1
|
Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
Collapse
Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| |
Collapse
|
2
|
Jamaluddin, Riyanti EI, Mubarik NR, Listanto E. Construction of Novel Yeast Strains from Candida tropicalis KBKTI 10.5.1 and Saccharomyces cerevisiae DBY1 to Improve the Performance of Ethanol Production Using Lignocellulosic Hydrolysate. Trop Life Sci Res 2023; 34:81-107. [PMID: 38144374 PMCID: PMC10735269 DOI: 10.21315/tlsr2023.34.2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/19/2022] [Indexed: 12/26/2023] Open
Abstract
Increased consumption of xylose-glucose and yeast tolerance to lignocellulosic hydrolysate are the keys to the success of second-generation bioethanol production. Candida tropicalis KBKTI 10.5.1 is a new isolated strain that has the ability to ferment xylose. In contrast to Saccharomyces cerevisiae DBY1 which only can produce ethanol from glucose fermentation. The research objective is the application of the genome shuffling method to increase the performance of ethanol production using lignocellulosic hydrolysate. Mutants were selected on xylose and glucose substrates separately and using random amplified polymorphic DNA (RAPD) analysis. The ethanol production using lignocellulosic hydrolysate by parents and mutants was evaluated using a batch fermentation system. Concentrations of ethanol, residual sugars, and by-products such as glycerol, lactate and acetate were measured using HPLC machine equipped with Hiplex H for carbohydrate column and a refraction index detector (RID). Ethanol produced by Fcs1 and Fcs4 mutants on acid hydrolysate increased by 26.58% and 24.17% from parent DBY1, by 14.94% and 21.84% from parent KBKTI 10.5.1. In contrast to the increase in ethanol production on alkaline hydrolysate, Fcs1 and Fcs4 mutants only experienced an increase in ethanol production by 1.35% from the parent KBKTI 10.5.1. Ethanol productivity by Fcs1 and Fcs4 mutants on acid hydrolysate reached 0.042 g/L/h and 0.044 g/L/h. The recombination of the genomes of different yeast species resulted in novel yeast strains that improved resistance performance and ethanol production on lignocellulosic hydrolysates.
Collapse
Affiliation(s)
- Jamaluddin
- Graduate School of IPB University, IPB University, Jl. Raya Dramaga, Kampus IPB Dramaga Bogor 16680 West Java, Indonesia
| | - Eny Ida Riyanti
- National Research and Innovation Agency (BRIN), Jl. Tentara Pelajar No 3A, Bogor 16111, Indonesia
| | - Nisa Rachmania Mubarik
- Department of Biology, Faculty of Mathematics and Natural Science, IPB University, Jl. Raya Dramaga, Kampus IPB Dramaga, Bogor 16680 West Java, Indonesia
| | - Edy Listanto
- National Research and Innovation Agency (BRIN), Jl. Tentara Pelajar No 3A, Bogor 16111, Indonesia
| |
Collapse
|
3
|
Gardner JM, Alperstein L, Walker ME, Zhang J, Jiranek V. Modern yeast development: finding the balance between tradition and innovation in contemporary winemaking. FEMS Yeast Res 2023; 23:6762920. [PMID: 36255399 PMCID: PMC9990983 DOI: 10.1093/femsyr/foac049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/11/2022] [Accepted: 02/01/2023] [Indexed: 11/13/2022] Open
Abstract
A key driver of quality in wines is the microbial population that undertakes fermentation of grape must. Winemakers can utilise both indigenous and purposefully inoculated yeasts to undertake alcoholic fermentation, imparting wines with aromas, flavours and palate structure and in many cases contributing to complexity and uniqueness. Importantly, having a toolbox of microbes helps winemakers make best use of the grapes they are presented with, and tackle fermentation difficulties with flexibility and efficiency. Each year the number of strains available commercially expands and more recently, includes strains of non-Saccharomyces, strains that have been improved using both classical and modern yeast technology and mixed cultures. Here we review what is available commercially, and what may be in the future, by exploring recent advances in fermentation relevant strain improvement technologies. We also report on the current use of microbes in the Australian wine industry, as reported by winemakers, as well as regulations around, and sentiment about the potential use of genetically modified organisms in the future.
Collapse
Affiliation(s)
- Jennifer M Gardner
- Department of Wine Science, School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond 5064, South Australia, Australia
| | - Lucien Alperstein
- Department of Wine Science, School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond 5064, South Australia, Australia
| | - Michelle E Walker
- Department of Wine Science, School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond 5064, South Australia, Australia
| | - Jin Zhang
- Department of Wine Science, School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond 5064, South Australia, Australia
| | - Vladimir Jiranek
- Department of Wine Science, School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond 5064, South Australia, Australia.,Australian Research Council Training Centre for Innovative Wine Production, Urrbrae 5064, South Australia, Australia
| |
Collapse
|
4
|
Geng B, Liu S, Chen Y, Wu Y, Wang Y, Zhou X, Li H, Li M, Yang S. A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor. Front Bioeng Biotechnol 2022; 10:1110513. [PMID: 36619397 PMCID: PMC9816438 DOI: 10.3389/fbioe.2022.1110513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Genome minimization is an effective way for industrial chassis development. In this study, Zymomonas mobilis ZMNP, a plasmid-free mutant strain of Z. mobilis ZM4 with four native plasmids deleted, was constructed using native type I-F CRISPR-Cas system. Cell growth of ZMNP under different temperatures and industrial effluent of xylose mother liquor were examined to investigate the impact of native plasmid removal. Despite ZMNP grew similarly as ZM4 under different temperatures, ZMNP had better xylose mother liquor utilization than ZM4. In addition, genomic, transcriptomic, and proteomic analyses were applied to unravel the molecular changes between ZM4 and ZMNP. Whole-genome resequencing result indicated that an S267P mutation in the C-terminal of OxyR, a peroxide-sensing transcriptional regulator, probably alters the transcription initiation of antioxidant genes for stress responses. Transcriptomic and proteomic studies illustrated that the reason that ZMNP utilized the toxic xylose mother liquor better than ZM4 was probably due to the upregulation of genes in ZMNP involving in stress responses as well as cysteine biosynthesis to accelerate the intracellular ROS detoxification and nucleic acid damage repair. This was further confirmed by lower ROS levels in ZMNP compared to ZM4 in different media supplemented with furfural or ethanol. The upregulation of stress response genes due to the OxyR mutation to accelerate ROS detoxification and DNA/RNA repair not only illustrates the underlying mechanism of the robustness of ZMNP in the toxic xylose mother liquor, but also provides an idea for the rational design of synthetic inhibitor-tolerant microorganisms for economic lignocellulosic biochemical production.
Collapse
Affiliation(s)
- Binan Geng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Shuyi Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yalun Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Yi Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Xuan Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Han Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., Ltd., Quzhou, Zhejiang, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, School of Life Sciences, Hubei University, Wuhan, China,*Correspondence: Shihui Yang,
| |
Collapse
|
5
|
Iqbal Z, Sadaf S. A patent-based consideration of latest platforms in the art of directed evolution: a decade long untold story. Biotechnol Genet Eng Rev 2022; 38:133-246. [PMID: 35200115 DOI: 10.1080/02648725.2021.2017638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Directed (or in vitro) evolution of proteins and metabolic pathways requires tools for creating genetic diversity and identifying protein variants with new or improved functional properties. Besides simplicity, reliability, speed, versatility, universal applicability and economy of the technique, the new science of synthetic biology requires improved means for construction of smart and high-quality mutant libraries to better navigate the sequence diversity. In vitro CRISPR/Cas9-mediated mutagenic (ICM) system and machine-learning (ML)-assisted approaches to directed evolution are now in the field to achieve the goal. This review describes the gene diversification strategies, screening and selection methods, in silico (computer-aided), Cas9-mediated and ML-based approaches to mutagenesis, developed especially in the last decade, and their patent position. The objective behind is to emphasize researchers the need for noting which mutagenesis, screening or selection method is patented and then selecting a suitable restriction-free approach to sequence diversity. Techniques and evolved products subject to patent rights need commercial license if their use is for purposes other than private or experimental research.
Collapse
Affiliation(s)
- Zarina Iqbal
- IP Litigation Department, PakPat World Intellectual Property Protection Services, Lahore, Pakistan
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
6
|
Whole-Genome Transformation of Yeast Promotes Rare Host Mutations with a Single Causative SNP Enhancing Acetic Acid Tolerance. Mol Cell Biol 2022; 42:e0056021. [PMID: 35311587 PMCID: PMC9022575 DOI: 10.1128/mcb.00560-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Whole-genome (WG) transformation (WGT) with DNA from the same or another species has been used to obtain strains with superior traits. Very few examples have been reported in eukaryotes—most apparently involving integration of large fragments of foreign DNA into the host genome. We show that WGT of a haploid acetic acid-sensitive Saccharomyces cerevisiae strain with DNA from a tolerant strain, but not from nontolerant strains, generated many tolerant transformants, some of which were stable upon subculturing under nonselective conditions. The most tolerant stable transformant contained no foreign DNA but only seven nonsynonymous single nucleotide polymorphisms (SNPs), of which none was present in the donor genome. The SNF4 mutation c.[805G→T], generating Snf4E269*, was the main causative SNP. Allele exchange of SNF4E269* or snf4Δ in industrial strains with unrelated genetic backgrounds enhanced acetic acid tolerance during fermentation under industrially relevant conditions. Our work reveals a surprisingly small number of mutations introduced by WGT, which do not bear any sequence relatedness to the genomic DNA (gDNA) of the donor organism, including the causative mutation. Spontaneous mutagenesis under protection of a transient donor gDNA fragment, maintained as extrachromosomal circular DNA (eccDNA), might provide an explanation. Support for this mechanism was obtained by transformation with genomic DNA of a yeast strain containing NatMX and selection on medium with nourseothricin. Seven transformants were obtained that gradually lost their nourseothricin resistance upon subculturing in nonselective medium. Our work shows that WGT is an efficient strategy for rapidly generating and identifying superior alleles capable of improving selectable traits of interest in industrial yeast strains.
Collapse
|
7
|
Rice Industry By-Products as Adsorbent Materials for Removing Fluoride and Arsenic from Drinking Water—A Review. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12063166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In drinking water, high concentrations of fluoride and arsenic can have adverse effects on human health. Waste deriving from the rice industry (rice husk, rice straw, rice bran) can be promising adsorbent materials, because they are (i) produced in large quantities in many parts of the world, (ii) recoverable in a circular economy perspective, (iii) at low cost if compared to expensive conventional activated carbon, and (iv) easily manageable even in developing countries. For the removal of fluoride, rice husk and rice straw allowed to obtain adsorption capacities in the range of 7.9–15.2 mg/g. Using rice husk for arsenic adsorption, excellent results were achieved with adsorption capacities above 19 mg/g. The best results both for fluorides and arsenic (>50 mg/g) were found with metal- or chemical-modified rice straw and rice husk. Identifying the next steps of future research to ensure the upscaling of biochar from recovered by-products, it is fundamental to perform: (i) tests on real waters for multicomponent adsorption; (ii) experiments with pilot plants in continuous operation; (iii) cost analysis/real applicability of modification treatments such as metal coupling or chemical synthesis; (iv) more studies on the biochar stability and on its regeneration or recovery after use.
Collapse
|
8
|
Terra-Matos J, Teixeira MO, Santos-Pereira C, Noronha H, Domingues L, Sieiro C, Gerós H, Chaves SR, Sousa MJ, Côrte-Real M. Saccharomyces cerevisiae Cells Lacking the Zinc Vacuolar Transporter Zrt3 Display Improved Ethanol Productivity in Lignocellulosic Hydrolysates. J Fungi (Basel) 2022; 8:78. [PMID: 35050019 PMCID: PMC8779672 DOI: 10.3390/jof8010078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/29/2022] Open
Abstract
Yeast-based bioethanol production from lignocellulosic hydrolysates (LH) is an attractive and sustainable alternative for biofuel production. However, the presence of acetic acid (AA) in LH is still a major problem. Indeed, above certain concentrations, AA inhibits yeast fermentation and triggers a regulated cell death (RCD) process mediated by the mitochondria and vacuole. Understanding the mechanisms involved in AA-induced RCD (AA-RCD) may thus help select robust fermentative yeast strains, providing novel insights to improve lignocellulosic ethanol (LE) production. Herein, we hypothesized that zinc vacuolar transporters are involved in vacuole-mediated AA-RCD, since zinc enhances ethanol production and zinc-dependent catalase and superoxide dismutase protect from AA-RCD. In this work, zinc limitation sensitized wild-type cells to AA-RCD, while zinc supplementation resulted in a small protective effect. Cells lacking the vacuolar zinc transporter Zrt3 were highly resistant to AA-RCD, exhibiting reduced vacuolar dysfunction. Moreover, zrt3Δ cells displayed higher ethanol productivity than their wild-type counterparts, both when cultivated in rich medium with AA (0.29 g L-1 h-1 versus 0.11 g L-1 h-1) and in an LH (0.73 g L-1 h-1 versus 0.55 g L-1 h-1). Overall, the deletion of ZRT3 emerges as a promising strategy to increase strain robustness in LE industrial production.
Collapse
Affiliation(s)
- Joana Terra-Matos
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Campus de Gualtar, University do Minho, 4710-057 Braga, Portugal; (J.T.-M.); (M.O.T.); (C.S.-P.); (H.N.); (H.G.); (S.R.C.); (M.J.S.)
| | - Marta Oliveira Teixeira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Campus de Gualtar, University do Minho, 4710-057 Braga, Portugal; (J.T.-M.); (M.O.T.); (C.S.-P.); (H.N.); (H.G.); (S.R.C.); (M.J.S.)
- Centre for Textile Science and Technology (2C2T), Department of Textile Engineering, Campus of Azurém, University of Minho, 4800-058 Guimarães, Portugal
| | - Cátia Santos-Pereira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Campus de Gualtar, University do Minho, 4710-057 Braga, Portugal; (J.T.-M.); (M.O.T.); (C.S.-P.); (H.N.); (H.G.); (S.R.C.); (M.J.S.)
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Henrique Noronha
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Campus de Gualtar, University do Minho, 4710-057 Braga, Portugal; (J.T.-M.); (M.O.T.); (C.S.-P.); (H.N.); (H.G.); (S.R.C.); (M.J.S.)
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
| | - Lucília Domingues
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Carmen Sieiro
- Biomedical Research Center (CINBIO), Department of Functional Biology and Health Sciences, Faculty of Biology, University of Vigo, 36310 Vigo, Spain;
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Campus de Gualtar, University do Minho, 4710-057 Braga, Portugal; (J.T.-M.); (M.O.T.); (C.S.-P.); (H.N.); (H.G.); (S.R.C.); (M.J.S.)
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
| | - Susana Rodrigues Chaves
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Campus de Gualtar, University do Minho, 4710-057 Braga, Portugal; (J.T.-M.); (M.O.T.); (C.S.-P.); (H.N.); (H.G.); (S.R.C.); (M.J.S.)
| | - Maria João Sousa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Campus de Gualtar, University do Minho, 4710-057 Braga, Portugal; (J.T.-M.); (M.O.T.); (C.S.-P.); (H.N.); (H.G.); (S.R.C.); (M.J.S.)
| | - Manuela Côrte-Real
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, Campus de Gualtar, University do Minho, 4710-057 Braga, Portugal; (J.T.-M.); (M.O.T.); (C.S.-P.); (H.N.); (H.G.); (S.R.C.); (M.J.S.)
| |
Collapse
|
9
|
Vanmarcke G, Deparis Q, Vanthienen W, Peetermans A, Foulquié-Moreno MR, Thevelein JM. A novel AST2 mutation generated upon whole-genome transformation of Saccharomyces cerevisiae confers high tolerance to 5-Hydroxymethylfurfural (HMF) and other inhibitors. PLoS Genet 2021; 17:e1009826. [PMID: 34624020 PMCID: PMC8500407 DOI: 10.1371/journal.pgen.1009826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/14/2021] [Indexed: 11/19/2022] Open
Abstract
Development of cell factories for conversion of lignocellulosic biomass hydrolysates into biofuels or bio-based chemicals faces major challenges, including the presence of inhibitory chemicals derived from biomass hydrolysis or pretreatment. Extensive screening of 2526 Saccharomyces cerevisiae strains and 17 non-conventional yeast species identified a Candida glabrata strain as the most 5-hydroxymethylfurfural (HMF) tolerant. Whole-genome (WG) transformation of the second-generation industrial S. cerevisiae strain MD4 with genomic DNA from C. glabrata, but not from non-tolerant strains, allowed selection of stable transformants in the presence of HMF. Transformant GVM0 showed the highest HMF tolerance for growth on plates and in small-scale fermentations. Comparison of the WG sequence of MD4 and GVM1, a diploid segregant of GVM0 with similarly high HMF tolerance, surprisingly revealed only nine non-synonymous SNPs, of which none were present in the C. glabrata genome. Reciprocal hemizygosity analysis in diploid strain GVM1 revealed AST2N406I as the only causative mutation. This novel SNP improved tolerance to HMF, furfural and other inhibitors, when introduced in different yeast genetic backgrounds and both in synthetic media and lignocellulose hydrolysates. It stimulated disappearance of HMF and furfural from the medium and enhanced in vitro furfural NADH-dependent reducing activity. The corresponding mutation present in AST1 (i.e. AST1D405I) the paralog gene of AST2, also improved inhibitor tolerance but only in combination with AST2N406I and in presence of high inhibitor concentrations. Our work provides a powerful genetic tool to improve yeast inhibitor tolerance in lignocellulosic biomass hydrolysates and other inhibitor-rich industrial media, and it has revealed for the first time a clear function for Ast2 and Ast1 in inhibitor tolerance.
Collapse
Affiliation(s)
- Gert Vanmarcke
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Ward Vanthienen
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Arne Peetermans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
- NovelYeast bv, Open Bio-Incubator, Erasmus High School, Brussels (Jette), Belgium
| |
Collapse
|
10
|
Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
Collapse
Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
11
|
Peetermans A, Foulquié-Moreno MR, Thevelein JM. Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae. MICROBIAL CELL 2021; 8:111-130. [PMID: 34055965 PMCID: PMC8144909 DOI: 10.15698/mic2021.06.751] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.
Collapse
Affiliation(s)
- Arne Peetermans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Flanders, Belgium.,Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven-Heverlee, Flanders, Belgium.,NovelYeast bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090 Brussels (Jette), Belgium
| |
Collapse
|
12
|
Deparis Q, Duitama J, Foulquié-Moreno MR, Thevelein JM. Whole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress. mBio 2021; 12:e03649-20. [PMID: 33758086 PMCID: PMC8092322 DOI: 10.1128/mbio.03649-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 11/20/2022] Open
Abstract
tRNAs are encoded by a large gene family, usually with several isogenic tRNAs interacting with the same codon. Mutations in the anticodon region of other tRNAs can overcome specific tRNA deficiencies. Phylogenetic analysis suggests that such mutations have occurred in evolution, but the driving force is unclear. We show that in yeast suppressor mutations in other tRNAs are able to overcome deficiency of the essential TRT2-encoded tRNAThrCGU at high temperature (40°C). Surprisingly, these tRNA suppressor mutations were obtained after whole-genome transformation with DNA from thermotolerant Kluyveromyces marxianus or Ogataea polymorpha strains but from which the mutations did apparently not originate. We suggest that transient presence of donor DNA in the host facilitates proliferation at high temperature and thus increases the chances for occurrence of spontaneous mutations suppressing defective growth at high temperature. Whole-genome sequence analysis of three transformants revealed only four to five nonsynonymous mutations of which one causing TRT2 anticodon stem stabilization and two anticodon mutations in non-threonyl-tRNAs, tRNALysCUU and tRNAeMetCAU, were causative. Both anticodon mutations suppressed lethality of TRT2 deletion and apparently caused the respective tRNAs to become novel substrates for threonyl-tRNA synthetase. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) data could not detect any significant mistranslation, and reverse transcription-quantitative PCR results contradicted induction of the unfolded protein response. We suggest that stress conditions have been a driving force in evolution for the selection of anticodon-switching mutations in tRNAs as revealed by phylogenetic analysis.IMPORTANCE In this work, we have identified for the first time the causative elements in a eukaryotic organism introduced by applying whole-genome transformation and responsible for the selectable trait of interest, i.e., high temperature tolerance. Surprisingly, the whole-genome transformants contained just a few single nucleotide polymorphisms (SNPs), which were unrelated to the sequence of the donor DNA. In each of three independent transformants, we have identified a SNP in a tRNA, either stabilizing the essential tRNAThrCGU at high temperature or switching the anticodon of tRNALysCUU or tRNAeMetCAU into CGU, which is apparently enough for in vivo recognition by threonyl-tRNA synthetase. LC-MS/MS analysis indeed indicated absence of significant mistranslation. Phylogenetic analysis showed that similar mutations have occurred throughout evolution and we suggest that stress conditions may have been a driving force for their selection. The low number of SNPs introduced by whole-genome transformation may favor its application for improvement of industrial yeast strains.
Collapse
Affiliation(s)
- Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Maria R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Flanders, Belgium
- NovelYeast bv, Open Bio-Incubator, Erasmus High School, Brussels (Jette), Belgium
| |
Collapse
|
13
|
Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
Collapse
Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| |
Collapse
|
14
|
Sharma S, Arora A. Tracking strategic developments for conferring xylose utilization/fermentation by Saccharomyces cerevisiae. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01590-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Purpose
Efficient ethanol production through lignocellulosic biomass hydrolysates could solve energy crisis as it is economically sustainable and ecofriendly. Saccharomyces cerevisiae is the work horse for lignocellulosic bioethanol production at industrial level. But its inability to ferment and utilize xylose limits the overall efficacy of the process.
Method
Data for the review was selected using different sources, such as Biofuels digest, Statista, International energy agency (IEA). Google scholar was used as a search engine to search literature for yeast metabolic engineering approaches. Keywords used were metabolic engineering of yeast for bioethanol production from lignocellulosic biomass.
Result
Through these approaches, interconnected pathways can be targeted randomly. Moreover, the improved strains genetic makeup can help us understand the mechanisms involved for this purpose.
Conclusion
This review discusses all possible approaches for metabolic engineering of yeast. These approaches may reveal unknown hidden mechanisms and construct ways for the researchers to produce novel and modified strains.
Collapse
|
15
|
Dasgupta A, Chowdhury N, De RK. Metabolic pathway engineering: Perspectives and applications. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 192:105436. [PMID: 32199314 DOI: 10.1016/j.cmpb.2020.105436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Metabolic engineering aims at contriving microbes as biocatalysts for enhanced and cost-effective production of countless secondary metabolites. These secondary metabolites can be treated as the resources of industrial chemicals, pharmaceuticals and fuels. Plants are also crucial targets for metabolic engineers to produce necessary secondary metabolites. Metabolic engineering of both microorganism and plants also contributes towards drug discovery. In order to implement advanced metabolic engineering techniques efficiently, metabolic engineers should have detailed knowledge about cell physiology and metabolism. Principle behind methodologies: Genome-scale mathematical models of integrated metabolic, signal transduction, gene regulatory and protein-protein interaction networks along with experimental validation can provide such knowledge in this context. Incorporation of omics data into these models is crucial in the case of drug discovery. Inverse metabolic engineering and metabolic control analysis (MCA) can help in developing such models. Artificial intelligence methodology can also be applied for efficient and accurate metabolic engineering. CONCLUSION In this review, we discuss, at the beginning, the perspectives of metabolic engineering and its application on microorganism and plant leading to drug discovery. At the end, we elaborate why inverse metabolic engineering and MCA are closely related to modern metabolic engineering. In addition, some crucial steps ensuring efficient and optimal metabolic engineering strategies have been discussed. Moreover, we explore the use of genomics data for the activation of silent metabolic clusters and how it can be integrated with metabolic engineering. Finally, we exhibit a few applications of artificial intelligence to metabolic engineering.
Collapse
Affiliation(s)
- Abhijit Dasgupta
- Department of Data Science, School of Interdisciplinary Studies, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India
| | - Nirmalya Chowdhury
- Department of Computer Science & Engineering, Jadavpur University, Kolkata 700032, India
| | - Rajat K De
- Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700108, India.
| |
Collapse
|
16
|
Yang Q, Yang Y, Tang Y, Wang X, Chen Y, Shen W, Zhan Y, Gao J, Wu B, He M, Chen S, Yang S. Development and characterization of acidic-pH-tolerant mutants of Zymomonas mobilis through adaptation and next-generation sequencing-based genome resequencing and RNA-Seq. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:144. [PMID: 32817760 PMCID: PMC7427070 DOI: 10.1186/s13068-020-01781-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 08/04/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Acid pretreatment is a common strategy used to break down the hemicellulose component of the lignocellulosic biomass to release pentoses, and a subsequent enzymatic hydrolysis step is usually applied to release hexoses from the cellulose. The hydrolysate after pretreatment and enzymatic hydrolysis containing both hexoses and pentoses can then be used as substrates for biochemical production. However, the acid-pretreated liquor can also be directly used as the substrate for microbial fermentation, which has an acidic pH and contains inhibitory compounds generated during pretreatment. Although the natural ethanologenic bacterium Zymomonas mobilis can grow in a broad range of pH 3.5 ~ 7.5, cell growth and ethanol fermentation are still affected under acidic-pH conditions below pH 4.0. RESULTS In this study, adaptive laboratory evolution (ALE) strategy was applied to adapt Z. mobilis under acidic-pH conditions. Two mutant strains named 3.6M and 3.5M with enhanced acidic pH tolerance were selected and confirmed, of which 3.5M grew better than ZM4 but worse than 3.6M in acidic-pH conditions that is served as a reference strain between 3.6M and ZM4 to help unravel the acidic-pH tolerance mechanism. Mutant strains 3.5M and 3.6M exhibited 50 ~ 130% enhancement on growth rate, 4 ~ 9 h reduction on fermentation time to consume glucose, and 20 ~ 63% improvement on ethanol productivity than wild-type ZM4 at pH 3.8. Next-generation sequencing (NGS)-based whole-genome resequencing (WGR) and RNA-Seq technologies were applied to unravel the acidic-pH tolerance mechanism of mutant strains. WGR result indicated that compared to wild-type ZM4, 3.5M and 3.6M have seven and five single nucleotide polymorphisms (SNPs), respectively, among which four are shared in common. Additionally, RNA-Seq result showed that the upregulation of genes involved in glycolysis and the downregulation of flagellar and mobility related genes would help generate and redistribute cellular energy to resist acidic pH while keeping normal biological processes in Z. mobilis. Moreover, genes involved in RND efflux pump, ATP-binding cassette (ABC) transporter, proton consumption, and alkaline metabolite production were significantly upregulated in mutants under the acidic-pH condition compared with ZM4, which could help maintain the pH homeostasis in mutant strains for acidic-pH resistance. Furthermore, our results demonstrated that in mutant 3.6M, genes encoding F1F0 ATPase to pump excess protons out of cells were upregulated under pH 3.8 compared to pH 6.2. This difference might help mutant 3.6M manage acidic conditions better than ZM4 and 3.5M. A few gene targets were then selected for genetics study to explore their role in acidic pH tolerance, and our results demonstrated that the expression of two operons in the shuttle plasmids, ZMO0956-ZMO0958 encoding cytochrome bc1 complex and ZMO1428-ZMO1432 encoding RND efflux pump, could help Z. mobilis tolerate acidic-pH conditions. CONCLUSION An acidic-pH-tolerant mutant 3.6M obtained through this study can be used for commercial bioethanol production under acidic fermentation conditions. In addition, the molecular mechanism of acidic pH tolerance of Z. mobilis was further proposed, which can facilitate future research on rational design of synthetic microorganisms with enhanced tolerance against acidic-pH conditions. Moreover, the strategy developed in this study combining approaches of ALE, genome resequencing, RNA-Seq, and classical genetics study for mutant evolution and characterization can be applied in other industrial microorganisms.
Collapse
Affiliation(s)
- Qing Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Ying Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Xia Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Wei Shen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Junjie Gao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Bo Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu, 610041 China
| | - Mingxiong He
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu, 610041 China
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province and School of Life Sciences, Hubei University, Wuhan, 430062 China
| |
Collapse
|
17
|
Otto M, Teixeira PG, Vizcaino MI, David F, Siewers V. Integration of a multi-step heterologous pathway in Saccharomyces cerevisiae for the production of abscisic acid. Microb Cell Fact 2019; 18:205. [PMID: 31767000 PMCID: PMC6876084 DOI: 10.1186/s12934-019-1257-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The sesquiterpenoid abscisic acid (ABA) is mostly known for regulating developmental processes and abiotic stress responses in higher plants. Recent studies show that ABA also exhibits a variety of pharmacological activities. Affordable and sustainable production will be required to utilize the compound in agriculture and as a potential pharmaceutical. Saccharomyces cerevisiae is an established workhorse for the biotechnological production of chemicals. In this study, we constructed and characterised an ABA-producing S. cerevisiae strain using the ABA biosynthetic pathway from Botrytis cinerea. RESULTS Expression of the B. cinerea genes bcaba1, bcaba2, bcaba3 and bcaba4 was sufficient to establish ABA production in the heterologous host. We characterised the ABA-producing strain further by monitoring ABA production over time and, since the pathway contains two cytochrome P450 enzymes, by investigating the effects of overexpressing the native S. cerevisiae or the B. cinerea cytochrome P450 reductase. Both, overexpression of the native or heterologous cytochrome P450 reductase, led to increased ABA titres. We were able to show that ABA production was not affected by precursor or NADPH supply, which suggested that the heterologous enzymes were limiting the flux towards the product. The B. cinerea cytochrome P450 monooxygenases BcABA1 and BcABA2 were identified as pathway bottlenecks and balancing the expression levels of the pathway enzymes resulted in 4.1-fold increased ABA titres while reducing by-product formation. CONCLUSION This work represents the first step towards a heterologous ABA cell factory for the commercially relevant sesquiterpenoid.
Collapse
Affiliation(s)
- Maximilian Otto
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Paulo Gonçalves Teixeira
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Maria Isabel Vizcaino
- Chalmers Mass Spectrometry Infrastructure, Chalmers University of Technology, Gothenburg, Sweden
| | - Florian David
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Novo Nordisk Foundation Center for Biosustainability, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| |
Collapse
|
18
|
Ruchala J, Kurylenko OO, Dmytruk KV, Sibirny AA. Construction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha). J Ind Microbiol Biotechnol 2019; 47:109-132. [PMID: 31637550 PMCID: PMC6970964 DOI: 10.1007/s10295-019-02242-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.
Collapse
Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland
| | - Olena O Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv, 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Biotechnology, University of Rzeszow, Zelwerowicza 4, 35-601, Rzeszow, Poland.
| |
Collapse
|
19
|
Zhai L, Manglekar RR, Geng A. Enzyme production and oil palm empty fruit bunch bioconversion to ethanol using a hybrid yeast strain. Biotechnol Appl Biochem 2019; 67:714-722. [PMID: 31498481 DOI: 10.1002/bab.1816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/05/2019] [Indexed: 11/08/2022]
Abstract
Oil palm empty fruit bunch (OPEFB) is a lignocellulosic biomass generated in palm oil mills. It is a sustainable resource for fuels and chemicals. In this study, OPEFB was converted to ethanol by an integrative OPEFB conversion process including dilute alkaline pretreatment, cellulolytic enzyme production, separate OPEFB hydrolysis, and cofermentation using a hybrid xylose-fermenting yeast. OPEFB was pretreated using 1% (w/v) NaOH solution followed by 1% (v/v) H2 O2 . Further, cellulolytic enzymes were produced by submerged fermentation using Trichoderma reesei Rut C30 and used for OPEFB hydrolysis. The filter paper cellulase activity of the crude cellulolytic enzymes was 15.1 IU/mL, which was higher than those obtained by reported Trichoderma strains under laboratory conditions. Glucose and xylose yields reached 66.9% and 74.2%, respectively, at 30 filter paper unit (FPU)/g-biomass enzyme dosage and 10% (w/v) biomass loading. The hybrid yeast strain ScF2 was previously constructed through recursive genome shuffling of Pichia stipitis and Saccharomyces cerevisiae and was used in OPEFB hydrolysate fermentation. About 16.9 g/L ethanol was produced with an ethanol yield of 0.34 g/g sugars, which was 67% of theoretical ethanol yield.
Collapse
Affiliation(s)
- Lili Zhai
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore
| | - Rupali Rahul Manglekar
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore
| | - Anli Geng
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore
| |
Collapse
|
20
|
Lin Y, Cai Y, Guo Y, Li X, Qi X, Qi Q, Wang Q. Development and genomic elucidation of hybrid yeast with improved glucose-xylose co-fermentation at high temperature. FEMS Yeast Res 2019; 19:5333307. [DOI: 10.1093/femsyr/foz015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/17/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Enhanced capability of co-fermenting glucose and xylose at high temperature is highly desirable for yeast application in second-generation bioethanol production. Here, we obtained hybrid strains with improved glucose-xylose co-fermentation properties at high temperature by combining genome shuffling and adaptive evolution. Genome resequencing of these strains suggested predominantly inherited genetic information from one parental strain Spathaspora passalidarum SP rather than the other parental strain Saccharomyces cerevisiae ScY01, possibly due to that the CUG codon system of S. passalidarum might have systematically eliminated most of the functional proteins from S. cerevisiae through misfolding. Compared to SP, one-copy loss of a 146-kb fragment was found in the hybrid strain and regained after being evolved for a while, whereas one-copy loss of an 11-kb fragment was only found after being evolved for a longer time. Besides, the genes affected by nonsynonymous variants were also identified, especially the mutation S540F in the endoplasmic reticulum chaperon Kar2. Structural prediction indicated that S540F might change the substrate binding activity of Kar2, and thus play a role in preventing protein aggregation in yeast at high temperature. Our results illustrated genomic alterations during this process and revealed some genomic factors that might be involved to determine yeast thermotolerance.
Collapse
Affiliation(s)
- Yuping Lin
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanqing Cai
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yufeng Guo
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xin Li
- Impossible Foods Inc., Redwood City, CA 94063, USA
| | - Xianni Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qi Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinhong Wang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| |
Collapse
|
21
|
Wang W, Wu B, Qin H, Liu P, Qin Y, Duan G, Hu G, He M. Genome shuffling enhances stress tolerance of Zymomonas mobilis to two inhibitors. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:288. [PMID: 31890016 PMCID: PMC6913010 DOI: 10.1186/s13068-019-1631-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 12/05/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Furfural and acetic acid are the two major inhibitors generated during lignocellulose pretreatment and hydrolysis, would severely inhibit the cell growth, metabolism, and ethanol fermentation efficiency of Zymomonas mobilis. Effective genome shuffling mediated by protoplast electrofusion was developed and then applied to Z. mobilis. RESULTS After two rounds of genome shuffling, 10 different mutants with improved cell growth and ethanol yield in the presence of 5.0 g/L acetic acid and 3.0 g/L furfural were obtained. The two most prominent genome-shuffled strains, 532 and 533, were further investigated along with parental strains in the presence of 7.0 g/L acetic acid and 3.0 g/L furfural. The results showed that mutants 532 and 533 were superior to the parental strain AQ8-1 in the presence of 7.0 g/L acetic acid, with a shorter fermentation time (30 h) and higher productivity than AQ8-1. Mutant 533 exhibited subtle differences from parental strain F34 in the presence of 3.0 g/L furfural. Mutations present in 10 genome-shuffled strains were identified via whole-genome resequencing, and the source of each mutation was identified as either de novo mutation or recombination of the parent genes. CONCLUSIONS These results indicate that genome shuffling is an efficient method for enhancing stress tolerance in Z. mobilis. The engineered strains generated in this study could be potential cellulosic ethanol producers in the future.
Collapse
Affiliation(s)
- Weiting Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
| | - Han Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
| | - Panting Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Yao Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610041 People’s Republic of China
| | - Guowei Duan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| |
Collapse
|
22
|
Jetti KD, GNS RR, Garlapati D, Nammi SK. Improved ethanol productivity and ethanol tolerance through genome shuffling of Saccharomyces cerevisiae and Pichia stipitis. Int Microbiol 2018; 22:247-254. [DOI: 10.1007/s10123-018-00044-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/03/2018] [Accepted: 11/06/2018] [Indexed: 01/26/2023]
|
23
|
Kordowska-Wiater M, Lisiecka U, Kostro K. Improvement of Candida parapsilosis by genome shuffling for the efficient production of arabitol from l-arabinose. Food Sci Biotechnol 2018; 27:1395-1403. [PMID: 30319849 PMCID: PMC6170280 DOI: 10.1007/s10068-018-0369-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/16/2018] [Accepted: 03/27/2018] [Indexed: 01/07/2023] Open
Abstract
Arabitol is used in the food industry as a low-calorie sweetener. It is produced by yeasts during the biotransformation process of l-arabinose. Genome shuffling was performed in Candida parapsilosis DSM 70125, an efficient producer of arabitol, to obtain fusants with improved arabitol production ability. Four mutants from the parental library were used for the first round of genome shuffling. The best fusants, GSI-1 and GSI-10A, were subjected to a second round of genome shuffling. Finally, two fusants, GSII-3 and GSII-16, produced concentrations of arabitol that were 50% higher than that of the wild-type strain during selection culture. Under the optimal conditions established for C. parapsilosis, the two fusants produced 11.83 and 11.75 g/L of arabitol and were approximately 15-16% more efficient than the wild-type strain. Flow cytometry analysis showed that the ploidy of the new strains did not change.
Collapse
Affiliation(s)
- Monika Kordowska-Wiater
- 1Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, Skromna 8, 20-704 Lublin, Poland
| | - Urszula Lisiecka
- 2Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences in Lublin, Głęboka 30, 20-950 Lublin, Poland
| | - Krzysztof Kostro
- 2Department of Epizootiology and Clinic of Infectious Diseases, University of Life Sciences in Lublin, Głęboka 30, 20-950 Lublin, Poland
| |
Collapse
|
24
|
Löbs AK, Schwartz C, Wheeldon I. Genome and metabolic engineering in non-conventional yeasts: Current advances and applications. Synth Syst Biotechnol 2017; 2:198-207. [PMID: 29318200 PMCID: PMC5655347 DOI: 10.1016/j.synbio.2017.08.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 12/26/2022] Open
Abstract
Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisiae is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.
Collapse
Affiliation(s)
- Ann-Kathrin Löbs
- Department of Chemical and Environmental Engineering, UC Riverside, Riverside, USA
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, UC Riverside, Riverside, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, UC Riverside, Riverside, USA
| |
Collapse
|
25
|
Wickramasinghe GHIM, Rathnayake PPAMSI, Chandrasekharan NV, Weerasinghe MSS, Wijesundera RLC, Wijesundera WSS. Expression, Docking, and Molecular Dynamics of Endo- β-1,4-xylanase I Gene of Trichoderma virens in Pichia stipitis. BIOMED RESEARCH INTERNATIONAL 2017; 2017:4658584. [PMID: 28856159 PMCID: PMC5569632 DOI: 10.1155/2017/4658584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/19/2017] [Indexed: 11/18/2022]
Abstract
It is essential that major carbohydrate polymers in the lignocellulosic biomass are converted into fermentable sugars for the economical production of energy. Xylan, the major component of hemicelluloses, is the second most naturally abundant carbohydrate polymer comprising 20-40% of the total biomass. Endoxylanase (EXN) hydrolyzes xylan into mixtures of xylooligosaccharides. The objective of this study was to genetically modify Pichia stipitis, a pentose sugar fermenting yeast species, to hydrolyze xylan into xylooligosaccharides via cloning and heterologous extracellular expression of EXNI gene from locally isolated Trichoderma virens species. Pichia stipitis was engineered to carry the EXNI gene of T. virens using pGAPZα expression vector. The open reading frame encodes 191 amino acids and SDS-PAGE analysis revealed a 24 kDA recombinant protein. The EXNI activity expressed by recombinant P. stipitis clone under standard conditions using 1% beechwood xylan was 31.7 U/ml. Molecular docking and molecular dynamics simulations were performed to investigate EXNI-xylan interactions. Free EXNI and xylan bound EXNI exhibited similar stabilities and structural behavior in aqueous medium. Furthermore, this in silico work opens avenues for the development of newer generation EXN proteins that can perform better and have enhanced catalytic activity.
Collapse
|
26
|
Deparis Q, Claes A, Foulquié-Moreno MR, Thevelein JM. Engineering tolerance to industrially relevant stress factors in yeast cell factories. FEMS Yeast Res 2017; 17:3861662. [PMID: 28586408 PMCID: PMC5812522 DOI: 10.1093/femsyr/fox036] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/04/2017] [Indexed: 01/01/2023] Open
Abstract
The main focus in development of yeast cell factories has generally been on establishing optimal activity of heterologous pathways and further metabolic engineering of the host strain to maximize product yield and titer. Adequate stress tolerance of the host strain has turned out to be another major challenge for obtaining economically viable performance in industrial production. Although general robustness is a universal requirement for industrial microorganisms, production of novel compounds using artificial metabolic pathways presents additional challenges. Many of the bio-based compounds desirable for production by cell factories are highly toxic to the host cells in the titers required for economic viability. Artificial metabolic pathways also turn out to be much more sensitive to stress factors than endogenous pathways, likely because regulation of the latter has been optimized in evolution in myriads of environmental conditions. We discuss different environmental and metabolic stress factors with high relevance for industrial utilization of yeast cell factories and the experimental approaches used to engineer higher stress tolerance. Improving stress tolerance in a predictable manner in yeast cell factories should facilitate their widespread utilization in the bio-based economy and extend the range of products successfully produced in large scale in a sustainable and economically profitable way.
Collapse
Affiliation(s)
- Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Arne Claes
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| |
Collapse
|
27
|
Zong H, Zhang C, Zhuge B, Lu X, Fang H, Sun J. Effects of xylitol dehydrogenase (XYL2) on xylose fermentation by engineeredCandida glycerinogenes. Biotechnol Appl Biochem 2017; 64:590-599. [DOI: 10.1002/bab.1514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 05/21/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Hong Zong
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Cheng Zhang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Huiying Fang
- The Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology; Research Centre of Industrial Microbiology; Jiangnan University; Wuxi People's Republic of China
| | - Jin Sun
- Zhejiang Condiments Industry Research Center; Zhejiang Zhengwei Food Co., Ltd.; Yiwu People's Republic of China
| |
Collapse
|
28
|
Li H, Xiong L, Chen X, Wang C, Qi G, Huang C, Luo M, Chen X. Enhanced enzymatic hydrolysis and acetone-butanol-ethanol fermentation of sugarcane bagasse by combined diluted acid with oxidate ammonolysis pretreatment. BIORESOURCE TECHNOLOGY 2017; 228:257-263. [PMID: 28081523 DOI: 10.1016/j.biortech.2016.12.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/30/2016] [Accepted: 12/31/2016] [Indexed: 05/24/2023]
Abstract
This study aims to propose a biorefinery pretreatment technology for the bioconversion of sugarcane bagasse (SB) into biofuels and N-fertilizers. Performance of diluted acid (DA), aqueous ammonia (AA), oxidate ammonolysis (OA) and the combined DA with AA or OA were compared in SB pretreatment by enzymatic hydrolysis, structural characterization and acetone-butanol-ethanol (ABE) fermentation. Results indicated that DA-OA pretreatment improves the digestibility of SB by sufficiently hydrolyzing hemicellulose into fermentable monosaccharides and oxidating lignin into soluble N-fertilizer with high nitrogen content (11.25%) and low C/N ratio (3.39). The enzymatic hydrolysates from DA-OA pretreated SB mainly composed of glucose was more suitable for the production of ABE solvents than the enzymatic hydrolysates from OA pretreated SB containing high ratio of xylose. The fermentation of enzymatic hydrolysates from DA-OA pretreated SB produced 12.12g/L ABE in 120h. These results suggested that SB could be utilized efficient, economic, and environmental by DA-OA pretreatment.
Collapse
Affiliation(s)
- Hailong Li
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Lian Xiong
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Xuefang Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Can Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Gaoxiang Qi
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Chao Huang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China
| | - Mutan Luo
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xinde Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, People's Republic of China; CAS Key Laboratory of Renewable Energy, Guangzhou 510640, People's Republic of China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, People's Republic of China; R&D Center of Xuyi Attapulgite Applied Technology, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Xuyi 211700, People's Republic of China.
| |
Collapse
|
29
|
Yi S, Wan Y. Separation performance of novel vinyltriethoxysilane (VTES)-g-silicalite-1/PDMS/PAN thin-film composite membrane in the recovery of bioethanol from fermentation broths by pervaporation. J Memb Sci 2017. [DOI: 10.1016/j.memsci.2016.11.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
30
|
Tramontina R, Franco Cairo JPL, Liberato MV, Mandelli F, Sousa A, Santos S, Rabelo SC, Campos B, Ienczak J, Ruller R, Damásio ARL, Squina FM. The Coptotermes gestroi aldo-keto reductase: a multipurpose enzyme for biorefinery applications. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:4. [PMID: 28053664 PMCID: PMC5209882 DOI: 10.1186/s13068-016-0688-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/14/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND In nature, termites can be considered as a model biological system for biofuel research based on their remarkable efficiency for lignocellulosic biomass conversion. Redox enzymes are of interest in second-generation ethanol production because they promote synergic enzymatic activity with classical hydrolases for lignocellulose saccharification and inactivate fermentation inhibitory compounds produced after lignocellulose pretreatment steps. RESULTS In the present study, the biochemical and structural characteristics of the Coptotermes gestroi aldo-keto reductase (CgAKR-1) were comprehensively investigated. CgAKR-1 displayed major structural differences compared with others AKRs, including the differences in the amino acid composition of the substrate-binding site, providing basis for classification as a founding member of a new AKR subfamily (family AKR1 I). Immunolocalization assays with anti-CgAKR-1 antibodies resulted in strong fluorescence in the salivary gland, proventriculus, and foregut. CgAKR-1 supplementation caused a 32% reduction in phenolic aldehydes, such as furfural, which act as fermentation inhibitors of hemicellulosic hydrolysates, and improved ethanol fermentation by the xylose-fermenting yeast Scheffersomyces stipitis by 45%. We observed synergistic enzymatic interactions between CgAKR-1 and commercial cellulosic cocktail for sugarcane bagasse saccharification, with a maximum synergism degree of 2.17 for sugar release. Our data indicated that additive enzymatic activity could be mediated by reactive oxygen species because CgAKR-1 could produce hydrogen peroxide. CONCLUSION In summary, we identified the founding member of an AKRI subfamily with a potential role in the termite digestome. CgAKR-1 was found to be a multipurpose enzyme with potential biotechnological applications. The present work provided a basis for the development and application of integrative and multipurpose enzymes in the bioethanol production chain.
Collapse
Affiliation(s)
- Robson Tramontina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
- Programa de Pós Graduação em Biociências e Tecnologia de Produtos Bioativos (BTPB)-Instituto de Biologia-CP 6109, Universidade Estadual de Campinas-UNICAMP, 13083-970 Campinas, SP Brazil
| | - João Paulo L. Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
| | - Marcelo V. Liberato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
| | - Fernanda Mandelli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
| | - Amanda Sousa
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
- Programa de Pós Graduação em Biociências e Tecnologia de Produtos Bioativos (BTPB)-Instituto de Biologia-CP 6109, Universidade Estadual de Campinas-UNICAMP, 13083-970 Campinas, SP Brazil
| | - Samantha Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
| | - Sarita Cândida Rabelo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
| | - Bruna Campos
- Brazilian Biosciences National Laboratory (LNBio), from the Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Jaciane Ienczak
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
| | - André R. L. Damásio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Fabio Marcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro, no 10000 Campinas, SP Brazil
| |
Collapse
|
31
|
Zhu Z, Wu X, Lv B, Wu G, Wang J, Jiang W, Li P, He J, Chen J, Chen M, Bao D, Zhang J, Tan Q, Tang X. A new approach for breeding low-temperature-resistantVolvariella volvaceastrains: Genome shuffling in edible fungi. Biotechnol Appl Biochem 2016; 63:605-615. [DOI: 10.1002/bab.1420] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 05/15/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Ziping Zhu
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- School of Life Science; Taizhou University; Taizhou People's Republic of China
| | - Xiao Wu
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Beibei Lv
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Guogan Wu
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Jinbin Wang
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Wei Jiang
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Peng Li
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Jianhua He
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Jianzhong Chen
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| | - Mingjie Chen
- National Engineering Research Center of Edible Fungi; Shanghai People's Republic of China
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi; Shanghai People's Republic of China
| | - Jinsong Zhang
- National Engineering Research Center of Edible Fungi; Shanghai People's Republic of China
| | - Qi Tan
- National Engineering Research Center of Edible Fungi; Shanghai People's Republic of China
| | - Xueming Tang
- Biotechnology Research Institute; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
- Key Laboratory of Agricultural Genetics and Breeding; Shanghai Academy of Agricultural Sciences; Shanghai People's Republic of China
| |
Collapse
|
32
|
Ren X, Wang J, Yu H, Peng C, Hu J, Ruan Z, Zhao S, Liang Y, Peng N. Anaerobic and sequential aerobic production of high-titer ethanol and single cell protein from NaOH-pretreated corn stover by a genome shuffling-modified Saccharomyces cerevisiae strain. BIORESOURCE TECHNOLOGY 2016; 218:623-630. [PMID: 27416512 DOI: 10.1016/j.biortech.2016.06.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 06/06/2023]
Abstract
In this study, a Saccharomyces cerevisiae recombinant strain 14 was constructed through genome shuffling method by transferring the whole genomic DNA of Candida intermedia strain 23 into a thermo-tolerant S. cerevisiae strain. The recombinant strain 14 combined the good natures of both parent strains that efficiently produced ethanol from glucose and single cell protein from xylose with 54.6% crude protein and all essential amino acids except cysteine at 35°C. Importantly, the recombinant strain 14 produced 64.07g/L ethanol from 25%(w/v) NaOH-pretreated and washed corn stover with the ethanol yield of 0.26g/g total stover by fed-batch simultaneous saccharification and fermentation and produced 66.50g/L dry cell mass subsequently from the residual hydrolysate and ethanol. Therefore, this study represents a feasible method to comprehensively utilize hexose and pentose in lignocellulosic materials.
Collapse
Affiliation(s)
- Xueliang Ren
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Juncong Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Hui Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Chunlan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Jinlong Hu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Shumiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China; Hubei Collaborative Innovation Center for Industrial Fermentation, Wuhan 430068, PR China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China; Hubei Collaborative Innovation Center for Industrial Fermentation, Wuhan 430068, PR China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China; Hubei Collaborative Innovation Center for Industrial Fermentation, Wuhan 430068, PR China; Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu 610041, Sichuan, PR China.
| |
Collapse
|
33
|
Mund NK, Dash D, Barik CR, Goud VV, Sahoo L, Mishra P, Nayak NR. Chemical composition, pretreatments and saccharification of Senna siamea (Lam.) H.S. Irwin & Barneby: An efficient biomass producing tree legume. BIORESOURCE TECHNOLOGY 2016; 207:205-212. [PMID: 26890795 DOI: 10.1016/j.biortech.2016.01.118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 06/05/2023]
Abstract
Protocols were developed for efficient release of glucose from the biomass of Senna siamea, one of the highly efficient biomass producing tree legumes. Composition of mature, 1year and 2years coppice biomass were analysed. For the hydrolysis of the glucan, two pretreatments, cellulose solvent- and organic solvent-based lignocellulose fractionation (COSLIF) and alkali (sodium hydroxide) were used; COSLIF (85% phosphoric acid, 45min incubation at 50°C) pretreated mature biomass exhibited best result in which 88.90% glucose released after 72h of incubation with the use of 5 filter paper units (FPU) of cellulase and 10 international units (IU) of β-glucosidase per gram of glucan. Of the biomass of different particle sizes (40-200mesh) used for saccharification, 40-60mesh shown the maximum glucose release. COSLIF pretreated mature, 1year and 2years coppice biomass showed equivalent glucose release profiles.
Collapse
Affiliation(s)
- Nitesh K Mund
- Regional Plant Resource Centre, Nayapalli, Bhubaneswar 751015, Odisha, India
| | - Debabrata Dash
- Regional Plant Resource Centre, Nayapalli, Bhubaneswar 751015, Odisha, India
| | - Chitta R Barik
- Centre for Energy, Indian Institute of Technology, Guwahati 781039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Vaibhav V Goud
- Centre for Energy, Indian Institute of Technology, Guwahati 781039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Lingaraj Sahoo
- Centre for Energy, Indian Institute of Technology, Guwahati 781039, Assam, India; Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Prasannajit Mishra
- AICRP on Agroforestry, College of Forestry, Orissa University of Agriculture and Technology, Bhubaneswar 751016, Odisha, India
| | - Nihar R Nayak
- Regional Plant Resource Centre, Nayapalli, Bhubaneswar 751015, Odisha, India.
| |
Collapse
|
34
|
Shalley Sharma, Sonia Sharma, Surender Singh, Lata, Anju Arora. Improving Yeast Strains for Pentose Hexose Co-fermentation: Successes and Hurdles. SPRINGER PROCEEDINGS IN ENERGY 2016. [DOI: 10.1007/978-81-322-2773-1_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
35
|
Characterization of a Novel Xylanase Gene from Rumen Content of Hu Sheep. Appl Biochem Biotechnol 2015; 177:1424-36. [DOI: 10.1007/s12010-015-1823-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/18/2015] [Indexed: 01/10/2023]
|
36
|
Zhang C, Zong H, Zhuge B, Lu X, Fang H, Zhuge J. Production of Xylitol from d-Xylose by Overexpression of Xylose Reductase in Osmotolerant Yeast Candida glycerinogenes WL2002-5. Appl Biochem Biotechnol 2015; 176:1511-27. [DOI: 10.1007/s12010-015-1661-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 05/06/2015] [Indexed: 12/23/2022]
|
37
|
Qi K, Xia XX, Zhong JJ. Enhanced anti-oxidative activity and lignocellulosic ethanol production by biotin addition to medium in Pichia guilliermondii fermentation. BIORESOURCE TECHNOLOGY 2015; 189:36-43. [PMID: 25864029 DOI: 10.1016/j.biortech.2015.02.089] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 02/21/2015] [Accepted: 02/23/2015] [Indexed: 06/04/2023]
Abstract
Commercialization of lignocellulosic ethanol fermentation requires its high titer, but the reactive oxygen species (ROS) accumulation during the bioprocess damaged the cells and compromised this goal. To improve the cellular anti-oxidative activity during non-detoxified corncob residue hydrolysate fermentation, seed cells were prepared to possess a higher level of intracellular biotin pool (IBP), which facilitated the biosyntheses of catalase and porphyrin. As a result, the catalase activity increased by 1.3-folds compared to control while the ROS level reduced by 50%. Cell viability in high-IBP cells was 1.7-folds of control and the final ethanol titer increased from 31.2 to 41.8 g L(-1) in batch fermentation. The high-IBP cells were further used for repeated-batch fermentation in the non-detoxified lignocellulosic hydrolysate, and the highest titer and average productivity of ethanol reached 63.7 g L(-1) and 1.2 g L(-1)h(-1). The results were favorable to future industrial application of this lignocellulosic bioethanol process.
Collapse
Affiliation(s)
- Kai Qi
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Xiao-Xia Xia
- State Key Laboratory of Microbial Metabolism, and Lab. of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
| | - Jian-Jiang Zhong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; State Key Laboratory of Microbial Metabolism, and Lab. of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.
| |
Collapse
|
38
|
Stabilization of mini-chromosome segregation during mitotic growth by overexpression of YCR041W and its application to chromosome engineering in Saccharomyces cerevisiae. J Biosci Bioeng 2014; 119:526-31. [PMID: 25454064 DOI: 10.1016/j.jbiosc.2014.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 10/07/2014] [Accepted: 10/10/2014] [Indexed: 11/22/2022]
Abstract
Chromosome engineering enables large-scale genome manipulation and can be used as a novel technology for breeding of yeasts. PCR-mediated chromosome splitting (PCS) offers a powerful tool for chromosome engineering by enabling a yeast chromosome to be split at any desired site. By applying PCS, a huge variety of chromosome combinations can be created and the best strain under specific conditions can be selected-a technology that we have called genome reorganization. Once the optimal strain is obtained, chromosome constitutions need to be maintained stably; however, mini-chromosomes of less than 50 kb are at relatively high frequency lost during cultivation. To overcome this problem, in this study we screened for multicopy suppressors of the high loss of mini-chromosomes by using a multicopy genomic library of Saccharomyces cerevisiae. We identified a novel gene, YCR041W, that stabilizes mini-chromosomes. The translational product of YCR041W was suggested to play an important role in increasing stability for mini-chromosome maintenance, probably by decreasing the rate of loss during mitotic cell division. The stabilization of mini-chromosomes conferred by YCR041W overexpression was completely dependent on the silencing protein Sir4, suggesting that a process related to telomere function might be involved in mini-chromosome stabilization. Overexpression of YCR041W stabilized not only a yeast artificial chromosome vector, but also a mini-chromosome derived from a natural chromosome. Taking these results together, we propose that YCR041W overexpression can be used as a novel chromosome engineering tool for controlling mini-chromosome maintenance and loss.
Collapse
|
39
|
Genetic improvement of native xylose-fermenting yeasts for ethanol production. J Ind Microbiol Biotechnol 2014; 42:1-20. [DOI: 10.1007/s10295-014-1535-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/02/2014] [Indexed: 12/27/2022]
|
40
|
Steensels J, Snoek T, Meersman E, Nicolino MP, Voordeckers K, Verstrepen KJ. Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev 2014; 38:947-95. [PMID: 24724938 PMCID: PMC4293462 DOI: 10.1111/1574-6976.12073] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 01/31/2014] [Accepted: 04/02/2014] [Indexed: 12/23/2022] Open
Abstract
Yeasts have been used for thousands of years to make fermented foods and beverages, such as beer, wine, sake, and bread. However, the choice for a particular yeast strain or species for a specific industrial application is often based on historical, rather than scientific grounds. Moreover, new biotechnological yeast applications, such as the production of second-generation biofuels, confront yeast with environments and challenges that differ from those encountered in traditional food fermentations. Together, this implies that there are interesting opportunities to isolate or generate yeast variants that perform better than the currently used strains. Here, we discuss the different strategies of strain selection and improvement available for both conventional and nonconventional yeasts. Exploiting the existing natural diversity and using techniques such as mutagenesis, protoplast fusion, breeding, genome shuffling and directed evolution to generate artificial diversity, or the use of genetic modification strategies to alter traits in a more targeted way, have led to the selection of superior industrial yeasts. Furthermore, recent technological advances allowed the development of high-throughput techniques, such as 'global transcription machinery engineering' (gTME), to induce genetic variation, providing a new source of yeast genetic diversity.
Collapse
Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Tim Snoek
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Esther Meersman
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Martina Picca Nicolino
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Karin Voordeckers
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU LeuvenLeuven, Belgium
- Laboratory for Systems Biology, VIBLeuven, Belgium
| |
Collapse
|
41
|
Lin J, Li S, Sun M, Zhang C, Yang W, Zhang Z, Li X, Li S. Microbial lipid production by oleaginous yeast ind-xylose solution using a two-stage culture mode. RSC Adv 2014. [DOI: 10.1039/c4ra01453g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
42
|
|
43
|
Direct ethanol production from lignocellulosic sugars and sugarcane bagasse by a recombinant Trichoderma reesei strain HJ48. ScientificWorldJournal 2014; 2014:798683. [PMID: 24995362 PMCID: PMC4060538 DOI: 10.1155/2014/798683] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/10/2014] [Indexed: 11/18/2022] Open
Abstract
Trichoderma reesei can be considered as a candidate for consolidated bioprocessing (CBP) microorganism. However, its ethanol yield needs to be improved significantly. Here the ethanol production of T. reesei CICC 40360 was improved by genome shuffling while simultaneously enhancing the ethanol resistance. The initial mutant population was generated by nitrosoguanidine treatment of the spores, and an improved population producing more than fivefold ethanol than wild type was obtained by genome shuffling. The results show that the shuffled strain HJ48 can efficiently convert lignocellulosic sugars to ethanol under aerobic conditions. Furthermore, it was able to produce ethanol directly from sugarcane bagasse, demonstrating that the shuffled strain HJ48 is a suitable microorganism for consolidated bioprocessing.
Collapse
|
44
|
Evolutionary engineering by genome shuffling. Appl Microbiol Biotechnol 2014; 98:3877-87. [PMID: 24595425 DOI: 10.1007/s00253-014-5616-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 01/28/2023]
Abstract
An upsurge in the bioeconomy drives the need for engineering microorganisms with increasingly complex phenotypes. Gains in productivity of industrial microbes depend on the development of improved strains. Classical strain improvement programmes for the generation, screening and isolation of such mutant strains have existed for several decades. An alternative to traditional strain improvement methods, genome shuffling, allows the directed evolution of whole organisms via recursive recombination at the genome level. This review deals chiefly with the technical aspects of genome shuffling. It first presents the diversity of organisms and phenotypes typically evolved using this technology and then reviews available sources of genetic diversity and recombination methodologies. Analysis of the literature reveals that genome shuffling has so far been restricted to microorganisms, both prokaryotes and eukaryotes, with an overepresentation of antibiotics- and biofuel-producing microbes. Mutagenesis is the main source of genetic diversity, with few studies adopting alternative strategies. Recombination is usually done by protoplast fusion or sexual recombination, again with few exceptions. For both diversity and recombination, prospective methods that have not yet been used are also presented. Finally, the potential of genome shuffling for gaining insight into the genetic basis of complex phenotypes is also discussed.
Collapse
|
45
|
Favaro L, Basaglia M, Casella S. Innately robust yeast strains isolated from grape marc have a great potential for lignocellulosic ethanol production. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0826-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
|
46
|
Demeke MM, Dumortier F, Li Y, Broeckx T, Foulquié-Moreno MR, Thevelein JM. Combining inhibitor tolerance and D-xylose fermentation in industrial Saccharomyces cerevisiae for efficient lignocellulose-based bioethanol production. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:120. [PMID: 23971950 PMCID: PMC3765968 DOI: 10.1186/1754-6834-6-120] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/20/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND In addition to efficient pentose utilization, high inhibitor tolerance is a key trait required in any organism used for economically viable industrial bioethanol production with lignocellulose biomass. Although recent work has succeeded in establishing efficient xylose fermentation in robust industrial Saccharomyces cerevisiae strains, the resulting strains still lacked sufficient inhibitor tolerance for efficient sugar fermentation in lignocellulose hydrolysates. The aim of the present work was to combine high xylose fermentation activity and high inhibitor tolerance in a single industrial yeast strain. RESULTS We have screened 580 yeast strains for high inhibitor tolerance using undetoxified acid-pretreated spruce hydrolysate and identified a triploid industrial baker's yeast strain as having the highest inhibitor tolerance. From this strain, a mating competent diploid segregant with even higher inhibitor tolerance was obtained. It was crossed with the recently developed D-xylose fermenting diploid industrial strain GS1.11-26, with the Ethanol Red genetic background. Screening of 819 diploid segregants from the tetraploid hybrid resulted in two strains, GSF335 and GSF767, combining high inhibitor tolerance and efficient xylose fermentation. In a parallel approach, meiotic recombination of GS1.11-26 with a haploid segregant of Ethanol Red and screening of 104 segregants resulted in a similar inhibitor tolerant diploid strain, GSE16. The three superior strains exhibited significantly improved tolerance to inhibitors in spruce hydrolysate, higher glucose consumption rates, higher aerobic growth rates and higher maximal ethanol accumulation capacity in very-high gravity fermentation, compared to GS1.11-26. In complex medium, the D-xylose utilization rate by the three superior strains ranged from 0.36 to 0.67 g/g DW/h, which was lower than that of GS1.11-26 (1.10 g/g DW/h). On the other hand, in batch fermentation of undetoxified acid-pretreated spruce hydrolysate, the three superior strains showed comparable D-xylose utilization rates as GS1.11-26, probably because of their higher inhibitor tolerance. They produced up to 23% more ethanol compared to Ethanol Red. CONCLUSIONS We have successfully constructed three superior industrial S. cerevisiae strains that combine efficient D-xylose utilization with high inhibitor tolerance. Since the background strain Ethanol Red has a proven record of successful industrial application, the three new superior strains have strong potential for direct application in industrial bioethanol production.
Collapse
Affiliation(s)
- Mekonnen M Demeke
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - Françoise Dumortier
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - Yingying Li
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - Tom Broeckx
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders B-3001, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Leuven-Heverlee, Flanders B-3001, Belgium
| |
Collapse
|
47
|
Demeke MM, Dietz H, Li Y, Foulquié-Moreno MR, Mutturi S, Deprez S, Den Abt T, Bonini BM, Liden G, Dumortier F, Verplaetse A, Boles E, Thevelein JM. Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:89. [PMID: 23800147 PMCID: PMC3698012 DOI: 10.1186/1754-6834-6-89] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 06/12/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The production of bioethanol from lignocellulose hydrolysates requires a robust, D-xylose-fermenting and inhibitor-tolerant microorganism as catalyst. The purpose of the present work was to develop such a strain from a prime industrial yeast strain, Ethanol Red, used for bioethanol production. RESULTS An expression cassette containing 13 genes including Clostridium phytofermentans XylA, encoding D-xylose isomerase (XI), and enzymes of the pentose phosphate pathway was inserted in two copies in the genome of Ethanol Red. Subsequent EMS mutagenesis, genome shuffling and selection in D-xylose-enriched lignocellulose hydrolysate, followed by multiple rounds of evolutionary engineering in complex medium with D-xylose, gradually established efficient D-xylose fermentation. The best-performing strain, GS1.11-26, showed a maximum specific D-xylose consumption rate of 1.1 g/g DW/h in synthetic medium, with complete attenuation of 35 g/L D-xylose in about 17 h. In separate hydrolysis and fermentation of lignocellulose hydrolysates of Arundo donax (giant reed), spruce and a wheat straw/hay mixture, the maximum specific D-xylose consumption rate was 0.36, 0.23 and 1.1 g/g DW inoculum/h, and the final ethanol titer was 4.2, 3.9 and 5.8% (v/v), respectively. In simultaneous saccharification and fermentation of Arundo hydrolysate, GS1.11-26 produced 32% more ethanol than the parent strain Ethanol Red, due to efficient D-xylose utilization. The high D-xylose fermentation capacity was stable after extended growth in glucose. Cell extracts of strain GS1.11-26 displayed 17-fold higher XI activity compared to the parent strain, but overexpression of XI alone was not enough to establish D-xylose fermentation. The high D-xylose consumption rate was due to synergistic interaction between the high XI activity and one or more mutations in the genome. The GS1.11-26 had a partial respiratory defect causing a reduced aerobic growth rate. CONCLUSIONS An industrial yeast strain for bioethanol production with lignocellulose hydrolysates has been developed in the genetic background of a strain widely used for commercial bioethanol production. The strain uses glucose and D-xylose with high consumption rates and partial cofermentation in various lignocellulose hydrolysates with very high ethanol yield. The GS1.11-26 strain shows highly promising potential for further development of an all-round robust yeast strain for efficient fermentation of various lignocellulose hydrolysates.
Collapse
Affiliation(s)
- Mekonnen M Demeke
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Heiko Dietz
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Yingying Li
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - María R Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Sarma Mutturi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Sylvie Deprez
- Laboratory of Enzyme, Fermentation and Brewing Technology, KAHO Sint-Lieven University College, KU Leuven Association, Gebroeders De Smetstraat 1, 9000, Ghent, Flanders, Belgium
| | - Tom Den Abt
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Beatriz M Bonini
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Gunnar Liden
- Department of Chemical Engineering, Lund University, P.O. Box 124, 22100 Lund, Sweden
| | - Françoise Dumortier
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| | - Alex Verplaetse
- Laboratory of Enzyme, Fermentation and Brewing Technology, KAHO Sint-Lieven University College, KU Leuven Association, Gebroeders De Smetstraat 1, 9000, Ghent, Flanders, Belgium
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven, Heverlee, Flanders, Belgium
| |
Collapse
|
48
|
Skretas G, Kolisis FN. Combinatorial approaches for inverse metabolic engineering applications. Comput Struct Biotechnol J 2013; 3:e201210021. [PMID: 24688681 PMCID: PMC3962077 DOI: 10.5936/csbj.201210021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/11/2013] [Accepted: 02/17/2013] [Indexed: 11/22/2022] Open
Abstract
Traditional metabolic engineering analyzes biosynthetic and physiological pathways, identifies bottlenecks, and makes targeted genetic modifications with the ultimate goal of increasing the production of high-value products in living cells. Such efforts have led to the development of a variety of organisms with industrially relevant properties. However, there are a number of cellular phenotypes important for research and the industry for which the rational selection of cellular targets for modification is not easy or possible. In these cases, strain engineering can be alternatively carried out using “inverse metabolic engineering”, an approach that first generates genetic diversity by subjecting a population of cells to a particular mutagenic process, and then utilizes genetic screens or selections to identify the clones exhibiting the desired phenotype. Given the availability of an appropriate screen for a particular property, the success of inverse metabolic engineering efforts usually depends on the level and quality of genetic diversity which can be generated. Here, we review classic and recently developed combinatorial approaches for creating such genetic diversity and discuss the use of these methodologies in inverse metabolic engineering applications.
Collapse
Affiliation(s)
- Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens - Zografou Campus, Athens, Greece
| |
Collapse
|
49
|
Systematic applications of metabolomics in metabolic engineering. Metabolites 2012; 2:1090-122. [PMID: 24957776 PMCID: PMC3901235 DOI: 10.3390/metabo2041090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/29/2012] [Accepted: 12/10/2012] [Indexed: 02/05/2023] Open
Abstract
The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules) to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.
Collapse
|