Limits...
Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain.

Poggi-Parodi D, Bidard F, Pirayre A, Portnoy T, Blugeon C, Seiboth B, Kubicek CP, Le Crom S, Margeot A - Biotechnol Biofuels (2014)

Bottom Line: Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated.The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei.Genes from two specific clusters might be potential targets for such genetic engineering.

View Article: PubMed Central - PubMed

Affiliation: IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France ; Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France.

ABSTRACT

Background: The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour.

Results: We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance.

Conclusions: This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.

No MeSH data available.


Related in: MedlinePlus

Differentially expressed genes of NG 14 and RUT C30 during lactose induction. (A) Venn diagram indicates the number of genes specific to each strain and the overlap between them. (B) The number of induced or repressed genes during induction by lactose is depicted in a bar chart. It displays the number of induced (red) and repressed (green) genes for the four time points (1, 3, 6 and 24 h) found during the induction in the RUT C30 and NG 14 strains compared to time 0. The differentially expressed genes have been selected using a 5% false discovery rate cut-off and with an absolute log2 fold change greater than 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4279801&req=5

Fig2: Differentially expressed genes of NG 14 and RUT C30 during lactose induction. (A) Venn diagram indicates the number of genes specific to each strain and the overlap between them. (B) The number of induced or repressed genes during induction by lactose is depicted in a bar chart. It displays the number of induced (red) and repressed (green) genes for the four time points (1, 3, 6 and 24 h) found during the induction in the RUT C30 and NG 14 strains compared to time 0. The differentially expressed genes have been selected using a 5% false discovery rate cut-off and with an absolute log2 fold change greater than 1.

Mentions: After consolidation of duplicates and statistical analysis, we obtained 568 genes that were differentially expressed compared to their corresponding time 0, both strains considered. The differentially expressed genes specific to each strain are indicated in Additional file 4: Table S1. The numbers of differentially expressed genes found specifically for each strain and shared in both strains are shown in Figure 2A. Interestingly, RUT C30 showed five times fewer differentially expressed genes than NG 14 and only 62 specific genes.Figure 2


Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain.

Poggi-Parodi D, Bidard F, Pirayre A, Portnoy T, Blugeon C, Seiboth B, Kubicek CP, Le Crom S, Margeot A - Biotechnol Biofuels (2014)

Differentially expressed genes of NG 14 and RUT C30 during lactose induction. (A) Venn diagram indicates the number of genes specific to each strain and the overlap between them. (B) The number of induced or repressed genes during induction by lactose is depicted in a bar chart. It displays the number of induced (red) and repressed (green) genes for the four time points (1, 3, 6 and 24 h) found during the induction in the RUT C30 and NG 14 strains compared to time 0. The differentially expressed genes have been selected using a 5% false discovery rate cut-off and with an absolute log2 fold change greater than 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4279801&req=5

Fig2: Differentially expressed genes of NG 14 and RUT C30 during lactose induction. (A) Venn diagram indicates the number of genes specific to each strain and the overlap between them. (B) The number of induced or repressed genes during induction by lactose is depicted in a bar chart. It displays the number of induced (red) and repressed (green) genes for the four time points (1, 3, 6 and 24 h) found during the induction in the RUT C30 and NG 14 strains compared to time 0. The differentially expressed genes have been selected using a 5% false discovery rate cut-off and with an absolute log2 fold change greater than 1.
Mentions: After consolidation of duplicates and statistical analysis, we obtained 568 genes that were differentially expressed compared to their corresponding time 0, both strains considered. The differentially expressed genes specific to each strain are indicated in Additional file 4: Table S1. The numbers of differentially expressed genes found specifically for each strain and shared in both strains are shown in Figure 2A. Interestingly, RUT C30 showed five times fewer differentially expressed genes than NG 14 and only 62 specific genes.Figure 2

Bottom Line: Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated.The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei.Genes from two specific clusters might be potential targets for such genetic engineering.

View Article: PubMed Central - PubMed

Affiliation: IFP Energies nouvelles, 1-4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France ; Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France.

ABSTRACT

Background: The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour.

Results: We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance.

Conclusions: This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.

No MeSH data available.


Related in: MedlinePlus