Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A

Couger, M. B.; Youssef, Noha H.; Struchtemeyer, Christopher G.; Liggenstoffer, Audra S.; Elshahed, Mostafa S.

doi:10.1186/s13068-015-0390-0

Biotechnology for Biofuels and Bioproducts

Table 2 Transcriptional levels of all CAZyme families when grown on glucose and lignocellulosic biomass substrates

From: Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A

Family	Number of transcripts	Normalized (FPKM) when grown on^a					Fold change in expression compared to glucose^b				Putative substrate
Family	Number of transcripts	Glucose	Alfalfa	Energy cane	Corn stover	Sorghum	Alfalfa	Energy cane	Corn stover	Sorghum	Putative substrate
Glycosyl hydrolase families
GH1	9	1771.34	3969.55	2979.04	3698.85	3909.06	1.16	0.75	1.06	1.14	Cellulose
GH2	1	5.92	8.56	1.30	1.05	4.12	0.53	−*2.19*	−*2.50*	−0.52	Xylan accessory
GH3	17	714.37	673.63	1050.78	3505.03	1394.83	−0.08	0.56	2.29	0.97	Cellulose
GH4	3	24.53	6.31	12.16	17.96	11.59	−*1.96*	−*1.01*	−0.45	−*1.08*	Other: catabolism
GH5	36	875.19	785.76	950.37	1080.05	844.70	−0.16	0.12	0.30	−0.05	Cellulose
GH6	18	1799.30	3264.96	3861.61	6956.76	4372.47	0.86	1.10	1.95	1.28	Cellulose
GH8	2	117.56	32.19	32.93	13.32	111.82	−*1.87*	−*1.84*	−*3.14*	−0.07	Cellulose, hemicellulose
GH9	21	607.91	887.25	1416.88	2192.44	2208.01	0.55	1.22	1.85	1.86	Cellulose
GH10	28	2347.94	2686.49	1930.29	2488.99	3482.82	0.19	−0.28	0.08	0.57	Xylan
GH11	24	1488.52	1007.52	1918.48	1979.64	6240.67	−0.56	0.37	0.41	2.07	Xylan
GH13	17	2427.14	337.37	2709.48	2410.50	2781.37	−*2.85*	0.16	−0.01	0.20	Starch
GH16	10	3323.52	1589.54	1295.78	1372.04	1217.24	−1.06	−1.36	−1.28	−1.45	Mixed glucan
GH17	1	0.00	0.00	0.68	1.18	0.69	0.00	19.38	20.17	19.40	Unknown
GH18	12	214.01	319.16	561.21	530.93	330.65	0.58	1.39	1.31	0.63	Chitin
GH20	1	2.89	2.07	4.41	5.20	3.29	−0.48	0.61	0.85	0.19	Other: N-acetyl-β-d-hexosamines
GH25	3	9.17	86.84	52.25	9.90	19.69	3.24	2.51	0.11	1.10	Peptidoglycan
GH26	7	136.35	167.23	73.65	94.95	46.23	0.29	−*0.89*	−0.52	−*1.56*	Mannan
GH28	5	107.74	67.83	65.97	65.68	85.86	−*0.67*	−*0.71*	−*0.71*	−0.33	Pectin
GH30	3	41.17	31.90	9.74	19.92	20.84	−0.37	−*2.08*	−*1.05*	−*0.98*	Xylan accessory
GH31	17	1730.49	371.79	621.35	1815.81	646.34	−*2.22*	−*1.48*	0.07	−*1.42*	Xylan accessory
GH32	2	26.28	10.46	27.34	14.64	17.18	−*1.33*	0.06	−0.84	−0.61	Other: fructan
GH36	1	3.41	1.85	6.92	8.23	4.80	−0.88	1.02	1.27	0.49	Other: fructan
GH37	1	12.40	6.41	9.35	8.58	4.14	−0.95	−0.41	−0.53	−1.58	Other: trehalose
GH38	1	3.26	1.06	7.18	4.16	3.38	−*1.62*	1.14	0.35	0.05	Other: anabolic
GH39	9	115.54	90.68	93.64	155.76	129.98	−0.35	−0.30	0.43	0.17	Xylan
GH43	32	711.65	822.50	465.65	494.55	747.27	0.21	−0.61	−0.53	0.07	Xylan
GH45	16	2974.32	2653.90	1981.70	1653.87	2315.32	−0.16	−0.59	−*0.85*	−0.36	Cellulose
GH47	3	12.98	5.33	32.56	19.49	14.89	−*1.28*	1.33	0.59	0.20	Other: anabolic
GH48	17	3609.25	1928.40	2587.13	3989.36	2077.62	−*0.90*	−0.48	0.14	−*0.80*	Cellulose
GH53	2	24.78	31.13	17.52	27.93	17.37	0.33	−0.50	0.17	−0.51	Pectin
GH55	1	6.91	17.95	10.63	9.13	15.71	1.38	0.62	0.40	1.18	β-1,3, Glucan (laminarin)
GH57	7	156.86	540.18	751.41	414.40	377.49	1.78	2.26	1.40	1.27	Starch
GH64	2	5.43	17.40	6.22	3.17	2.99	1.68	0.20	−*0.78*	−*0.86*	β-1,3, Glucan (laminarin)
GH67	1	0.99	6.39	1.61	2.11	2.92	2.69	0.71	1.10	1.57	Xyloglucan
GH74	4	50.30	94.58	65.58	64.75	31.52	0.91	0.38	0.36	−0.67	Xyloglucan
GH78	1	15.39	18.06	4.18	2.60	3.97	0.23	−*1.88*	−*2.56*	−*1.96*	Pectin
GH95	1	35.79	39.09	21.54	16.34	37.22	0.13	−*0.73*	−*1.13*	0.06	Xyloglucan
GH97	2	7.13	1.86	4.94	1.01	5.06	−*1.94*	−0.53	−*2.82*	−0.49	Xyloglucan
GH105	1	31.80	47.57	22.45	14.56	30.55	0.58	−0.50	−*1.13*	−0.06	Pectin
GH109	3	6.74	10.53	23.54	19.34	14.64	0.64	1.80	1.52	1.12	Polygalactosamine
GH114	16	70.57	355.00	213.95	121.41	123.15	2.33	1.60	0.78	0.80	Other (polygalactosamine)
GH115	4	89.40	27.51	7.26	2.56	6.07	−1.70	−*3.62*	−*5.12*	−*3.88*	Xylan accessory
GH119	20	3049.91	946.89	966.78	820.70	519.50	−*1.69*	−*1.66*	−*1.89*	−*2.55*	Starch
GH124	3	70.07	89.06	117.98	178.06	103.34	0.35	0.75	1.35	0.56	Cellulose
Polysaccharide lyase families
PL1	21	154.13	343.14	236.82	140.09	116.49	1.15	0.62	−0.14	−0.40	Pectate/pectin lyase
PL2	1	2.24	0.64	4.08	3.90	2.58	−*1.80*	0.87	0.80	0.21	Pectate lyase, exo-polygalacturonate lyase
PL3	9	46.40	177.00	46.85	75.80	29.12	1.93	0.01	0.71	−*0.67*	Pectate lyase
PL4	4	54.08	56.23	77.28	88.88	137.43	0.06	0.52	0.72	1.35	Rhamnogalacturonan lyase
PL9	1	9.09	28.83	6.25	3.16	7.53	1.67	−0.54	−*1.52*	−0.27	Pectate lyase, exo-polygalacturonate lyase
PL10	1	8.71	15.27	19.57	21.08	11.62	0.81	1.17	1.27	0.42	Pectate lyase
PL11	1	0.96	0.34	1.61	1.59	1.31	−*1.51*	0.74	0.73	0.45	Rhamnogalacturonan lyase
PL22	5	73.10	42.63	32.88	17.93	29.22	−*0.78*	−*1.15*	−*2.03*	−*1.32*	Oligogalacturonate lyase
Carboxyl esterase families
CE1	67	1064.51	1482.74	1331.78	824.56	2043.05	0.48	0.32	−0.37	0.94
CE2	4	18.08	59.94	61.97	84.97	41.02	1.73	1.78	2.23	1.18
CE3	9	190.73	200.04	258.23	170.58	311.61	0.07	0.44	−0.16	0.71
CE4	66	5195.95	3586.97	4918.19	5519.76	4410.55	−0.53	−0.08	0.09	−0.24
CE6	10	950.25	208.31	165.10	142.38	367.79	−*2.19*	−*2.52*	−*2.74*	−*1.37*
CE7	4	428.18	226.89	367.54	378.99	358.44	−*0.92*	−0.22	−0.18	−0.26
CE8	5	25.32	48.98	84.27	53.33	44.48	0.95	1.73	1.07	0.81
CE9	3	0.74	4.64	3.44	1.35	1.33	2.64	2.21	0.86	0.84
CE10	58	559.63	576.67	758.11	433.52	332.26	0.04	0.44	−0.37	−*0.75*
CE12	4	133.25	137.86	137.67	201.83	175.85	0.05	0.05	0.60	0.40
CE14	1	1.17	1.91	5.03	2.62	2.64	0.71	2.10	1.16	1.18
CE15	2	259.98	238.38	105.97	41.58	240.61	−0.13	−*1.29*	−*2.64*	−0.11
CE16	12	125.10	160.06	118.64	47.91	156.38	0.36	−0.08	−*1.38*	0.32
CEX	7	906.91	381.49	426.72	481.87	779.19	−*1.25*	−*1.09*	−*0.91*	−0.22

^aCorrected FPKM values normalized by the library size, as calculated using the estimateDispersions function in the R package DESeq [44]
^bFold change is shown as Log₂ expression levels compared to glucose. Italics represents significantly over-expressed (a differential expression p value <0.01 as calculated by the nbinomTest function in the R package DESeq), bold italics represents significantly under-expressed (a differential expression p value <0.01 as calculated by the nbinomTest function in the R package DESeq [44]

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