1
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Shen Y, Dinh HV, Cruz ER, Chen Z, Bartman CR, Xiao T, Call CM, Ryseck RP, Pratas J, Weilandt D, Baron H, Subramanian A, Fatma Z, Wu ZY, Dwaraknath S, Hendry JI, Tran VG, Yang L, Yoshikuni Y, Zhao H, Maranas CD, Wühr M, Rabinowitz JD. Mitochondrial ATP generation is more proteome efficient than glycolysis. Nat Chem Biol 2024:10.1038/s41589-024-01571-y. [PMID: 38448734 DOI: 10.1038/s41589-024-01571-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Metabolic efficiency profoundly influences organismal fitness. Nonphotosynthetic organisms, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. Although respiration is more energy efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (that is, faster). Through quantitative flux analysis and proteomics, we find, however, that mitochondrial respiration is actually more proteome efficient than aerobic glycolysis. This is shown across yeast strains, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which promotes hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth but outgrow respiratory cells during oxygen limitation. We accordingly propose that aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.
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Affiliation(s)
- Yihui Shen
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Hoang V Dinh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Edward R Cruz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zihong Chen
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA
| | - Caroline R Bartman
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA
| | - Tianxia Xiao
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Catherine M Call
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Rolf-Peter Ryseck
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jimmy Pratas
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Daniel Weilandt
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Heide Baron
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Arjuna Subramanian
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Zia Fatma
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zong-Yen Wu
- US Department of Energy Joint Genome Institute and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sudharsan Dwaraknath
- US Department of Energy Joint Genome Institute and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John I Hendry
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Vinh G Tran
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lifeng Yang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA.
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2
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Joehnk B, Ali N, Voorhies M, Walcott K, Sil A. Recyclable CRISPR/Cas9-mediated gene disruption and deletions in Histoplasma. mSphere 2023; 8:e0037023. [PMID: 37819140 PMCID: PMC10732100 DOI: 10.1128/msphere.00370-23] [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: 07/02/2023] [Accepted: 07/17/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Histoplasma is a primary fungal pathogen with the ability to infect otherwise healthy mammalian hosts, causing systemic and sometimes life-threatening disease. Thus far, molecular genetic manipulation of this organism has utilized RNA interference, random insertional mutagenesis, and a homologous recombination protocol that is highly variable and often inefficient. Targeted gene manipulations have been challenging due to poor rates of homologous recombination events in Histoplasma. Interrogation of the virulence strategies of this organism would be highly accelerated by a means of efficiently generating targeted mutations. We have developed a recyclable CRISPR/Cas9 system that can be used to introduce gene disruptions in Histoplasma with high efficiency, thereby allowing disruption of multiple genes.
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Affiliation(s)
- Bastian Joehnk
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Nebat Ali
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, USA
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3
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Opulente DA, Langdon QK, Jarzyna M, Buh KV, Haase MAB, Groenewald M, Hittinger CT. Taxogenomic analysis of a novel yeast species isolated from soil, Pichia galeolata sp. nov. Yeast 2023; 40:608-615. [PMID: 37921542 PMCID: PMC10841356 DOI: 10.1002/yea.3905] [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: 05/10/2022] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023] Open
Abstract
A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446T (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.
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Affiliation(s)
- Dana A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53726
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
- Department of Biology, Villanova University, Villanova, PA 19085
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53726
| | - Martin Jarzyna
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53726
| | - Kelly V. Buh
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53726
| | - Max A. B. Haase
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53726
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53726
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726
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4
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Gu L, Zhang R, Fan X, Wang Y, Ma K, Jiang J, Li G, Wang H, Fan F, Zhang X. Development of CRISPR/Cas9-Based Genome Editing Tools for Polyploid Yeast Cyberlindnera jadinii and Its Application in Engineering Heterologous Steroid-Producing Strains. ACS Synth Biol 2023; 12:2947-2960. [PMID: 37816156 DOI: 10.1021/acssynbio.3c00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
In this study, a suite of efficient CRISPR/Cas9 tools was developed to overcome the genetic manipulation challenges posed by the polyploid genome of industrial yeast Cyberlindnera jadinii. The developed CRISPR/Cas9 system can achieve a 100% single-gene knockdown efficiency in strain NBRC0988. Moreover, the integration of a single exogenous gene into the target locus using a 50 bp homology arm achieved near-100% efficiency. The efficiency of simultaneous integration of three genes into the chromosome is strongly influenced by the length of the homology arm, with the highest integration efficiency of 62.5% obtained when selecting a homology arm of about 500 bp. By utilizing the CRISPR/Cas system, this study demonstrated the potential of C. jadinii in producing heterologous sterols. Through shake-flask fermentation, the engineered strains produced 92.1 and 81.8 mg/L of campesterol and cholesterol, respectively. Furthermore, the production levels of these two sterols were further enhanced through high-cell-density fed-batch fermentation in a 5 L bioreactor. The highest titer of campesterol reached 807 mg/L [biomass OD600 = 294, productivity of 6.73 mg/(L·h)]. The titer of cholesterol reached 1.52 g/L [biomass OD600 = 380, productivity of 9.06 mg/(L·h)], marking the first gram-scale production of steroidal compounds in C. jadinii.
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Affiliation(s)
- Lishan Gu
- College of Chemistry and Life Science, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - Rongxin Zhang
- College of Chemistry and Life Science, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - Xuqian Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Yu Wang
- College of Biotechnology and Food Science, Tianjin University of Commerce, 409 Glorious Road, Beichen District, Tianjin 300134, P. R. China
| | - Kaiyu Ma
- College of Biotechnology, Tianjin University of Science and Technology, No. 29 of 13th Avenue, TEDA, Tianjin 300457, P. R. China
| | - Jingjing Jiang
- College of Biotechnology and Food Science, Tianjin University of Commerce, 409 Glorious Road, Beichen District, Tianjin 300134, P. R. China
| | - Gen Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Honglei Wang
- College of Chemistry and Life Science, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, P. R. China
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5
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Tran VG, Mishra S, Bhagwat SS, Shafaei S, Shen Y, Allen JL, Crosly BA, Tan SI, Fatma Z, Rabinowitz JD, Guest JS, Singh V, Zhao H. An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis. Nat Commun 2023; 14:6152. [PMID: 37788990 PMCID: PMC10547785 DOI: 10.1038/s41467-023-41616-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34-90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.
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Affiliation(s)
- Vinh G Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Somesh Mishra
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sarang S Bhagwat
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Saman Shafaei
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yihui Shen
- Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Jayne L Allen
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Benjamin A Crosly
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Joshua D Rabinowitz
- Department of Chemistry and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Jeremy S Guest
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Vijay Singh
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
- Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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6
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Joehnk B, Ali N, Voorhies M, Walcott K, Sil A. Recyclable CRISPR/Cas9 mediated gene disruption and deletions in Histoplasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547774. [PMID: 37461713 PMCID: PMC10350005 DOI: 10.1101/2023.07.05.547774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Targeted gene disruption is challenging in the dimorphic fungal pathogen Histoplasma due to the low frequency of homologous recombination. Transformed DNA is either integrated ectopically into the genome or maintained extra chromosomally by de novo addition of telomeric sequences. Based on a system developed in Blastomyces, we adapted a CRISPR/Cas9 system to facilitate targeted gene disruption in Histoplasma with high efficiency. We express a codon-optimized version of Cas9 as well as guide RNAs from a single ectopic vector carrying a selectable marker. Once the desired mutation is verified, one can screen for isolates that have lost the Cas9 vector by simply removing the selective pressure. Multiple mutations can then be generated in the same strain by retransforming the Cas9 vector carrying different guides. We used this system to disrupt a number of target genes including RYP2 and SRE1 where loss-of-function mutations could be monitored visually by colony morphology or color, respectively. Interestingly, expression of two guide RNAs targeting the 5' and 3' ends of a gene allowed isolation of deletion mutants where the sequence between the guide RNAs was removed from the genome. Whole-genome sequencing showed that the frequency of off-target mutations associated with the Cas9 nuclease was negligible. Finally, we increased the frequency of gene disruption by using an endogenous Histoplasma regulatory sequence to drive guide RNA expression. These tools transform our ability to generate targeted mutations in Histoplasma.
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Affiliation(s)
- Bastian Joehnk
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Nebat Ali
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Mark Voorhies
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - Anita Sil
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA 94158
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7
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Fatma Z, Tan SI, Boob AG, Zhao H. A landing pad system for multicopy gene integration in Issatchenkia orientalis. Metab Eng 2023; 78:200-208. [PMID: 37343658 DOI: 10.1016/j.ymben.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/18/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023]
Abstract
The robust nature of the non-conventional yeast Issatchenkia orientalis allows it to grow under highly acidic conditions and therefore, has gained increasing interest in producing organic acids using a variety of carbon sources. Recently, the development of a genetic toolbox for I. orientalis, including an episomal plasmid, characterization of multiple promoters and terminators, and CRISPR-Cas9 tools, has eased the metabolic engineering efforts in I. orientalis. However, multiplex engineering is still hampered by the lack of efficient multicopy integration tools. To facilitate the construction of large, complex metabolic pathways by multiplex CRISPR-Cas9-mediated genome editing, we developed a bioinformatics pipeline to identify and prioritize genome-wide intergenic loci and characterized 47 gRNAs located in 21 intergenic regions. These loci are screened for guide RNA cutting efficiency, integration efficiency of a gene cassette, the resulting cellular fitness, and GFP expression level. We further developed a landing pad system using components from these well-characterized loci, which can aid in the integration of multiple genes using single guide RNA and multiple repair templates of the user's choice. We have demonstrated the use of the landing pad for simultaneous integrations of 2, 3, 4, or 5 genes to the target loci with efficiencies greater than 80%. As a proof of concept, we showed how the production of 5-aminolevulinic acid can be improved by integrating five copies of genes at multiple sites in one step. We have further demonstrated the efficiency of this tool by constructing a metabolic pathway for succinic acid production by integrating five gene expression cassettes using a single guide RNA along with five different repair templates, leading to the production of 9 g/L of succinic acid in batch fermentations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in a non-conventional yeast. This landing pad system will be a valuable tool for the metabolic engineering of I. orientalis.
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Affiliation(s)
- Zia Fatma
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
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8
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Zhao Y, Coelho C, Lauer S, Majewski M, Laurent JM, Brosh R, Boeke JD. CREEPY: CRISPR-mediated editing of synthetic episomes in yeast. Nucleic Acids Res 2023:gkad491. [PMID: 37326023 PMCID: PMC10359617 DOI: 10.1093/nar/gkad491] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023] Open
Abstract
Use of synthetic genomics to design and build 'big' DNA has revolutionized our ability to answer fundamental biological questions by employing a bottom-up approach. Saccharomyces cerevisiae, or budding yeast, has become the major platform to assemble large synthetic constructs thanks to its powerful homologous recombination machinery and the availability of well-established molecular biology techniques. However, introducing designer variations to episomal assemblies with high efficiency and fidelity remains challenging. Here we describe CRISPR Engineering of EPisomes in Yeast, or CREEPY, a method for rapid engineering of large synthetic episomal DNA constructs. We demonstrate that CRISPR editing of circular episomes presents unique challenges compared to modifying native yeast chromosomes. We optimize CREEPY for efficient and precise multiplex editing of >100 kb yeast episomes, providing an expanded toolkit for synthetic genomics.
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Affiliation(s)
- Yu Zhao
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Camila Coelho
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Stephanie Lauer
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Miłosz Majewski
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
- Maastricht Science Programme, Maastricht University, Maastricht6200MD, The Netherlands
| | - Jon M Laurent
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY11201, USA
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9
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Wu ZY, Sun W, Shen Y, Pratas J, Suthers PF, Hsieh PH, Dwaraknath S, Rabinowitz JD, Maranas CD, Shao Z, Yoshikuni Y. Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalate. Metab Eng Commun 2023; 16:e00220. [PMID: 36860699 PMCID: PMC9969067 DOI: 10.1016/j.mec.2023.e00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Methyl methacrylate (MMA) is an important petrochemical with many applications. However, its manufacture has a large environmental footprint. Combined biological and chemical synthesis (semisynthesis) may be a promising alternative to reduce both cost and environmental impact, but strains that can produce the MMA precursor (citramalate) at low pH are required. A non-conventional yeast, Issatchenkia orientalis, may prove ideal, as it can survive extremely low pH. Here, we demonstrate the engineering of I. orientalis for citramalate production. Using sequence similarity network analysis and subsequent DNA synthesis, we selected a more active citramalate synthase gene (cimA) variant for expression in I. orientalis. We then adapted a piggyBac transposon system for I. orientalis that allowed us to simultaneously explore the effects of different cimA gene copy numbers and integration locations. A batch fermentation showed the genome-integrated-cimA strains produced 2.0 g/L citramalate in 48 h and a yield of up to 7% mol citramalate/mol consumed glucose. These results demonstrate the potential of I. orientalis as a chassis for citramalate production.
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Affiliation(s)
- Zong-Yen Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Wan Sun
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yihui Shen
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Jimmy Pratas
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Patrick F. Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA,Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ping-Hung Hsieh
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sudharsan Dwaraknath
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA,Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Zengyi Shao
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA,Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA,Bioeconomy Institute, Iowa State University, Ames, IA, 50011, USA,The Ames Laboratory, Ames, IA, 50011, USA,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA,Corresponding author. Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA.
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Global Center for Food, Land, and Water Resources, Hokkaido University, Hokkaido, 060-8589, Japan,Corresponding author. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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10
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Advances in the Application of the Non-Conventional Yeast Pichia kudriavzevii in Food and Biotechnology Industries. J Fungi (Basel) 2023; 9:jof9020170. [PMID: 36836285 PMCID: PMC9961021 DOI: 10.3390/jof9020170] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Pichia kudriavzevii is an emerging non-conventional yeast which has attracted increased attention for its application in food and biotechnology areas. It is widespread in various habitats and often occurs in the spontaneous fermentation process of traditional fermented foods and beverages. The contributions of P. kudriavzevii in degrading organic acid, releasing various hydrolase and flavor compounds, and displaying probiotic properties make it a promising starter culture in the food and feed industry. Moreover, its inherent characteristics, including high tolerance to extreme pH, high temperature, hyperosmotic stress and fermentation inhibitors, allow it the potential to address technical challenges in industrial applications. With the development of advanced genetic engineering tools and system biology techniques, P. kudriavzevii is becoming one of the most promising non-conventional yeasts. This paper systematically reviews the recent progress in the application of P. kudriavzevii to food fermentation, the feed industry, chemical biosynthesis, biocontrol and environmental engineering. In addition, safety issues and current challenges to its use are discussed.
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11
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Volk MJ, Tran VG, Tan SI, Mishra S, Fatma Z, Boob A, Li H, Xue P, Martin TA, Zhao H. Metabolic Engineering: Methodologies and Applications. Chem Rev 2022; 123:5521-5570. [PMID: 36584306 DOI: 10.1021/acs.chemrev.2c00403] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Metabolic engineering aims to improve the production of economically valuable molecules through the genetic manipulation of microbial metabolism. While the discipline is a little over 30 years old, advancements in metabolic engineering have given way to industrial-level molecule production benefitting multiple industries such as chemical, agriculture, food, pharmaceutical, and energy industries. This review describes the design, build, test, and learn steps necessary for leading a successful metabolic engineering campaign. Moreover, we highlight major applications of metabolic engineering, including synthesizing chemicals and fuels, broadening substrate utilization, and improving host robustness with a focus on specific case studies. Finally, we conclude with a discussion on perspectives and future challenges related to metabolic engineering.
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Affiliation(s)
- Michael J Volk
- 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
| | - Vinh G Tran
- 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
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, 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 Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shekhar Mishra
- 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
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, 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
| | - Aashutosh Boob
- 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
| | - Hongxiang Li
- 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.,Department of Chemistry, 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
| | - Teresa A Martin
- 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
| | - 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
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12
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Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications.
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13
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Lee YG, Kim C, Kuanyshev N, Kang NK, Fatma Z, Wu ZY, Cheng MH, Singh V, Yoshikuni Y, Zhao H, Jin YS. Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12085-12094. [PMID: 36103687 DOI: 10.1021/acs.jafc.2c04251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Issatchenkia orientalis, exhibiting high tolerance against harsh environmental conditions, is a promising metabolic engineering host for producing fuels and chemicals from cellulosic hydrolysates containing fermentation inhibitors under acidic conditions. Although genetic tools for I. orientalis exist, they require auxotrophic mutants so that the selection of a host strain is limited. We developed a drug resistance gene (cloNAT)-based genome-editing method for engineering any I. orientalis strains and engineered I. orientalis strains isolated from various sources for xylose fermentation. Specifically, xylose reductase, xylitol dehydrogenase, and xylulokinase from Scheffersomyces stipitis were integrated into an intended chromosomal locus in four I. orientalis strains (SD108, IO21, IO45, and IO46) through Cas9-based genome editing. The resulting strains (SD108X, IO21X, IO45X, and IO46X) efficiently produced ethanol from cellulosic and hemicellulosic hydrolysates even though the pH adjustment and nitrogen source were not provided. As they presented different fermenting capacities, selection of a host I. orientalis strain was crucial for producing fuels and chemicals using cellulosic hydrolysates.
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Affiliation(s)
- Ye-Gi Lee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, South Korea
| | - Chanwoo Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nurzhan Kuanyshev
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Nam Kyu Kang
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zong-Yen Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ming-Hsun Cheng
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vijay Singh
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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14
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Baisya D, Ramesh A, Schwartz C, Lonardi S, Wheeldon I. Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica. Nat Commun 2022; 13:922. [PMID: 35177617 PMCID: PMC8854577 DOI: 10.1038/s41467-022-28540-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica. A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide's ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.
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Affiliation(s)
- Dipankar Baisya
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
- iBio Inc., San Diego, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California, Riverside, CA, 92521, USA.
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15
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Shan L, Dai Z, Wang Q. Advances and Opportunities of CRISPR/Cas Technology in Bioengineering Non-conventional Yeasts. Front Bioeng Biotechnol 2021; 9:765396. [PMID: 34708030 PMCID: PMC8542773 DOI: 10.3389/fbioe.2021.765396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Non-conventional yeasts have attracted a growing interest on account of their excellent characteristics. In recent years, the emerging of CRISPR/Cas technology has improved the efficiency and accuracy of genome editing. Utilizing the advantages of CRISPR/Cas in bioengineering of non-conventional yeasts, quite a few advancements have been made. Due to the diversity in their genetic background, the ways for building a functional CRISPR/Cas system of various species non-conventional yeasts were also species-specific. Herein, we have summarized the different strategies for optimizing CRISPR/Cas systems in different non-conventional yeasts and their biotechnological applications in the construction of cell factories. In addition, we have proposed some potential directions for broadening and improving the application of CRISPR/Cas technology in non-conventional yeasts.
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Affiliation(s)
- Lu Shan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zongjie Dai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
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16
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Tran VG, Zhao H. Engineering robust microorganisms for organic acid production. J Ind Microbiol Biotechnol 2021; 49:6373449. [PMID: 34549297 PMCID: PMC9118992 DOI: 10.1093/jimb/kuab067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/11/2021] [Indexed: 11/24/2022]
Abstract
Organic acids are an important class of compounds that can be produced by microbial conversion of renewable feedstocks and have huge demands and broad applications in food, chemical, and pharmaceutical industries. An economically viable fermentation process for production of organic acids requires robust microbial cell factories with excellent tolerance to low pH conditions, high concentrations of organic acids, and lignocellulosic inhibitors. In this review, we summarize various strategies to engineer robust microorganisms for organic acid production and highlight their applications in a few recent examples.
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Affiliation(s)
- Vinh G Tran
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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17
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Xi Y, Zhan T, Xu H, Chen J, Bi C, Fan F, Zhang X. Characterization of JEN family carboxylate transporters from the acid-tolerant yeast Pichia kudriavzevii and their applications in succinic acid production. Microb Biotechnol 2021; 14:1130-1147. [PMID: 33629807 PMCID: PMC8085920 DOI: 10.1111/1751-7915.13781] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/26/2021] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
The unconventional yeast Pichia kudriavzevii is renowned for its ability to survive at low pH and has been exploited for the industrial production of various organic acids, especially succinic acid (SA). However, P. kudriavzevii can also utilize the di- and tricarboxylate intermediates of the Krebs cycle as the sole carbon sources for cell growth, which may adversely affect the extracellular accumulation of SA. Because the carboxylic acid transport machinery of P. kudriavzevii remains poorly understood, here, we focused on studying its SA transportation process from the perspective of mining and characterization of dicarboxylate transporters in a newly isolated acid-tolerant P. kudriavzevii strain CY902. Through genome sequencing and transcriptome analysis, two JEN family carboxylate transporters (PkJEN2-1 and PkJEN2-2) were found to be involved in SA transport. Substrate specificity analysis revealed that both PkJEN proteins are active dicarboxylate transporters, that can effectively import succinate, fumarate and L-malate into the cell. In addition, PkJEN2-1 can transport α-ketoglutarate, while PkJEN2-2 cannot. Since PkJEN2-1 shows higher transcript abundance than PkJEN2-2, its role in dicarboxylate transport is more important than PkJEN2-2. In addition, PKJEN2-2 is also responsible for the uptake of citrate. To our best knowledge, this is the first study to show that a JEN2 subfamily transporter is involved in tricarboxylate transport in yeast. A combination of model-based structure analysis and rational mutagenesis further proved that amino acid residues 392-403 of the tenth transmembrane span (TMS-X) of PkJEN2-2 play an important role in determining the specificity of the tricarboxylate substrate. Moreover, these two PkJEN transporters only exhibited inward transport activity for SA, and simultaneous inactivation of both PkJEN transporters reduced the SA influx, resulting in enhanced extracellular accumulation of SA in the late stage of fermentation. This work provides useful information on the mechanism of di-/tricarboxylic acid utilization in P. kudriavzevii, which will help improve the organic acid production performance of this microbial chassis.
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Affiliation(s)
- Yongyan Xi
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tao Zhan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Hongtao Xu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Jing Chen
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Changhao Bi
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Feiyu Fan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Xueli Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
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18
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Zwirzitz A, Alteio L, Sulzenbacher D, Atanasoff M, Selg M. Ethanol Production from Wheat Straw Hydrolysate by Issatchenkia Orientalis Isolated from Waste Cooking Oil. J Fungi (Basel) 2021; 7:jof7020121. [PMID: 33562172 PMCID: PMC7915885 DOI: 10.3390/jof7020121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/29/2022] Open
Abstract
The interest in using non-conventional yeasts to produce value-added compounds from low cost substrates, such as lignocellulosic materials, has increased in recent years. Setting out to discover novel microbial strains that can be used in biorefineries, an Issatchenkia orientalis strain was isolated from waste cooking oil (WCO) and its capability to produce ethanol from wheat straw hydrolysate (WSHL) was analyzed. As with previously isolated I. orientalis strains, WCO-isolated I. orientalis KJ27-7 is thermotolerant. It grows well at elevated temperatures up to 42 °C. Furthermore, spot drop tests showed that it is tolerant to various chemical fermentation inhibitors that are derived from the pre-treatment of lignocellulosic materials. I. orientalis KJ27-7 is particularly tolerant to acetic acid (up to 75 mM) and tolerates 10 mM formic acid, 5 mM furfural and 10 mM hydroxymethylfurfural. Important for biotechnological cellulosic ethanol production, I. orientalis KJ27-7 grows well on plates containing up to 10% ethanol and media containing up to 90% WSHL. As observed in shake flask fermentations, the specific ethanol productivity correlates with WSHL concentrations. In 90% WSHL media, I. orientalis KJ27-7 produced 10.3 g L−1 ethanol within 24 h. This corresponds to a product yield of 0.50 g g−1 glucose (97% of the theoretical maximum) and a volumetric productivity of 0.43 g L−1 h−1. Therefore, I. orientalis KJ27-7 is an efficient producer of lignocellulosic ethanol from WSHL.
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Affiliation(s)
- Alexander Zwirzitz
- Biosciences Research Group, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria; (D.S.); (M.A.); (M.S.)
- Correspondence:
| | - Lauren Alteio
- Centre of Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria;
| | - Daniel Sulzenbacher
- Biosciences Research Group, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria; (D.S.); (M.A.); (M.S.)
| | - Michael Atanasoff
- Biosciences Research Group, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria; (D.S.); (M.A.); (M.S.)
| | - Manuel Selg
- Biosciences Research Group, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria; (D.S.); (M.A.); (M.S.)
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19
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Abstract
Modern industrial winemaking is based on the use of specific starters of wine strains. Commercial wine strains present several advantages over natural isolates, and it is their use that guarantees the stability and reproducibility of industrial winemaking technologies. For the highly competitive wine market with new demands for improved wine quality and wine safety, it has become increasingly critical to develop new yeast strains. In the last decades, new possibilities arose for creating upgraded wine yeasts in the laboratory, resulting in the development of strains with better fermentation abilities, able to improve the sensory quality of wines and produce wines targeted to specific consumers, considering their health and nutrition requirements. However, only two genetically modified (GM) wine yeast strains are officially registered and approved for commercial use. Compared with traditional genetic engineering methods, CRISPR/Cas9 is described as efficient, versatile, cheap, easy-to-use, and able to target multiple sites. This genetic engineering technique has been applied to Saccharomyces cerevisiae since 2013. In this review, we aimed to overview the use of CRISPR/Cas9 editing technique in wine yeasts to combine develop phenotypes able to increase flavor compounds in wine without the development of off-flavors and aiding in the creation of “safer wines.”
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20
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Yang Z, Blenner M. Genome editing systems across yeast species. Curr Opin Biotechnol 2020; 66:255-266. [PMID: 33011454 PMCID: PMC7744358 DOI: 10.1016/j.copbio.2020.08.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/23/2020] [Accepted: 08/29/2020] [Indexed: 02/07/2023]
Abstract
Yeasts are used to produce a myriad of value-added compounds. Engineering yeasts into cost-efficient cell factories is greatly facilitated by the availability of genome editing tools. While traditional engineering techniques such as homologous recombination-based gene knockout and pathway integration continue to be widely used, novel genome editing systems including multiplexed approaches, bacteriophage integrases, CRISPR-Cas systems, and base editors are emerging as more powerful toolsets to accomplish rapid genome scale engineering and phenotype screening. In this review, we summarized the techniques which have been successfully implemented in model yeast Saccharomyces cerevisiae as well as non-conventional yeast species. The mechanisms and applications of various genome engineering systems are discussed and general guidelines to expand genome editing systems from S. cerevisiae to other yeast species are also highlighted.
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Affiliation(s)
- Zhiliang Yang
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, United States
| | - Mark Blenner
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, United States.
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21
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Lacerda MP, Oh EJ, Eckert C. The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels. Life (Basel) 2020; 10:E299. [PMID: 33233378 PMCID: PMC7700301 DOI: 10.3390/life10110299] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023] Open
Abstract
Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.
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Affiliation(s)
- Maria Priscila Lacerda
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, CO 80303, USA;
| | - Eun Joong Oh
- Department of Food Science, Purdue University, West Lafayette, IN 47907, USA;
| | - Carrie Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado, Boulder, CO 80303, USA;
- National Renewable Energy Laboratory (NREL), Biosciences Center, Golden, CO 80401, USA
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22
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Suthers PF, Dinh HV, Fatma Z, Shen Y, Chan SHJ, Rabinowitz JD, Zhao H, Maranas CD. Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. Metab Eng Commun 2020; 11:e00148. [PMID: 33134082 PMCID: PMC7586132 DOI: 10.1016/j.mec.2020.e00148] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/08/2020] [Accepted: 10/05/2020] [Indexed: 12/18/2022] Open
Abstract
Many platform chemicals can be produced from renewable biomass by microorganisms, with organic acids making up a large fraction. Intolerance to the resulting low pH growth conditions, however, remains a challenge for the industrial production of organic acids by microorganisms. Issatchenkia orientalis SD108 is a promising host for industrial production because it is tolerant to acidic conditions as low as pH 2.0. With the goal to systematically assess the metabolic capabilities of this non-model yeast, we developed a genome-scale metabolic model for I. orientalis SD108 spanning 850 genes, 1826 reactions, and 1702 metabolites. In order to improve the model’s quantitative predictions, organism-specific macromolecular composition and ATP maintenance requirements were determined experimentally and implemented. We examined its network topology, including essential genes and flux coupling analysis and drew comparisons with the Yeast 8.3 model for Saccharomyces cerevisiae. We explored the carbon substrate utilization and examined the organism’s production potential for the industrially-relevant succinic acid, making use of the OptKnock framework to identify gene knockouts which couple production of the targeted chemical to biomass production. The genome-scale metabolic model iIsor850 is a data-supported curated model which can inform genetic interventions for overproduction. Genome-scale metabolic model iIsor850 describes metabolism of I. orientalis SD108. Customized biomass reaction highlights differences with S. cerevisiae. Chemostat data elucidate growth-associated ATP maintenance. Substrate utilization and CRISPR/Cas9 gene knockout phenotypes validate model. Model pinpoints candidate gene deletions coupling succinic acid production to growth.
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Affiliation(s)
- Patrick F Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hoang V Dinh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yihui Shen
- Department of Chemistry, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Siu Hung Joshua Chan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champagne, Urbana, IL, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
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23
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Ji H, Xu K, Dong X, Sun D, Peng R, Lin S, Zhang K, Jin L. Transcriptional profiling reveals molecular basis and the role of arginine in response to low-pH stress in Pichia kudriavzevii. J Biosci Bioeng 2020; 130:588-595. [PMID: 32798135 DOI: 10.1016/j.jbiosc.2020.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/11/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022]
Abstract
The non-conventional yeast Pichia kudriavzevii is considered to be a promising biotechnological host for the production of organic acids under low-pH conditions. However, little is known about the low-pH stress response in P. kudriavzevii, which significantly restricts its future development. In this study, P. kudriavzevii N-X showed great tolerance to low-pH stress, but the cell aggregation upon extremely acidic conditions might be unfavorable for low-pH fermentation. We therefore conducted RNA-Seq to compare global gene expression of P. kudriavzevii N-X in response to different pH stresses. Totally 434 genes were identified to be differentially expressed genes (DEGs), and annotation and enrichment analysis suggested that multiple genes associated with regulation of membrane lipid composition, filamentous growth and arginine metabolism were differentially expressed. The increased specific activity of arginase and intracellular ammonia concentration of P. kudriavzevii cultured at pH 2.0 further implied potential roles of arginine in response to extreme low-pH conditions. Extracellular supplementation of 5 mM arginine resulted in increased pHi and cell growth at pH 2.0, meanwhile the cell aggregation was partially suppressed. Additionally, overexpression of ARG J involving in arginine synthesis can also enhance the cell growth and reduce the aggregation effect. These results suggested that increasing arginine flux might be an alternative approach in the developing of P. kudriavzevii as a platform host for production of organic acids under low-pH conditions.
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Affiliation(s)
- Hao Ji
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China.
| | - Ke Xu
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Xiameng Dong
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang 325006, PR China
| | - Da Sun
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Renyi Peng
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Kailun Zhang
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
| | - Libo Jin
- Institute of Life Sciences, Wenzhou University, Wenzhou, Zhejiang 325035, PR China; Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Biomedical Collaborative Innovation Center of Wenzhou, Wenzhou, Zhejiang 325035, PR China
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24
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Ding W, Zhang Y, Shi S. Development and Application of CRISPR/Cas in Microbial Biotechnology. Front Bioeng Biotechnol 2020; 8:711. [PMID: 32695770 PMCID: PMC7338305 DOI: 10.3389/fbioe.2020.00711] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has been rapidly developed as versatile genomic engineering tools with high efficiency, accuracy and flexibility, and has revolutionized traditional methods for applications in microbial biotechnology. Here, key points of building reliable CRISPR/Cas system for genome engineering are discussed, including the Cas protein, the guide RNA and the donor DNA. Following an overview of various CRISPR/Cas tools for genome engineering, including gene activation, gene interference, orthogonal CRISPR systems and precise single base editing, we highlighted the application of CRISPR/Cas toolbox for multiplexed engineering and high throughput screening. We then summarize recent applications of CRISPR/Cas systems in metabolic engineering toward production of chemicals and natural compounds, and end with perspectives of future advancements.
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Affiliation(s)
- Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.,Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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25
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Varela C, Bartel C, Onetto C, Borneman A. Targeted gene deletion in Brettanomyces bruxellensis with an expression-free CRISPR-Cas9 system. Appl Microbiol Biotechnol 2020; 104:7105-7115. [DOI: 10.1007/s00253-020-10750-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
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26
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Fatma Z, Schultz JC, Zhao H. Recent advances in domesticating non‐model microorganisms. Biotechnol Prog 2020; 36:e3008. [DOI: 10.1002/btpr.3008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Zia Fatma
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - J. Carl Schultz
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Departments of Chemistry, Biochemistry, and Bioengineering University of Illinois at Urbana‐Champaign Urbana Illinois USA
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27
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Ramesh A, Ong T, Garcia JA, Adams J, Wheeldon I. Guide RNA Engineering Enables Dual Purpose CRISPR-Cpf1 for Simultaneous Gene Editing and Gene Regulation in Yarrowia lipolytica. ACS Synth Biol 2020; 9:967-971. [PMID: 32208677 DOI: 10.1021/acssynbio.9b00498] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Yarrowia lipolytica has fast become a biotechnologically significant yeast for its ability to accumulate lipids to high levels. While there exists a suite of synthetic biology tools for genetic engineering in this yeast, there is a need for multipurposed tools for rapid strain generation. Here, we describe a dual purpose CRISPR-Cpf1 system that is capable of simultaneous gene disruption and gene regulation. Truncating guide RNA spacer length to 16 nt inhibited nuclease activity but not binding to the target loci, enabling gene activation and repression with Cpf1-fused transcriptional regulators. Gene repression was demonstrated using a Cpf1-Mxi1 fusion achieving a 7-fold reduction in mRNA, while CRISPR-activation with Cpf1-VPR increased hrGFP expression by 10-fold. High efficiency disruptions were achieved with gRNAs 23-25 bp in length, and efficiency and repression levels were maintained with multiplexed expression of truncated and full-length gRNAs. The developed CRISPR-Cpf1 system should prove useful in metabolic engineering, genome wide screening, and functional genomics studies.
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Affiliation(s)
- Adithya Ramesh
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Thomas Ong
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Jaime A Garcia
- Department of Physics and Environmental Science, St. Mary's University, San Antonio, Texas 78228, United States
| | - Jessica Adams
- Molecular and Cell Biology Department, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
- Center for Industrial Biotechnology, Bourns College of Engineering, University of California Riverside, Riverside, California 92521, United States
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28
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A genetic toolbox for metabolic engineering of Issatchenkia orientalis. Metab Eng 2020; 59:87-97. [PMID: 32007615 DOI: 10.1016/j.ymben.2020.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 01/01/2023]
Abstract
The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.
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