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Reilly MC, Kim J, Lynn J, Simmons BA, Gladden JM, Magnuson JK, Baker SE. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger. Appl Microbiol Biotechnol 2018; 102:1797-1807. [PMID: 29305699 PMCID: PMC5794824 DOI: 10.1007/s00253-017-8717-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 12/12/2022]
Abstract
Plant biomass, once reduced to its composite sugars, can be converted to fuel substitutes. One means of overcoming the recalcitrance of lignocellulose is pretreatment followed by enzymatic hydrolysis. However, currently available commercial enzyme cocktails are inhibited in the presence of residual pretreatment chemicals. Recent studies have identified a number of cellulolytic enzymes from bacteria that are tolerant to pretreatment chemicals such as ionic liquids. The challenge now is generation of these enzymes in copious amounts, an arena where fungal organisms such as Aspergillus niger have proven efficient. Fungal host strains still need to be engineered to increase production titers of heterologous protein over native enzymes, which has been a difficult task. Here, we developed a forward genetics screen coupled with whole-genome resequencing to identify specific lesions responsible for a protein hyper-production phenotype in A. niger. This strategy successfully identified novel targets, including a low-affinity glucose transporter, MstC, whose deletion significantly improved secretion of recombinant proteins driven by a glucoamylase promoter.
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Affiliation(s)
- Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jed Lynn
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Naval Medical Research Unit Dayton, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biomass Science and Conversion Technologies Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Jon K Magnuson
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Scott E Baker
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Biosystems Design and Simulation Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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Mukherjee S, Chandrababunaidu MM, Panda A, Khowala S, Tripathy S. Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. Front Microbiol 2016; 7:596. [PMID: 27242677 PMCID: PMC4865484 DOI: 10.3389/fmicb.2016.00596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 04/11/2016] [Indexed: 01/24/2023] Open
Abstract
This study catalogs production of industrially important enzymes and changes in transcript expression caused by 2-deoxy D-glucose (2-DG) treatment in Arthrinium malaysianum cultures. Carbon Catabolite Repression (CCR) induced by 2-DG in this species is cAMP independent unlike many other organisms. Higher levels of secreted endoglucanase (EG), β-glucosidase (BGL), β-xylosidase (BXL), and filter paper activity assay (FPase) enzymes under 2-DG treatment can be exploited for commercial purposes. An integrated RNA sequencing and quantitative proteomic analysis was performed to investigate the cellular response to 2-DG in A. malaysianum. Analysis of RNASeq data under 2-DG treated and control condition reveals that 56% of the unigenes do not have any known similarity to proteins in non-redundant database. Gene Ontology IDs were assigned to 36% of the transcripts (13260) and about 5207 (14%) were mapped to Kyoto Encyclopedia of Genes and Genomes pathway (KEGG). About 1711 genes encoding 2691 transcripts were differentially expressed in treated vs. control samples. Out of the 2691 differentially expressed transcripts, only 582 have any known function. The most up regulated genes belonged to Pentose Phosphate Pathways and carbohydrate degradation class as expected. In addition, genes involved in protein folding, binding, catalytic activity, DNA repair, and secondary metabolites were up-regulated under 2-DG treatment. Whereas genes encoding glycosylation pathways, growth, nutrient reservoir activity was repressed. Gene ontology analysis of the differentially expressed genes indicates metabolic process (35%) is the pre-dominant class followed by carbohydrate degradation (11%), protein folding, and trafficking (6.2%) and transport (5.3%) classes. Unlike other organisms, conventional unfolded protein response (UPR) was not activated in either control or treated conditions. Major enzymes secreted by A. malaysianum are those degrading plant polysaccharides, the most dominant ones being β-glucosidase, as demonstrated by the 2D gel analysis. A set of 7 differentially expressed mRNAs were validated by qPCR. Transmission electron microscopy analyses demonstrated that the 2-DG treated cell walls of hyphae showed significant differences in the cell-wall thickness. Overall 2-DG treatment in A. malaysianum induced secretion of large amount of commercially viable enzymes compared to other known species.
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Affiliation(s)
- Soumya Mukherjee
- Drug Development Diagnostic and Biotechnology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Mathu Malar Chandrababunaidu
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Arijit Panda
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Suman Khowala
- Drug Development Diagnostic and Biotechnology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research-Indian Institute of Chemical BiologyKolkata, India
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