Transcriptomic Analysis Reveals Opposing Roles of CEL1B in Sophorose- and Lactose-Induced Cellulase Expression in Trichoderma reesei Rut C30
Abstract
1. Introduction
2. Materials and Methods
2.1. Strains
2.2. Construction of CEL1B Gene Knockout T. reesei
2.3. Cellulase Production
2.4. RNA Isolation and High-Throughput RNA-Seq
2.5. Determination of Copy Numbers by qPCR Analysis
2.6. Analytical Methods
3. Results
3.1. Gene Knockout and Phenotypic Analysis of CEL1B in Trichoderma reesei RUT C30
3.2. Impact of CEL1B Gene Knockout on Cellulase Production
3.3. Transcriptome Analysis
3.4. GH Family
3.5. Transporters
3.6. Transcription Factors
3.7. Endoplasmic Reticulum (ER) Protein Processing Pathway
3.8. RT-qPCR
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
MGD | Glucose–sophorose mixture |
GH families | Glycoside Hydrolase families |
T. reesei | Trichoderma reesei |
SLF | Submerged liquid fermentation |
Sophorose | β-1,2-linked disaccharide |
CRISPR-Cas9 | Clustered Regularly Interspaced Short Palindromic Repeats associated with Cas9 |
sgRNA | single guide RNA |
DEGs | Differentially expressed genes |
GO | Gene Ontology |
KOG | Eukaryotic Orthologous Groups |
SRA | Sequence Read Archive |
qPCR | Quantitative Polymerase Chain Reaction |
DNS | 3,5-dinitrosalicylic acid |
pNPC | p-nitrophenyl-β-D-cellobioside |
pNP | p-nitrophenol |
CMC | Carboxymethyl cellulose |
BCA | Bicinchoninic acid |
SDS-PAGE | Sulfate polyacrylamide gel electrophoresis |
5-FOA | 5-fluoroorotic acid |
PCA | Principal Component Analysis |
FPKM | Fragments per kilobase of transcript per million mapped reads |
TFs | Transcription factors |
GNAT | Gcn5-related N-acetyltransferase |
ER | Endoplasmic reticulum |
ARS | Agricultural Research Service |
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Category | Gene ID | Description/Name | MGD Log2FC | Lac Log2FC |
---|---|---|---|---|
Cellulase | 125125 | Exoglucanase I/CEL7A | −1.3 | 2.4 |
122470 | Exoglucanase II/CEL6A | −1.7 | 2.6 | |
5304 | Endoglucanase I/CEL7B | −1.6 | 3.4 | |
72489 | Endoglucanase III/CEL5A | −1.7 | 2.5 | |
124438 | Endoglucanase II/CEL12A | −1.4 | 3.3 | |
74496 | Endoglucanase V/CEL45A | NS | NS | |
136547 | β-glucosidase/CEL3A | −0.8 | 3.0 | |
82126 | β-glucosidase/CEL3H | −1.6 | NS | |
Auxiliary protein | 104220 | Swollenin | −1.5 | 2.3 |
139633 | Endoglucanase IV (AA9) | NS | 2.0 | |
122518 | Endoglucanase VII (AA9) | −1.2 | 1.8 | |
121449 | Cellulose binding domain/CIP1 | −1.5 | 2.2 | |
125575 | Cellulose binding domain/CIP2 | −1.6 | 2.3 |
Gene ID | Name | MGD Up/Dwon | Lac Up/Dwon | Description |
---|---|---|---|---|
97259 | Hgt1 | NS | Up | Glucose transporter |
109243 | Crt1 | NS | Up | Cellulose sensor |
136988 | Stp1 | NS | Up | Cellobiose transporter |
138519 | Str1 | Down | Up | Xylose transporter |
33630 | Xlt1 | Down | Up | Xylose transporter |
38765 | NS | Up | Xylose transporter | |
91594 | Down | Up | Cellobiose/Xylose transporter | |
127980 | Down | Up | Cellodextrin transporter | |
55710 | NS | Up | Permease of the major facilitator superfamily | |
137001 | Crt2 | NS | Up | Cellulose sensor |
137795 | NS | Up | Cellobiose transporter | |
79984 | NS | Up | Cellobiose transporter | |
124396 | Hxt1 | NS | Down | Glucose transporter |
Gene ID | Name | Positive/Negative-Acting | MGD Up/Down | MGD Log2FC | Lac Up/Down | Lac Log2FC |
---|---|---|---|---|---|---|
98788 | Xyr1 | Positive | NS | −0.1 | Up | 1.7 |
98455 | Ace3 | Positive | NS | −0.7 | Up | 1.8 |
125610 | Vib1 | Positive | NS | −0.2 | Up | 1.3 |
122363 | Ace1 | Negative | NS | 0.2 | NS | −0.6 |
32395 | Ace2 | Positive | NS | −0.1 | NS | 0.5 |
93466 | Hap2 | Positive | NS | 0.1 | NS | −0.1 |
24298 | Hap3 | Positive | NS | −0.1 | NS | 0.2 |
95791 | Pacc | Negative | NS | 0.6 | NS | −0.2 |
140814 | Area | Positive | NS | 0.3 | NS | 0.1 |
91236 | Bglr | Positive | NS | 0.3 | NS | 0.1 |
68701 | Clr-1 | Positive | NS | 0.3 | NS | 0.3 |
76250 | Clr-2 | Positive | NS | −0.2 | NS | 0.7 |
93861 | Ypr1 | Positive | NS | −0.5 | NS | 0.8 |
112571 | Tmac1 | Positive | NS | 0.2 | NS | −0.3 |
23706 | Cre1 | Negative | NS | −0.6 | NS | 0.7 |
6520 | Rce1 | Negative | NS | −0.2 | NS | 0.7 |
Gene ID | Name | MGD Up/Dwon | Lac Up/Dwon | Description |
---|---|---|---|---|
124246 | Fes1 | NS | Up | Hsp70 nucleotide exchange factor |
121926 | NS | Up | Heat shock protein 70 kDa | |
102206 | NS | Up | Heat shock protein 90 | |
122594 | NS | Up | DnaJ domain-containing protein | |
25648 | Bip1 | Down | Up | Heat shock protein 70 kDa |
83445 | ERManI | NS | Up | 1, 2-α-mannosidase |
137683 | NEF | NS | Up | Armadillo/beta-catenin-like repeat-containing protein |
101105 | ERManI | NS | Up | 1, 2-α-mannosidase |
116265 | SPCS1 | Down | NS | Microsomal signal peptidase 12 kDa subunit |
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Wang, L.; Fan, J.; He, X.; Cheng, J.; Zhang, X.; Tian, T.; Li, Y. Transcriptomic Analysis Reveals Opposing Roles of CEL1B in Sophorose- and Lactose-Induced Cellulase Expression in Trichoderma reesei Rut C30. Fermentation 2025, 11, 439. https://doi.org/10.3390/fermentation11080439
Wang L, Fan J, He X, Cheng J, Zhang X, Tian T, Li Y. Transcriptomic Analysis Reveals Opposing Roles of CEL1B in Sophorose- and Lactose-Induced Cellulase Expression in Trichoderma reesei Rut C30. Fermentation. 2025; 11(8):439. https://doi.org/10.3390/fermentation11080439
Chicago/Turabian StyleWang, Lu, Junping Fan, Xiao He, Jian Cheng, Xinyan Zhang, Tian Tian, and Yonghao Li. 2025. "Transcriptomic Analysis Reveals Opposing Roles of CEL1B in Sophorose- and Lactose-Induced Cellulase Expression in Trichoderma reesei Rut C30" Fermentation 11, no. 8: 439. https://doi.org/10.3390/fermentation11080439
APA StyleWang, L., Fan, J., He, X., Cheng, J., Zhang, X., Tian, T., & Li, Y. (2025). Transcriptomic Analysis Reveals Opposing Roles of CEL1B in Sophorose- and Lactose-Induced Cellulase Expression in Trichoderma reesei Rut C30. Fermentation, 11(8), 439. https://doi.org/10.3390/fermentation11080439