1
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Knoshaug EP, Sun P, Nag A, Nguyen H, Mattoon EM, Zhang N, Liu J, Chen C, Cheng J, Zhang R, St. John P, Umen J. Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis. Plant Direct 2023; 7:e527. [PMID: 38044962 PMCID: PMC10690477 DOI: 10.1002/pld3.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 12/05/2023]
Abstract
The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome-wide protein-coding gene annotation. A substantial fraction of protein-coding genes in all plant genomes are poorly annotated or unannotated and remain functionally uncharacterized. We identified unannotated proteins in three model organisms representing distinct branches of the green lineage (Viridiplantae): Arabidopsis thaliana (eudicot), Setaria viridis (monocot), and Chlamydomonas reinhardtii (Chlorophyte alga). Using similarity searching, we identified a subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Bioinformatic, genomic, and structural predictions were performed to begin classifying Deep Green genes and proteins. Compared to whole proteomes for each species, the Deep Green set was enriched for proteins with predicted chloroplast targeting signals predictive of photosynthetic or plastid functions, a result that was consistent with enrichment for daylight phase diurnal expression patterning. Structural predictions using AlphaFold and comparisons to known structures showed that a significant proportion of Deep Green proteins may possess novel folds. Though only available for three organisms, the Deep Green genes and proteins provide a starting resource of high-value targets for further investigation of potentially new protein structures and functions conserved across the green lineage.
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Affiliation(s)
- Eric P. Knoshaug
- Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - Peipei Sun
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Ambarish Nag
- Computational Sciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - Huong Nguyen
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil ScienceTexas Tech UniversityLubbockTexasUSA
| | - Erin M. Mattoon
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical SciencesWashington University in Saint LouisSt. LouisMissouriUSA
| | | | - Jian Liu
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Chen Chen
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Ru Zhang
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Peter St. John
- Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - James Umen
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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2
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McGowen J, Knoshaug EP, Laurens LM, Forrester J. Outdoor annual algae productivity improvements at the pre-pilot scale through crop rotation and pond operational management strategies. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.102995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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3
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Huesemann MH, Knoshaug EP, Laurens LM, Dale T, Lane TW, McGowen J. Development of integrated screening, cultivar optimization, and verification research (DISCOVR): A coordinated research-driven approach to improve microalgal productivity, composition, and culture stability for commercially viable biofuels production. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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4
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Kruger JS, Wiatrowski M, Davis RE, Dong T, Knoshaug EP, Nagle NJ, Laurens LML, Pienkos PT. Enabling Production of Algal Biofuels by Techno-Economic Optimization of Co-Product Suites. Front Chem Eng 2022. [DOI: 10.3389/fceng.2021.803513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recent techno-economic analysis (TEA) has underscored that for algal biofuels to be cost competitive with petroleum fuels, co-products are necessary to offset the cost of fuel production. The co-product suite must scale with fuel production while also maximizing value from the non-fuel precursor components. The co-product suite also depends on algal biomass composition, which is highly dynamic and depends on environmental conditions during cultivation. Intentional shifts in composition during cultivation are often associated with reduced biomass productivity, which can increase feedstock production costs for the algae-based biorefinery. The optimal algae-based biorefinery configuration is thus a function of many factors. We have found that comprehensive TEA, which requires the construction of process models with detailed mass and energy balances, along with a complete accounting of capital and operating expenditures for a commercial-scale production facility, provides invaluable insight into the viability of a proposed biorefinery configuration. This insight is reflected in improved viability for one biorefining approach that we have developed over the last 10 years, namely, the Combined Algal Processing (CAP) approach. This approach fractionates algal biomass into carbohydrate-, lipid-, and protein-rich fractions, and tailors upgrading chemistry to the composition of each fraction. In particular, transitioning from valorization of only the lipids to a co-product suite from multiple components of high-carbohydrate algal biomass can reduce the minimum fuel selling price (MFSP) from more than $8/gallon of gasoline equivalent (GGE) to $2.50/GGE. This paper summarizes that progress and discusses several surprising implications in this optimization approach.
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Wei H, Wang W, Knoshaug EP, Chen X, Van Wychen S, Bomble YJ, Himmel ME, Zhang M. Disruption of the Snf1 Gene Enhances Cell Growth and Reduces the Metabolic Burden in Cellulase-Expressing and Lipid-Accumulating Yarrowia lipolytica. Front Microbiol 2022; 12:757741. [PMID: 35003001 PMCID: PMC8733397 DOI: 10.3389/fmicb.2021.757741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/19/2021] [Indexed: 12/01/2022] Open
Abstract
Yarrowia lipolytica is known to be capable of metabolizing glucose and accumulating lipids intracellularly; however, it lacks the cellulolytic enzymes needed to break down cellulosic biomass directly. To develop Y. lipolytica as a consolidated bioprocessing (CBP) microorganism, we previously expressed the heterologous CBH I, CBH II, and EG II cellulase enzymes both individually and collectively in this microorganism. We concluded that the coexpression of these cellulases resulted in a metabolic drain on the host cells leading to reduced cell growth and lipid accumulation. The current study aims to build a new cellulase coexpressing platform to overcome these hinderances by (1) knocking out the sucrose non-fermenting 1 (Snf1) gene that represses the energetically expensive lipid and protein biosynthesis processes, and (2) knocking in the cellulase cassette fused with the recyclable selection marker URA3 gene in the background of a lipid-accumulating Y. lipolytica strain overexpressing ATP citrate lyase (ACL) and diacylglycerol acyltransferase 1 (DGA1) genes. We have achieved a homologous recombination insertion rate of 58% for integrating the cellulases-URA3 construct at the disrupted Snf1 site in the genome of host cells. Importantly, we observed that the disruption of the Snf1 gene promoted cell growth and lipid accumulation and lowered the cellular saturated fatty acid level and the saturated to unsaturated fatty acid ratio significantly in the transformant YL163t that coexpresses cellulases. The result suggests a lower endoplasmic reticulum stress in YL163t, in comparison with its parent strain Po1g ACL-DGA1. Furthermore, transformant YL163t increased in vitro cellulolytic activity by 30%, whereas the “total in vivo newly formed FAME (fatty acid methyl esters)” increased by 16% in comparison with a random integrative cellulase-expressing Y. lipolytica mutant in the same YNB-Avicel medium. The Snf1 disruption platform demonstrated in this study provides a potent tool for the further development of Y. lipolytica as a robust host for the expression of cellulases and other commercially important proteins.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Eric P Knoshaug
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Xiaowen Chen
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stefanie Van Wychen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
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6
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Kruger JS, Knoshaug EP, Dong T, Hull TC, Pienkos PT. Catalytic Hydroprocessing of Single-Cell Oils to Hydrocarbon Fuels : Converting microbial lipids to fuels is a promising approach to replace fossil fuels. Johnson Matthey Technology Review 2021. [DOI: 10.1595/205651321x16024905831259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial lipids hold great promise as biofuel precursors, and research efforts to convert such lipids to renewable diesel fuels have been increasing in recent years. In contrast to the numerous literature reviews on growing, characterising and extracting lipids from oleaginous microbes,
and on converting vegetable oils to hydrocarbon fuels, this review aims to provide insight into aspects that are specific to hydroprocessing microbial lipids. While standard hydrotreating catalysts generally perform well with terrestrial oils, differences in lipid speciation and the presence
of co-extracted compounds, such as chlorophyll and sterols, introduce additional complexities into the process for microbial lipids. Lipid cleanup steps can be introduced to produce suitable feedstocks for catalytic upgrading.
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Affiliation(s)
- Jacob S. Kruger
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Eric P. Knoshaug
- Bioscience Center, National Renewable Energy Laboratory 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Tao Dong
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Tobias C. Hull
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory 15013 Denver West Parkway, Golden, CO 80401 USA
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8
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Douchi D, Mosey M, Astling DP, Knoshaug EP, Nag A, McGowen J, Laurens LM. Nuclear and chloroplast genome engineering of a productive non-model alga Desmodesmus armatus: Insights into unusual and selective acquisition mechanisms for foreign DNA. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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9
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Alahuhta M, Xu Q, Knoshaug EP, Wang W, Wei H, Amore A, Baker JO, Vander Wall T, Himmel ME, Zhang M. Chimeric cellobiohydrolase I expression, activity, and biochemical properties in three oleaginous yeast. Biotechnol Biofuels 2021; 14:6. [PMID: 33407766 PMCID: PMC7789491 DOI: 10.1186/s13068-020-01856-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/10/2020] [Indexed: 05/16/2023]
Abstract
Consolidated bioprocessing using oleaginous yeast is a promising modality for the economic conversion of plant biomass to fuels and chemicals. However, yeast are not known to produce effective biomass degrading enzymes naturally and this trait is essential for efficient consolidated bioprocessing. We expressed a chimeric cellobiohydrolase I gene in three different oleaginous, industrially relevant yeast: Yarrowia lipolytica, Lipomyces starkeyi, and Saccharomyces cerevisiae to study the biochemical and catalytic properties and biomass deconstruction potential of these recombinant enzymes. Our results showed differences in glycosylation, surface charge, thermal and proteolytic stability, and efficacy of biomass digestion. L. starkeyi was shown to be an inferior active cellulase producer compared to both the Y. lipolytica and S. cerevisiae enzymes, whereas the cellulase expressed in S. cerevisiae displayed the lowest activity against dilute-acid-pretreated corn stover. Comparatively, the chimeric cellobiohydrolase I enzyme expressed in Y. lipolytica was found to have a lower extent of glycosylation, better protease stability, and higher activity against dilute-acid-pretreated corn stover.
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Affiliation(s)
- Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Antonella Amore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Todd Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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10
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Wang W, Knoshaug EP, Wei H, Van Wychen S, Lin CY, Wall TV, Xu Q, Himmel ME, Zhang M. High titer fatty alcohol production in Lipomyces starkeyi by fed-batch fermentation. Current Research in Biotechnology 2020. [DOI: 10.1016/j.crbiot.2020.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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11
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Qiu M, Shen W, Yan X, He Q, Cai D, Chen S, Wei H, Knoshaug EP, Zhang M, Himmel ME, Yang S. Metabolic engineering of Zymomonas mobilis for anaerobic isobutanol production. Biotechnol Biofuels 2020; 13:15. [PMID: 31998408 PMCID: PMC6982386 DOI: 10.1186/s13068-020-1654-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/11/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Biofuels and value-added biochemicals derived from renewable biomass via biochemical conversion have attracted considerable attention to meet global sustainable energy and environmental goals. Isobutanol is a four-carbon alcohol with many advantages that make it attractive as a fossil-fuel alternative. Zymomonas mobilis is a highly efficient, anaerobic, ethanologenic bacterium making it a promising industrial platform for use in a biorefinery. RESULTS In this study, the effect of isobutanol on Z. mobilis was investigated, and various isobutanol-producing recombinant strains were constructed. The results showed that the Z. mobilis parental strain was able to grow in the presence of isobutanol below 12 g/L while concentrations greater than 16 g/L inhibited cell growth. Integration of the heterologous gene encoding 2-ketoisovalerate decarboxylase such as kdcA from Lactococcus lactis is required for isobutanol production in Z. mobilis. Moreover, isobutanol production increased from nearly zero to 100-150 mg/L in recombinant strains containing the kdcA gene driven by the tetracycline-inducible promoter Ptet. In addition, we determined that overexpression of a heterologous als gene and two native genes (ilvC and ilvD) involved in valine metabolism in a recombinant Z. mobilis strain expressing kdcA can divert pyruvate from ethanol production to isobutanol biosynthesis. This engineering improved isobutanol production to above 1 g/L. Finally, recombinant strains containing both a synthetic operon, als-ilvC-ilvD, driven by Ptet and the kdcA gene driven by the constitutive strong promoter, Pgap, were determined to greatly enhance isobutanol production with a maximum titer about 4.0 g/L. Finally, isobutanol production was negatively affected by aeration with more isobutanol being produced in more poorly aerated flasks. CONCLUSIONS This study demonstrated that overexpression of kdcA in combination with a synthetic heterologous operon, als-ilvC-ilvD, is crucial for diverting pyruvate from ethanol production for enhanced isobutanol biosynthesis. Moreover, this study also provides a strategy for harnessing the valine metabolic pathway for future production of other pyruvate-derived biochemicals in Z. mobilis.
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Affiliation(s)
- Mengyue Qiu
- 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
| | - Xiongyin Yan
- 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
| | - Qiaoning He
- 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
| | - Dongbo Cai
- 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
| | - 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
| | - Hui Wei
- Biosciences Centers, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Eric P. Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Min Zhang
- Biosciences Centers, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Centers, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - 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
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12
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Wu C, Herold RA, Knoshaug EP, Wang B, Xiong W, Laurens LML. Author Correction: Fluxomic Analysis Reveals Central Carbon Metabolism Adaptation for Diazotroph Azotobacter vinelandii Ammonium Excretion. Sci Rep 2019; 9:18010. [PMID: 31767908 PMCID: PMC6877564 DOI: 10.1038/s41598-019-54633-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Chao Wu
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Ryan A Herold
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Bo Wang
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Wei Xiong
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA.
| | - Lieve M L Laurens
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA.
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Wu C, Herold RA, Knoshaug EP, Wang B, Xiong W, Laurens LML. Fluxomic Analysis Reveals Central Carbon Metabolism Adaptation for Diazotroph Azotobacter vinelandii Ammonium Excretion. Sci Rep 2019; 9:13209. [PMID: 31520074 PMCID: PMC6744558 DOI: 10.1038/s41598-019-49717-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/30/2019] [Indexed: 11/09/2022] Open
Abstract
Diazotrophic bacteria are an attractive biological alternative to synthetic nitrogen fertilizers due to their remarkable capacity to fix atmospheric nitrogen gas to ammonium via nitrogenase enzymes. However, how diazotrophic bacteria tailor central carbon catabolism to accommodate the energy requirement for nitrogenase activity is largely unknown. In this study, we used Azotobacter vinelandii DJ and an ammonium excreting mutant, AV3 (ΔNifL), to investigate central carbon metabolism fluxes and central cell bioenergetics in response to ammonium availability and nitrogenase activity. Enabled by the powerful and reliable methodology of 13C-metabolic flux analysis, we show that the respiratory TCA cycle is upregulated in association with increased nitrogenase activity and causes a monotonic decrease in specific growth rate. Whereas the activity of the glycolytic Entner-Doudoroff pathway is positively correlated with the cell growth rate. These new observations are formulated into a 13C-metabolic flux model which further improves the understanding and interpretation of intracellular bioenergetics. This analysis leads to the conclusion that, under aerobic conditions, respiratory TCA metabolism is responsible for the supply of additional ATP and reducing equivalents required for elevated nitrogenase activity. This study provides a quantitative relationship between central carbon and nitrogen metabolism in an aerobic diazotroph for the first time.
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Affiliation(s)
- Chao Wu
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Ryan A Herold
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Bo Wang
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA
| | - Wei Xiong
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA.
| | - Lieve M L Laurens
- Bioenergy Science and Technology Directorate, National Renewable Energy Laboratory (NREL), 15013, Denver West Parkway, Golden, CO, 80401, USA.
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14
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Wei H, Wang W, Alper HS, Xu Q, Knoshaug EP, Van Wychen S, Lin CY, Luo Y, Decker SR, Himmel ME, Zhang M. Ameliorating the Metabolic Burden of the Co-expression of Secreted Fungal Cellulases in a High Lipid-Accumulating Yarrowia lipolytica Strain by Medium C/N Ratio and a Chemical Chaperone. Front Microbiol 2019; 9:3276. [PMID: 30687267 PMCID: PMC6333634 DOI: 10.3389/fmicb.2018.03276] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Yarrowia lipolytica, known to accumulate lipids intracellularly, lacks the cellulolytic enzymes needed to break down solid biomass directly. This study aimed to evaluate the potential metabolic burden of expressing core cellulolytic enzymes in an engineered high lipid-accumulating strain of Y. lipolytica. Three fungal cellulases, Talaromyces emersonii-Trichoderma reesei chimeric cellobiohydrolase I (chimeric-CBH I), T. reesei cellobiohydrolase II (CBH II), and T. reesei endoglucanase II (EG II) were expressed using three constitutive strong promoters as a single integrative expression block in a recently engineered lipid hyper-accumulating strain of Y. lipolytica (HA1). In yeast extract-peptone-dextrose (YPD) medium, the resulting cellulase co-expressing transformant YL165-1 had the chimeric-CBH I, CBH II, and EG II secretion titers being 26, 17, and 132 mg L-1, respectively. Cellulase co-expression in YL165-1 in culture media with a moderate C/N ratio of ∼4.5 unexpectedly resulted in a nearly two-fold reduction in cellular lipid accumulation compared to the parental control strain, a sign of cellular metabolic drain. Such metabolic drain was ameliorated when grown in media with a high C/N ratio of 59 having a higher glucose utilization rate that led to approximately twofold more cell mass and threefold more lipid production per liter culture compared to parental control strain, suggesting cross-talk between cellulase and lipid production, both of which involve the endoplasmic reticulum (ER). Most importantly, we found that the chemical chaperone, trimethylamine N-oxide dihydride increased glucose utilization, cell mass and total lipid titer in the transformants, suggesting further amelioration of the metabolic drain. This is the first study examining lipid production in cellulase-expressing Y. lipolytica strains under various C/N ratio media and with a chemical chaperone highlighting the metabolic complexity for developing robust, cellulolytic and lipogenic yeast strains.
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Affiliation(s)
- Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Hal S Alper
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stefanie Van Wychen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Chien-Yuan Lin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yonghua Luo
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.,National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
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Xu Q, Alahuhta M, Wei H, Knoshaug EP, Wang W, Baker JO, Vander Wall T, Himmel ME, Zhang M. Expression of an endoglucanase-cellobiohydrolase fusion protein in Saccharomyces cerevisiae, Yarrowia lipolytica, and Lipomyces starkeyi. Biotechnol Biofuels 2018; 11:322. [PMID: 30524504 PMCID: PMC6278004 DOI: 10.1186/s13068-018-1301-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/25/2018] [Indexed: 05/28/2023]
Abstract
The low secretion levels of cellobiohydrolase I (CBHI) in yeasts are one of the key barriers preventing yeast from directly degrading and utilizing lignocellulose. To overcome this obstacle, we have explored the approach of genetically linking an easily secreted protein to CBHI, with CBHI being the last to be folded. The Trichoderma reesei eg2 (TrEGII) gene was selected as the leading gene due to its previously demonstrated outstanding secretion in yeast. To comprehensively characterize the effects of this fusion protein, we tested this hypothesis in three industrially relevant yeasts: Saccharomyces cerevisiae, Yarrowia lipolytica, and Lipomyces starkeyi. Our initial assays with the L. starkeyi secretome expressing differing TrEGII domains fused to a chimeric Talaromyces emersonii-T. reesei CBHI (TeTrCBHI) showed that the complete TrEGII enzyme, including the glycoside hydrolase (GH) 5 domain is required for increased expression level of the fusion protein when linked to CBHI. We found that this new construct (TrEGII-TeTrCBHI, Fusion 3) had an increased secretion level of at least threefold in L. starkeyi compared to the expression level of the chimeric TeTrCBHI. However, the same improvements were not observed when Fusion 3 construct was expressed in S. cerevisiae and Y. lipolytica. Digestion of pretreated corn stover with the secretomes of Y. lipolytica and L. starkeyi showed that conversion was much better using Y. lipolytica secretomes (50% versus 29%, respectively). In Y. lipolytica, TeTrCBHI performed better than the fusion construct. Furthermore, S. cerevisiae expression of Fusion 3 construct was poor and only minimal activity was observed when acting on the substrate, pNP-cellobiose. No activity was observed for the pNP-lactose substrate. Clearly, this approach is not universally applicable to all yeasts, but works in specific cases. With purified protein and soluble substrates, the exoglucanase activity of the GH7 domain embedded in the Fusion 3 construct in L. starkeyi was significantly higher than that of the GH7 domain in TeTrCBHI expressed alone. It is probable that a higher fraction of fusion construct CBHI is in an active form in Fusion 3 compared to just TeTrCBHI. We conclude that the strategy of leading TeTrCBHI expression with a linked TrEGII module significantly improved the expression of active CBHI in L. starkeyi.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Eric P. Knoshaug
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - John O. Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Todd Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
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16
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Knoshaug EP, Dong T, Spiller R, Nagle N, Pienkos PT. Pretreatment and fermentation of salt-water grown algal biomass as a feedstock for biofuels and high-value biochemicals. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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17
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Knoshaug EP, Wolfrum E, Laurens LML, Harmon VL, Dempster TA, McGowen J. Unified field studies of the algae testbed public-private partnership as the benchmark for algae agronomics. Sci Data 2018; 5:180267. [PMID: 30480663 PMCID: PMC6257041 DOI: 10.1038/sdata.2018.267] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/10/2018] [Indexed: 11/09/2022] Open
Abstract
National scale agronomic projections are an important input for assessing potential benefits of algae cultivation on the future of innovative agriculture. The Algae Testbed Public-Private Partnership was established with the goal of investigating open pond algae cultivation across different geographic, climatic, seasonal, and operational conditions while setting the benchmark for quality data collection, analysis, and dissemination. Identical algae cultivation systems and data analysis methodologies were established at testbed sites across the continental United States and Hawaii. Within this framework, the Unified Field Studies were designed for algae cultivation during all 4 seasons across the testbed network. With increasingly diverse algae research and development, and field deployment strategies, the challenges associated with data collection, quality, and dissemination increase dramatically. The dataset presented here is the complete, curated, climatic, cultivation, harvest, and biomass composition data for each season at each site. These data enable others to do in-depth cultivation, harvest, techno-economic, life cycle, resource, and predictive growth modelling analysis, as well as development of crop protection strategies throughout the algae cultivation industry.
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Affiliation(s)
- Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, USA
| | - Ed Wolfrum
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Lieve M L Laurens
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, USA
| | - Valerie L Harmon
- Harmon Consulting Inc., 64-5162C Kamamalu Street, Kamuela, HI 96743, USA
| | - Thomas A Dempster
- Arizona Center for Algae Technology and Innovation, Arizona State University, Mesa, Arizona, 85212, USA
| | - John McGowen
- Arizona Center for Algae Technology and Innovation, Arizona State University, Mesa, Arizona, 85212, USA
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18
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He Q, Yang Y, Yang S, Donohoe BS, Van Wychen S, Zhang M, Himmel ME, Knoshaug EP. Oleaginicity of the yeast strain Saccharomyces cerevisiae D5A. Biotechnol Biofuels 2018; 11:258. [PMID: 30258492 PMCID: PMC6151946 DOI: 10.1186/s13068-018-1256-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/10/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND The model yeast, Saccharomyces cerevisiae, is not known to be oleaginous. However, an industrial wild-type strain, D5A, was shown to accumulate over 20% storage lipids from glucose when growth is nitrogen-limited compared to no more than 7% lipid accumulation without nitrogen stress. METHODS AND RESULTS To elucidate the mechanisms of S. cerevisiae D5A oleaginicity, we compared physiological and metabolic changes; as well as the transcriptional profiles of the oleaginous industrial strain, D5A, and a non-oleaginous laboratory strain, BY4741, under normal and nitrogen-limited conditions using analytic techniques and next-generation sequencing-based RNA-Seq transcriptomics. Transcriptional levels for genes associated with fatty acid biosynthesis, nitrogen metabolism, amino acid catabolism, as well as the pentose phosphate pathway and ethanol oxidation in central carbon (C) metabolism, were up-regulated in D5A during nitrogen deprivation. Despite increased carbon flux to lipids, most gene-encoding enzymes involved in triacylglycerol (TAG) assembly were expressed at similar levels regardless of the varying nitrogen concentrations in the growth media and strain backgrounds. Phospholipid turnover also contributed to TAG accumulation through increased precursor production with the down-regulation of subsequent phospholipid synthesis steps. Our results also demonstrated that nitrogen assimilation via the glutamate-glutamine pathway and amino acid metabolism, as well as the fluxes of carbon and reductants from central C metabolism, are integral to the general oleaginicity of D5A, which resulted in the enhanced lipid storage during nitrogen deprivation. CONCLUSION This work demonstrated the disequilibrium and rebalance of carbon and nitrogen contribution to the accumulation of lipids in the oleaginous yeast S. cerevisiae D5A. Rather than TAG assembly from acyl groups, the major switches for the enhanced lipid accumulation of D5A (i.e., fatty acid biosynthesis) are the increases of cytosolic pools of acetyl-CoA and NADPH, as well as alternative nitrogen assimilation.
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Affiliation(s)
- Qiaoning He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | | | - Min Zhang
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, 80401 USA
| | - Eric P. Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, 80401 USA
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19
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Guarnieri MT, Levering J, Henard CA, Boore JL, Betenbaugh MJ, Zengler K, Knoshaug EP. Genome Sequence of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395. Front Bioeng Biotechnol 2018; 6:37. [PMID: 29675409 PMCID: PMC5895722 DOI: 10.3389/fbioe.2018.00037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Jennifer Levering
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Calvin A Henard
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Karsten Zengler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
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20
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Guarnieri MT, Gerritsen AT, Henard CA, Knoshaug EP. Phosphoproteome of the Oleaginous Green Alga, Chlorella vulgaris UTEX 395, under Nitrogen-Replete and -Deplete Conditions. Front Bioeng Biotechnol 2018; 6:19. [PMID: 29560349 PMCID: PMC5845665 DOI: 10.3389/fbioe.2018.00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/12/2018] [Indexed: 11/30/2022] Open
Affiliation(s)
- Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Alida T Gerritsen
- Computational Science Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Calvin A Henard
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, United States
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21
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Xu Q, Knoshaug EP, Wang W, Alahuhta M, Baker JO, Yang S, Vander Wall T, Decker SR, Himmel ME, Zhang M, Wei H. Expression and secretion of fungal endoglucanase II and chimeric cellobiohydrolase I in the oleaginous yeast Lipomyces starkeyi. Microb Cell Fact 2017; 16:126. [PMID: 28738851 PMCID: PMC5525229 DOI: 10.1186/s12934-017-0742-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/13/2017] [Indexed: 11/29/2022] Open
Abstract
Background Lipomyces starkeyi is one of the leading lipid-producing microorganisms reported to date; its genetic transformation was only recently reported. Our aim is to engineer L. starkeyi to serve in consolidated bioprocessing (CBP) to produce lipid or fatty acid-related biofuels directly from abundant and low-cost lignocellulosic substrates. Results To evaluate L. starkeyi in this role, we first conducted a genome analysis, which revealed the absence of key endo- and exocellulases in this yeast, prompting us to select and screen four signal peptides for their suitability for the overexpression and secretion of cellulase genes. To compensate for the cellulase deficiency, we chose two prominent cellulases, Trichoderma reesei endoglucanase II (EG II) and a chimeric cellobiohydrolase I (TeTrCBH I) formed by fusion of the catalytic domain from Talaromyces emersonii CBH I with the linker peptide and cellulose-binding domain from T. reesei CBH I. The systematically tested signal peptides included three peptides from native L. starkeyi and one from Yarrowia lipolytica. We found that all four signal peptides permitted secretion of active EG II. We also determined that three of these signal peptides worked for expression of the chimeric CBH I; suggesting that our design criteria for selecting these signal peptides was effective. Encouragingly, the Y. lipolytica signal peptide was able to efficiently guide secretion of the chimeric TeTrCBH I protein from L. starkeyi. The purified chimeric TeTrCBH I showed high activity against the cellulose in pretreated corn stover and the purified EG II showed high endocellulase activity measured by the CELLG3 (Megazyme) method. Conclusions Our results suggest that L. starkeyi is capable of expressing and secreting core fungal cellulases. Moreover, the purified EG II and chimeric TeTrCBH I displayed significant and potentially useful enzymatic activities, demonstrating that engineered L. starkeyi has the potential to function as an oleaginous CBP strain for biofuel production. The effectiveness of the tested secretion signals will also benefit future secretion of other heterologous proteins in L. starkeyi and, given the effectiveness of the cross-genus secretion signal, possibly other oleaginous yeasts as well. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0742-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qi Xu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Wei Wang
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - John O Baker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Todd Vander Wall
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Stephen R Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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22
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McGowen J, Knoshaug EP, Laurens LM, Dempster TA, Pienkos PT, Wolfrum E, Harmon VL. The Algae Testbed Public-Private Partnership (ATP3) framework; establishment of a national network of testbed sites to support sustainable algae production. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.05.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Henard CA, Guarnieri MT, Knoshaug EP. The Chlorella vulgaris S-Nitrosoproteome under Nitrogen-Replete and -Deplete Conditions. Front Bioeng Biotechnol 2017; 4:100. [PMID: 28144611 PMCID: PMC5239800 DOI: 10.3389/fbioe.2016.00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/27/2016] [Indexed: 01/12/2023] Open
Affiliation(s)
- Calvin A Henard
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, CO , USA
| | - Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, CO , USA
| | - Eric P Knoshaug
- National Bioenergy Center, National Renewable Energy Laboratory , Golden, CO , USA
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24
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Dong T, Knoshaug EP, Davis R, Laurens LM, Van Wychen S, Pienkos PT, Nagle N. Combined algal processing: A novel integrated biorefinery process to produce algal biofuels and bioproducts. ALGAL RES 2016. [DOI: 10.1016/j.algal.2015.12.021] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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25
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Zuñiga C, Li CT, Huelsman T, Levering J, Zielinski DC, McConnell BO, Long CP, Knoshaug EP, Guarnieri MT, Antoniewicz MR, Betenbaugh MJ, Zengler K. Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. Plant Physiol 2016; 172:589-602. [PMID: 27372244 PMCID: PMC5074608 DOI: 10.1104/pp.16.00593] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/26/2016] [Indexed: 05/21/2023]
Abstract
The green microalga Chlorella vulgaris has been widely recognized as a promising candidate for biofuel production due to its ability to store high lipid content and its natural metabolic versatility. Compartmentalized genome-scale metabolic models constructed from genome sequences enable quantitative insight into the transport and metabolism of compounds within a target organism. These metabolic models have long been utilized to generate optimized design strategies for an improved production process. Here, we describe the reconstruction, validation, and application of a genome-scale metabolic model for C. vulgaris UTEX 395, iCZ843. The reconstruction represents the most comprehensive model for any eukaryotic photosynthetic organism to date, based on the genome size and number of genes in the reconstruction. The highly curated model accurately predicts phenotypes under photoautotrophic, heterotrophic, and mixotrophic conditions. The model was validated against experimental data and lays the foundation for model-driven strain design and medium alteration to improve yield. Calculated flux distributions under different trophic conditions show that a number of key pathways are affected by nitrogen starvation conditions, including central carbon metabolism and amino acid, nucleotide, and pigment biosynthetic pathways. Furthermore, model prediction of growth rates under various medium compositions and subsequent experimental validation showed an increased growth rate with the addition of tryptophan and methionine.
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Affiliation(s)
- Cristal Zuñiga
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Chien-Ting Li
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Tyler Huelsman
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Jennifer Levering
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Brian O McConnell
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Christopher P Long
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Eric P Knoshaug
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Michael T Guarnieri
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Maciek R Antoniewicz
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Michael J Betenbaugh
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093-0412 (C.Z., T.H., J.L., D.C.Z., K.Z.);Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (C.-T.L., M.J.B.);Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, Delaware 19716 (B.O.M., C.P.L., M.R.A.); andNational Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401 (E.P.K., M.T.G.)
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26
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Knoshaug EP, Vidgren V, Magalhães F, Jarvis EE, Franden MA, Zhang M, Singh A. Novel transporters from
Kluyveromyces marxianus
and
Pichia guilliermondii
expressed in
Saccharomyces cerevisiae
enable growth on
l
‐arabinose and
d
‐xylose. Yeast 2015; 32:615-28. [DOI: 10.1002/yea.3084] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/11/2015] [Accepted: 06/23/2015] [Indexed: 11/08/2022] Open
Affiliation(s)
- Eric P. Knoshaug
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Virve Vidgren
- VTT Technical Research Centre of Finland PO Box 1000 FI‐02044 VTT Finland
| | | | - Eric E. Jarvis
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Mary Ann Franden
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Min Zhang
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Arjun Singh
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
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Gerken HG, Donohoe B, Knoshaug EP. Enzymatic cell wall degradation of Chlorella vulgaris and other microalgae for biofuels production. Planta 2013; 237:239-53. [PMID: 23011569 DOI: 10.1007/s00425-012-1765-0] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 09/04/2012] [Indexed: 05/03/2023]
Abstract
Cell walls of microalgae consist of a polysaccharide and glycoprotein matrix providing the cells with a formidable defense against its environment. We characterized enzymes that can digest the cell wall and weaken this defense for the purpose of protoplasting or lipid extraction. A growth inhibition screen demonstrated that chitinase, lysozyme, pectinase, sulfatase, β-glucuronidase, and laminarinase had the broadest effect across the various Chlorella strains tested and also inhibited Nannochloropsis and Nannochloris strains. Chlorella is typically most sensitive to chitinases and lysozymes, both enzymes that degrade polymers containing N-acetylglucosamine. Using a fluorescent DNA stain, we developed rapid methodology to quantify changes in permeability in response to enzyme digestion and found that treatment with lysozyme in conjunction with other enzymes has a drastic effect on cell permeability. Transmission electron microscopy of enzymatically treated Chlorella vulgaris indicates that lysozyme degrades the outer surface of the cell wall and removes hair-like fibers protruding from the surface, which differs from the activity of chitinase. This action on the outer surface of the cell causes visible protuberances on the cell surface and presumably leads to the increased settling rate when cells are treated with lysozyme. We demonstrate radical ultrastructural changes to the cell wall in response to treatment with various enzyme combinations which, in some cases, causes a greater than twofold increase in the thickness of the cell wall. The enzymes characterized in this study should prove useful in the engineering and extraction of oils from microalgae.
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Affiliation(s)
- Henri G Gerken
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Parkway, Golden, CO 80401, USA
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Selig MJ, Knoshaug EP, Adney WS, Himmel ME, Decker SR. Synergistic enhancement of cellobiohydrolase performance on pretreated corn stover by addition of xylanase and esterase activities. Bioresour Technol 2008; 99:4997-5005. [PMID: 18006303 DOI: 10.1016/j.biortech.2007.09.064] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 09/06/2007] [Accepted: 09/06/2007] [Indexed: 05/05/2023]
Abstract
Significant increases in the depolymerization of corn stover cellulose by cellobiohydrolase I (Cel7A) from Trichoderma reesei were observed using small quantities of non-cellulolytic cell wall-degrading enzymes. Purified endoxylanase (XynA), ferulic acid esterase (FaeA), and acetyl xylan esterase (Axe1) all enhanced Cel7A performance on corn stover subjected to hot water pretreatment. In all cases, the addition of these activities improved the effectiveness of the enzymatic hydrolysis in terms of the quantity of cellulose converted per milligram of total protein. Improvement in cellobiose release by the addition of the non-cellulolytic enzymes ranged from a 13-84% increase over Cel7A alone. The most effective combinations included the addition of both XynA and Axe1, which synergistically enhance xylan conversions resulting in additional synergistic improvements in glucan conversion. Additionally, we note a direct relationship between enzymatic xylan removal in the presence of XynA and the enhancement of cellulose hydrolysis by Cel7A.
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Affiliation(s)
- Michael J Selig
- National Renewable Energy Laboratory, Chemical and BioSciences Center, 1617 Cole Boulevard, Golden, CO 80401, United States.
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Knoshaug EP, Selig MJ, Baker JO, Decker SR, Himmel ME, Adney WS. Heterologous Expression of Two Ferulic Acid Esterases from Penicillium funiculosum. Appl Biochem Biotechnol 2007; 146:79-87. [DOI: 10.1007/s12010-007-8074-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 09/27/2007] [Indexed: 11/24/2022]
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Knoshaug EP, Ahlgren JA, Trempy JE. Exopolysaccharide expression in Lactococcus lactis subsp. cremoris Ropy352: evidence for novel gene organization. Appl Environ Microbiol 2006; 73:897-905. [PMID: 17122391 PMCID: PMC1800743 DOI: 10.1128/aem.01945-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis subsp. cremoris Ropy352 produces two distinct heteropolysaccharides, phenotypically described as ropy and mucoid, when cultured in nonfat milk. One exopolysaccharide precipitated with 50% ethanol as a series of elongated threads and was composed of glucose and galactose in a molar ratio of 3:2. The second exopolysaccharide precipitated with 75% ethanol as a fine flocculant and consisted of galactose, glucose, and mannose with a molar ratio of 67:21:12. A mutant strain, L. lactis subsp. cremoris EK240, lacking the ropy phenotype did not produce the exopolysaccharide that precipitated with 50% ethanol; however, it produced the exopolysaccharide that precipitated with 75% ethanol, indicating that the former exopolysaccharide is essential for the ropy phenotype. Cultures of L. lactis subsp. cremoris Ropy352 in 10% nonfat milk reached a viscosity of 25 Pa-s after 24 h, while those of the nonropy L. lactis subsp. cremoris EK240 mutant did not change. A mutation abolishing ropy exopolysaccharide expression mapped to a region on a plasmid containing two open reading frames, epsM and epsN, encoding novel glycosyltransferases bordered by ISS1 elements oriented in the same direction. Sequencing of this plasmid revealed two other regions involved in exopolysaccharide expression, an operon located between partial IS981 and IS982 elements, and an independent gene, epsU. Two and possibly three of these regions are involved in L. lactis subsp. cremoris Ropy352 exopolysaccharide expression and are arranged in a novel fashion different from that of typical lactococcal exopolysaccharide loci, and this provides genetic evidence for exopolysaccharide gene reorganization and evolution in Lactococcus.
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Affiliation(s)
- Eric P Knoshaug
- Department of Microbiology, Nash Hall 220, Oregon State University, Corvallis, OR 97331-3804, USA
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Abstract
A natural lactococcal isolate, Lactococcus lactis ssp. cremoris Ropy352, has been previously shown to express two phenotypically distinct exopolysaccharides (ropy and mucoid). This natural isolate was cultured on various media to explore the carbon requirements for exopolysaccharide expression. Ropy exopolysaccharide expression was optimal when grown in defined media rather than on M17-based media. Ropy352 was examined for inducible lysogenic phages. No lytic burst was observed in Ropy352 with ultraviolet light or mitomycin C for phage induction. The sugar compositions of the two phenotypically distinct exopolysaccharides were determined. The ropy exopolysaccharide is composed of galactose and glucose in the molar percents of 42 and 58%, respectively. The mucoid exopolysaccharide is composed of galactose, glucose, and mannose in the molar percents of 58, 29, and 13%, respectively. Mutational analysis revealed that mutations impairing ropy exopolysaccharide expression but not affecting mucoid exopolysaccharide expression could be isolated.
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Affiliation(s)
- E P Knoshaug
- Department of Microbiology, Oregon State University, Corvallis 97331, USA
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