Alpha-L-arabinofuranosidaseB / 17.3 / 64.7 / 72.1 / 26.6 / 74.5
Clo1313_2805 / CelO / Glycoside hydrolase family 5 / 27.3 / 48.8 / 41.1 / 76.3 / 50.5
Clo1313_2843 / Pectatelyase/Amballergen / 67.8 / 31.4 / 30.1 / 32.5 / 35.5
Clo1313_2856 / CtXyl5A / Carbohydrate binding family 6 / 68.4 / 80.0 / 88.6 / 77.0 / 88.1
Clo1313_2858 / Carbohydrate binding family 6 / 22.4 / 33.1 / 32.1 / 24.0 / 23.8
Clo1313_2859 / Carbohydrate binding family 6 / 12.5 / 17.4 / 18.8 / 18.3 / 13.3
Clo1313_2860 / Glycoside hydrolase family 43 / 9.2 / 15.3 / 17.7 / 18.5 / 14.5
Clo1313_2861 / Glycoside hydrolase family 2 sugar binding protein / 6.9 / 8.3 / 9.8 / 15.3 / 12.5
Clo1313_2944 / Dockerin type 1 / 4.4 / 7.1 / 6.8 / 12.7 / 7.4
Clo1313_3023 / CelU / Glycoside hydrolase family 9 / 53.5 / 81.2 / 92.3 / 97.9 / 93.1
Free enzyme system
Clo1313_0133 / Alpha-L-arabinofuranosidase domain protein / 35.9 / 33.5 / 34.4 / 41.1 / 36.7
Clo1313_0333 / Lytic transglycosylasecatalytic / 75.5 / 45.9 / 40.3 / 60.1 / 40.9
Clo1313_0395 / CelC / Glycoside hydrolase family 5 / 45.6 / 36.8 / 47.8 / 89.2 / 56.9
Clo1313_0397 / LicA / Glucan endo-1,3-beta-D-glucosidase / 85.3 / 80.3 / 84.8 / 98.4 / 92.7
Clo1313_0436 / Glycoside hydrolase family 18 / 52.0 / 45.0 / 56.3 / 45.7 / 52.1
Clo1313_0539 / Glycosyltransferase36 / 82.5 / 84.4 / 81.8 / 79.8 / 87.3
Clo1313_0613 / Cephalosporin-C deacetylase / 32.4 / 47.0 / 36.1 / 39.2 / 24.5
Clo1313_0714 / Carbohydrate binding family 25 / 92.4 / 82.3 / 83.0 / 71.8 / 87.1
Clo1313_0820 / Beta-glucosidase / 15.0 / 14.9 / 16.1 / 20.8 / 12.8
Clo1313_1002 / bglB / Glycoside hydrolase family 3 domain protein / 77.6 / 53.9 / 54.2 / 99.5 / 61.2
Clo1313_1336 / Lytic transglycosylasecatalytic / 46.7 / 42.3 / 44.1 / 99.8 / 43.3
Clo1313_1426 / Alpha amylase catalytic region / 41.7 / 49.3 / 45.6 / 70.6 / 53.6
Clo1313_1904 / Glycoside hydrolase family 3 domain protein / 39.3 / 46.1 / 50.0 / 40.6 / 44.0
Clo1313_1954 / Glycosyltransferase36 / 90.8 / 82.7 / 87.1 / 85.1 / 93.1
Clo1313_1958 / Type 3a cellulose-binding domain protein / 94.6 / 99.1 / 98.8 / 97.7 / 98.8
Clo1313_2020 / bglA / Beta-galactosidase / 60.5 / 50.9 / 71.7 / 68.1 / 77.1
Clo1313_2161 / CelY / Cellulose 1,4-beta-cellobiosidase / 57.5 / 83.0 / 80.0 / 87.7 / 82.2
Clo1313_2192 / CelI / Glycoside hydrolase family 9 / 40.0 / 35.7 / 46.8 / 43.1 / 48.8
Clo1313_2233 / Glycoside hydrolase family 5 / 53.9 / 64.0 / 63.8 / 98.8 / 67.8
Clo1313_2382 / Hypothetical protein / 5.1 / 4.9 / 5.7 / 5.1 / 3.2
Clo1313_2450 / Amidohydrolase / 72.8 / 74.7 / 75.5 / 62.0 / 79.6
Clo1313_2460 / Glycoside hydrolase 15-related protein / 72.1 / 57.0 / 75.9 / 95.0 / 79.0
Clo1313_2473 / Peptidoglycan-binding lysindomain / 49.9 / 56.2 / 49.1 / 81.1 / 42.9
Clo1313_2584 / Carbohydrate binding family 6 / 62.3 / 63.4 / 63.1 / 43.5 / 63.5
Clo1313_2777 / Glycoside hydrolase family 10 / 70.1 / 81.1 / 84.8 / 86.1 / 85.4
Clo1313_2853 / N-acetylglucosamine-6-phosphate deacetylase / 34.6 / 36.2 / 38.0 / 86.4 / 47.1
Clo1313_2854 / 1,4-alpha-glucan branching enzyme / 66.9 / 60.9 / 48.0 / 60.8 / 56.8

Ranked abundance was calculated by ranking all genes (see Supplementary Table 2) from highest expression to lowest expression based on the LS means normalized value of averaged replicates. The most highly expressed gene was assigned a rank of 2664 with decreasing values given down to a rank of 1 for the least expressed gene. These rankings are expressed as a percentage in the column labelled “rank abundance” with a value of 100 indicating the most highly expressed gene in a particular strain. Boldface values indicate that these genes were significantly (FDR adjusted p-value <0.05), differentially expressed (greater than +/- 1 log2 transformed ratio) in a given strain relative to the parental DS3 strain. A value of del. in the ranked abundance columns indicates that this gene was deleted and the level of gene expression was equivalent to the background signal of the microarray (See Supplementary Table 2)