1
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Scown CD, Baral NR, Tanjore D, Rapp V. Matching diverse feedstocks to conversion processes for the future bioeconomy. Curr Opin Biotechnol 2023; 84:103017. [PMID: 37935087 DOI: 10.1016/j.copbio.2023.103017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/10/2023] [Accepted: 10/07/2023] [Indexed: 11/09/2023]
Abstract
A wide variety of wasted or underutilized organic feedstocks can be leveraged to build a sustainable bioeconomy, ranging from crop residues to food processor residues and municipal wastes. Leveraging these feedstocks is both high-risk and high-reward. Converting mixed, variable, and/or highly contaminated feedstocks can pose engineering and economic challenges. However, converting these materials to fuels and chemicals can divert waste from landfills, reduce fugitive methane emissions, and enable more responsible forest management to reduce the frequency and severity of wildfires. Historically, low-value components, including ash and lignin, are poised to become valuable coproducts capable of supplementing cement and valuable chemicals. Here, we evaluate the challenges and opportunities associated with converting a range of feedstocks to renewable fuels and chemicals.
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Affiliation(s)
- Corinne D Scown
- Life-cycle, Economics, and Agronomy Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Energy Analysis and Environmental Impacts Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Energy & Biosciences Institute, University of California, Berkeley, CA 94720, United States.
| | - Nawa R Baral
- Life-cycle, Economics, and Agronomy Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, United States
| | - Vi Rapp
- Building Technologies and Urban Systems Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
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2
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Liu D, Hwang HJ, Otoupal PB, Geiselman GM, Kim J, Pomraning KR, Kim YM, Munoz N, Nicora CD, Gao Y, Burnum-Johnson KE, Jacobson O, Coradetti S, Kim J, Deng S, Dai Z, Prahl JP, Tanjore D, Lee TS, Magnuson JK, Gladden JM. Engineering Rhodosporidium toruloides for production of 3-hydroxypropionic acid from lignocellulosic hydrolysate. Metab Eng 2023; 78:72-83. [PMID: 37201565 DOI: 10.1016/j.ymben.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Microbial production of valuable bioproducts is a promising route towards green and sustainable manufacturing. The oleaginous yeast, Rhodosporidium toruloides, has emerged as an attractive host for the production of biofuels and bioproducts from lignocellulosic hydrolysates. 3-hydroxypropionic acid (3HP) is an attractive platform molecule that can be used to produce a wide range of commodity chemicals. This study focuses on establishing and optimizing the production of 3HP in R. toruloides. As R. toruloides naturally has a high metabolic flux towards malonyl-CoA, we exploited this pathway to produce 3HP. Upon finding the yeast capable of catabolizing 3HP, we then implemented functional genomics and metabolomic analysis to identify the catabolic pathways. Deletion of a putative malonate semialdehyde dehydrogenase gene encoding an oxidative 3HP pathway was found to significantly reduce 3HP degradation. We further explored monocarboxylate transporters to promote 3HP transport and identified a novel 3HP transporter in Aspergillus pseudoterreus by RNA-seq and proteomics. Combining these engineering efforts with media optimization in a fed-batch fermentation resulted in 45.4 g/L 3HP production. This represents one of the highest 3HP titers reported in yeast from lignocellulosic feedstocks. This work establishes R. toruloides as a host for 3HP production from lignocellulosic hydrolysate at high titers, and paves the way for further strain and process optimization towards enabling industrial production of 3HP in the future.
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Affiliation(s)
- Di Liu
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA.
| | - Hee Jin Hwang
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA
| | - Peter B Otoupal
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Gina M Geiselman
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Joonhoon Kim
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kyle R Pomraning
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathalie Munoz
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Oslo Jacobson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Samuel Coradetti
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA
| | - Jinho Kim
- DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shuang Deng
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ziyu Dai
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jan-Philip Prahl
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Deepti Tanjore
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taek Soon Lee
- DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jon K Magnuson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - John M Gladden
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
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3
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Bilbao A, Munoz N, Kim J, Orton DJ, Gao Y, Poorey K, Pomraning KR, Weitz K, Burnet M, Nicora CD, Wilton R, Deng S, Dai Z, Oksen E, Gee A, Fasani RA, Tsalenko A, Tanjore D, Gardner J, Smith RD, Michener JK, Gladden JM, Baker ES, Petzold CJ, Kim YM, Apffel A, Magnuson JK, Burnum-Johnson KE. PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements. Nat Commun 2023; 14:2461. [PMID: 37117207 PMCID: PMC10147702 DOI: 10.1038/s41467-023-37031-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 02/24/2023] [Indexed: 04/30/2023] Open
Abstract
Multidimensional measurements using state-of-the-art separations and mass spectrometry provide advantages in untargeted metabolomics analyses for studying biological and environmental bio-chemical processes. However, the lack of rapid analytical methods and robust algorithms for these heterogeneous data has limited its application. Here, we develop and evaluate a sensitive and high-throughput analytical and computational workflow to enable accurate metabolite profiling. Our workflow combines liquid chromatography, ion mobility spectrometry and data-independent acquisition mass spectrometry with PeakDecoder, a machine learning-based algorithm that learns to distinguish true co-elution and co-mobility from raw data and calculates metabolite identification error rates. We apply PeakDecoder for metabolite profiling of various engineered strains of Aspergillus pseudoterreus, Aspergillus niger, Pseudomonas putida and Rhodosporidium toruloides. Results, validated manually and against selected reaction monitoring and gas-chromatography platforms, show that 2683 features could be confidently annotated and quantified across 116 microbial sample runs using a library built from 64 standards.
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Affiliation(s)
- Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, WA, USA.
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA.
| | - Nathalie Munoz
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Joonhoon Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Daniel J Orton
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | | | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Karl Weitz
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Meagan Burnet
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Rosemarie Wilton
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Argonne National Laboratory, Lemont, IL, USA
| | - Shuang Deng
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Ziyu Dai
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Ethan Oksen
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aaron Gee
- Agilent Research Laboratories, Agilent Technologies, Santa Clara, CA, USA
| | - Rick A Fasani
- Agilent Research Laboratories, Agilent Technologies, Santa Clara, CA, USA
| | - Anya Tsalenko
- Agilent Research Laboratories, Agilent Technologies, Santa Clara, CA, USA
| | - Deepti Tanjore
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James Gardner
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Joshua K Michener
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John M Gladden
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Sandia National Laboratory, Livermore, CA, USA
| | - Erin S Baker
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher J Petzold
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Alex Apffel
- Agilent Research Laboratories, Agilent Technologies, Santa Clara, CA, USA
| | - Jon K Magnuson
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Kristin E Burnum-Johnson
- Pacific Northwest National Laboratory, Richland, WA, USA.
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA.
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4
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Martin HG, Radivojevic T, Zucker J, Bouchard K, Sustarich J, Peisert S, Arnold D, Hillson N, Babnigg G, Marti JM, Mungall CJ, Beckham GT, Waldburger L, Carothers J, Sundaram S, Agarwal D, Simmons BA, Backman T, Banerjee D, Tanjore D, Ramakrishnan L, Singh A. Perspectives for self-driving labs in synthetic biology. Curr Opin Biotechnol 2023; 79:102881. [PMID: 36603501 DOI: 10.1016/j.copbio.2022.102881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023]
Abstract
Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments. Taken to their ultimate expression, SDLs could usher a new paradigm of scientific research, where the world is probed, interpreted, and explained by machines for human benefit. While there are functioning SDLs in the fields of chemistry and materials science, we contend that synthetic biology provides a unique opportunity since the genome provides a single target for affecting the incredibly wide repertoire of biological cell behavior. However, the level of investment required for the creation of biological SDLs is only warranted if directed toward solving difficult and enabling biological questions. Here, we discuss challenges and opportunities in creating SDLs for synthetic biology.
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Affiliation(s)
- Hector G Martin
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States; BCAM, Basque Center for Applied Mathematics, Bilbao, Spain.
| | - Tijana Radivojevic
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Jeremy Zucker
- Earth and Biological Sciences Division, Pacific Northwest National Laboratories, Richland, WA, United States
| | - Kristofer Bouchard
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States; Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience, Berkeley, CA, United States
| | - Jess Sustarich
- Joint BioEnergy Institute, Emeryville, CA, United States; Biomaterials and Biomanufacturing Division, Sandia National Laboratories, Livermore, CA, United States
| | - Sean Peisert
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States; University of California, Davis, Department of Computer Science, Davis, CA, United States
| | - Dan Arnold
- Lawrence Berkeley National Laboratory, Energy Storage and Distributed Resources Division, Berkeley, CA, United States
| | - Nathan Hillson
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Gyorgy Babnigg
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Jose M Marti
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States; Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Christopher J Mungall
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States
| | - Gregg T Beckham
- Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, United States
| | - Lucas Waldburger
- Department of Bioengineering, University of California, Berkeley, CA, United States
| | - James Carothers
- Department of Chemical Engineering, Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, WA, United States
| | - ShivShankar Sundaram
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States; Center for Bioengineering, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Deb Agarwal
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States
| | - Blake A Simmons
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Tyler Backman
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepanwita Banerjee
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepti Tanjore
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, United States; Department of Energy, Agile BioFoundry, Emeryville, CA, United States; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lavanya Ramakrishnan
- Lawrence Berkeley National Laboratory, Scientific Data Division, Berkeley, CA, United States
| | - Anup Singh
- Joint BioEnergy Institute, Emeryville, CA, United States; Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
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5
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Eng T, Banerjee D, Lau AK, Bowden E, Herbert RA, Trinh J, Prahl JP, Deutschbauer A, Tanjore D, Mukhopadhyay A. Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor. Metab Eng 2021; 66:229-238. [PMID: 33964456 DOI: 10.1016/j.ymben.2021.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022]
Abstract
Pseudomonas putida KT2440 is an emerging biomanufacturing host amenable for use with renewable carbon streams including aromatics such as para-coumarate. We used a pooled transposon library disrupting nearly all (4,778) non-essential genes to characterize this microbe under common stirred-tank bioreactor parameters with quantitative fitness assays. Assessing differential fitness values by monitoring changes in mutant strain abundance identified 33 gene mutants with improved fitness across multiple stirred-tank bioreactor formats. Twenty-one deletion strains from this subset were reconstructed, including GacA, a regulator, TtgB, an ABC transporter, and PP_0063, a lipid A acyltransferase. Thirteen deletion strains with roles in varying cellular functions were evaluated for conversion of para-coumarate, to a heterologous bioproduct, indigoidine. Several mutants, such as the ΔgacA strain improved fitness in a bioreactor by 35 fold and showed an 8-fold improvement in indigoidine production (4.5 g/L, 0.29 g/g, 23% of maximum theoretical yield) from para-coumarate as the carbon source.
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Affiliation(s)
- Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Andrew K Lau
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Emily Bowden
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Jessica Trinh
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Hollis Street, Emeryville, CA, 5885, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Hollis Street, Emeryville, CA, 5885, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885, Hollis Street, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, USA.
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6
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Kirby J, Geiselman GM, Yaegashi J, Kim J, Zhuang X, Tran-Gyamfi MB, Prahl JP, Sundstrom ER, Gao Y, Munoz N, Burnum-Johnson KE, Benites VT, Baidoo EEK, Fuhrmann A, Seibel K, Webb-Robertson BJM, Zucker J, Nicora CD, Tanjore D, Magnuson JK, Skerker JM, Gladden JM. Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass. Biotechnol Biofuels 2021; 14:101. [PMID: 33883010 PMCID: PMC8058980 DOI: 10.1186/s13068-021-01950-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/07/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Mitigation of climate change requires that new routes for the production of fuels and chemicals be as oil-independent as possible. The microbial conversion of lignocellulosic feedstocks into terpene-based biofuels and bioproducts represents one such route. This work builds upon previous demonstrations that the single-celled carotenogenic basidiomycete, Rhodosporidium toruloides, is a promising host for the production of terpenes from lignocellulosic hydrolysates. RESULTS This study focuses on the optimization of production of the monoterpene 1,8-cineole and the sesquiterpene α-bisabolene in R. toruloides. The α-bisabolene titer attained in R. toruloides was found to be proportional to the copy number of the bisabolene synthase (BIS) expression cassette, which in turn influenced the expression level of several native mevalonate pathway genes. The addition of more copies of BIS under a stronger promoter resulted in production of α-bisabolene at 2.2 g/L from lignocellulosic hydrolysate in a 2-L fermenter. Production of 1,8-cineole was found to be limited by availability of the precursor geranylgeranyl pyrophosphate (GPP) and expression of an appropriate GPP synthase increased the monoterpene titer fourfold to 143 mg/L at bench scale. Targeted mevalonate pathway metabolite analysis suggested that 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGR), mevalonate kinase (MK) and phosphomevalonate kinase (PMK) may be pathway bottlenecks are were therefore selected as targets for overexpression. Expression of HMGR, MK, and PMK orthologs and growth in an optimized lignocellulosic hydrolysate medium increased the 1,8-cineole titer an additional tenfold to 1.4 g/L. Expression of the same mevalonate pathway genes did not have as large an impact on α-bisabolene production, although the final titer was higher at 2.6 g/L. Furthermore, mevalonate pathway intermediates accumulated in the mevalonate-engineered strains, suggesting room for further improvement. CONCLUSIONS This work brings R. toruloides closer to being able to make industrially relevant quantities of terpene from lignocellulosic biomass.
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Affiliation(s)
- James Kirby
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Gina M Geiselman
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Junko Yaegashi
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Chemical and Biological Processing Group, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joonhoon Kim
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Chemical and Biological Processing Group, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Xun Zhuang
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Mary Bao Tran-Gyamfi
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Jan-Philip Prahl
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Eric R Sundstrom
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Yuqian Gao
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nathalie Munoz
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- The Environmental Molecular Sciences Laboratory, Richland, WA, 99354, USA
| | - Kristin E Burnum-Johnson
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- The Environmental Molecular Sciences Laboratory, Richland, WA, 99354, USA
| | - Veronica T Benites
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Fuhrmann
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Katharina Seibel
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Bobbie-Jo M Webb-Robertson
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jeremy Zucker
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Carrie D Nicora
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Deepti Tanjore
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jon K Magnuson
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA
- Chemical and Biological Processing Group, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jeffrey M Skerker
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- QB3-Berkeley, University of California, Berkeley, CA, 94704, USA
| | - John M Gladden
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA.
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94550, USA.
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7
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Lawson CE, Martí JM, Radivojevic T, Jonnalagadda SVR, Gentz R, Hillson NJ, Peisert S, Kim J, Simmons BA, Petzold CJ, Singer SW, Mukhopadhyay A, Tanjore D, Dunn JG, Garcia Martin H. Machine learning for metabolic engineering: A review. Metab Eng 2020; 63:34-60. [PMID: 33221420 DOI: 10.1016/j.ymben.2020.10.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/22/2020] [Accepted: 10/31/2020] [Indexed: 12/14/2022]
Abstract
Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner in terms of data management, algorithm libraries, computational resources, and important non-technical issues. A variety of applications ranging from pathway construction and optimization, to genetic editing optimization, cell factory testing, and production scale-up are discussed. Moreover, the promising relationship between machine learning and mechanistic models is thoroughly reviewed. Finally, the future perspectives and most promising directions for this combination of disciplines are examined.
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Affiliation(s)
- Christopher E Lawson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Jose Manuel Martí
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Tijana Radivojevic
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sai Vamshi R Jonnalagadda
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Reinhard Gentz
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sean Peisert
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; University of California Davis, Davis, CA, 95616, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Pacific Northwest National Laboratory, Richland, 99354, WA, USA
| | - Blake A Simmons
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Steven W Singer
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA
| | - Deepti Tanjore
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, 94608, USA
| | | | - Hector Garcia Martin
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Basque Center for Applied Mathematics, 48009, Bilbao, Spain; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA.
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8
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Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl JP, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nat Commun 2020; 11:5385. [PMID: 33097726 PMCID: PMC7584609 DOI: 10.1038/s41467-020-19171-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We compute MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From the 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. We implement a total of 14 genes knockdowns using multiplex-CRISPRi. MCS-based solution shifts production from stationary to exponential phase. We achieve 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose). These phenotypes are maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr®, and 2-L bioreactors).
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Andrew K Lau
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yusuke Sasaki
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brenda Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Vasanth R Singan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA, 94608, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970, Horsholm, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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9
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Wehrs M, Thompson MG, Banerjee D, Prahl JP, Morella NM, Barcelos CA, Moon J, Costello Z, Keasling JD, Shih PM, Tanjore D, Mukhopadhyay A. Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation. Microb Cell Fact 2020; 19:167. [PMID: 32811554 PMCID: PMC7437010 DOI: 10.1186/s12934-020-01423-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 05/12/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Despite the latest advancements in metabolic engineering for genome editing and characterization of host performance, the successful development of robust cell factories used for industrial bioprocesses and accurate prediction of the behavior of microbial systems, especially when shifting from laboratory-scale to industrial conditions, remains challenging. To increase the probability of success of a scale-up process, data obtained from thoroughly performed studies mirroring cellular responses to typical large-scale stimuli may be used to derive crucial information to better understand potential implications of large-scale cultivation on strain performance. This study assesses the feasibility to employ a barcoded yeast deletion library to assess genome-wide strain fitness across a simulated industrial fermentation regime and aims to understand the genetic basis of changes in strain physiology during industrial fermentation, and the corresponding roles these genes play in strain performance. Results We find that mutant population diversity is maintained through multiple seed trains, enabling large scale fermentation selective pressures to act upon the community. We identify specific deletion mutants that were enriched in all processes tested in this study, independent of the cultivation conditions, which include MCK1, RIM11, MRK1, and YGK3 that all encode homologues of mammalian glycogen synthase kinase 3 (GSK-3). Ecological analysis of beta diversity between all samples revealed significant population divergence over time and showed feed specific consequences of population structure. Further, we show that significant changes in the population diversity during fed-batch cultivations reflect the presence of significant stresses. Our observations indicate that, for this yeast deletion collection, the selection of the feeding scheme which affects the accumulation of the fermentative by-product ethanol impacts the diversity of the mutant pool to a higher degree as compared to the pH of the culture broth. The mutants that were lost during the time of most extreme population selection suggest that specific biological processes may be required to cope with these specific stresses. Conclusions Our results demonstrate the feasibility of Bar-seq to assess fermentation associated stresses in yeast populations under industrial conditions and to understand critical stages of a scale-up process where variability emerges, and selection pressure gets imposed. Overall our work highlights a promising avenue to identify genetic loci and biological stress responses required for fitness under industrial conditions.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Mitchell G Thompson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Deepanwita Banerjee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Norma M Morella
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carolina A Barcelos
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jadie Moon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Zak Costello
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Energy Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK 2970, Horsholm, Denmark.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Patrick M Shih
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Biology, University of California-Davis, Davis, CA, 95616, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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10
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Liu D, Geiselman GM, Coradetti S, Cheng YF, Kirby J, Prahl JP, Jacobson O, Sundstrom ER, Tanjore D, Skerker JM, Gladden J. Exploiting nonionic surfactants to enhance fatty alcohol production in Rhodosporidium toruloides. Biotechnol Bioeng 2020; 117:1418-1425. [PMID: 31981215 PMCID: PMC7187362 DOI: 10.1002/bit.27285] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 10/08/2019] [Revised: 12/23/2019] [Accepted: 01/22/2020] [Indexed: 01/13/2023]
Abstract
Fatty alcohols (FOHs) are important feedstocks in the chemical industry to produce detergents, cosmetics, and lubricants. Microbial production of FOHs has become an attractive alternative to production in plants and animals due to growing energy demands and environmental concerns. However, inhibition of cell growth caused by intracellular FOH accumulation is one major issue that limits FOH titers in microbial hosts. In addition, identification of FOH‐specific exporters remains a challenge and previous studies towards this end are limited. To alleviate the toxicity issue, we exploited nonionic surfactants to promote the export of FOHs in Rhodosporidium toruloides, an oleaginous yeast that is considered an attractive next‐generation host for the production of fatty acid‐derived chemicals. Our results showed FOH export efficiency was dramatically improved and the growth inhibition was alleviated in the presence of small amounts of tergitol and other surfactants. As a result, FOH titers increase by 4.3‐fold at bench scale to 352.6 mg/L. With further process optimization in a 2‐L bioreactor, the titer was further increased to 1.6 g/L. The method we show here can potentially be applied to other microbial hosts and may facilitate the commercialization of microbial FOH production.
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Affiliation(s)
- Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Gina M Geiselman
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Samuel Coradetti
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Ya-Fang Cheng
- QB3-Berkeley, University of California, Berkeley, California
| | - James Kirby
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California
| | - Jan-Philip Prahl
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Oslo Jacobson
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Eric R Sundstrom
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | - Deepti Tanjore
- Department of Energy, Agile BioFoundry, Emeryville, California.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, California
| | | | - John Gladden
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, California.,Department of Energy, Agile BioFoundry, Emeryville, California.,Joint BioEnergy Institute, Emeryville, California
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11
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Geiselman GM, Zhuang X, Kirby J, Tran-Gyamfi MB, Prahl JP, Sundstrom ER, Gao Y, Munoz Munoz N, Nicora CD, Clay DM, Papa G, Burnum-Johnson KE, Magnuson JK, Tanjore D, Skerker JM, Gladden JM. Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides. Microb Cell Fact 2020; 19:24. [PMID: 32024522 PMCID: PMC7003354 DOI: 10.1186/s12934-020-1293-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 09/05/2019] [Accepted: 01/23/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Rhodosporidium toruloides has emerged as a promising host for the production of bioproducts from lignocellulose, in part due to its ability to grow on lignocellulosic feedstocks, tolerate growth inhibitors, and co-utilize sugars and lignin-derived monomers. Ent-kaurene derivatives have a diverse range of potential applications from therapeutics to novel resin-based materials. RESULTS The Design, Build, Test, and Learn (DBTL) approach was employed to engineer production of the non-native diterpene ent-kaurene in R. toruloides. Following expression of kaurene synthase (KS) in R. toruloides in the first DBTL cycle, a key limitation appeared to be the availability of the diterpene precursor, geranylgeranyl diphosphate (GGPP). Further DBTL cycles were carried out to select an optimal GGPP synthase and to balance its expression with KS, requiring two of the strongest promoters in R. toruloides, ANT (adenine nucleotide translocase) and TEF1 (translational elongation factor 1) to drive expression of the KS from Gibberella fujikuroi and a mutant version of an FPP synthase from Gallus gallus that produces GGPP. Scale-up of cultivation in a 2 L bioreactor using a corn stover hydrolysate resulted in an ent-kaurene titer of 1.4 g/L. CONCLUSION This study builds upon previous work demonstrating the potential of R. toruloides as a robust and versatile host for the production of both mono- and sesquiterpenes, and is the first demonstration of the production of a non-native diterpene in this organism.
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Affiliation(s)
- Gina M Geiselman
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA.,Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Xun Zhuang
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA.,Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - James Kirby
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA.,Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Mary B Tran-Gyamfi
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA.,Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Jan-Philip Prahl
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Eric R Sundstrom
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuqian Gao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Nathalie Munoz Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Carrie D Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Derek M Clay
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA.,Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA
| | - Gabriella Papa
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kristin E Burnum-Johnson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jon K Magnuson
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Deepti Tanjore
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - John M Gladden
- Department of Energy, Agile BioFoundry, Emeryville, CA, 94608, USA. .,Department of Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Ave, Livermore, CA, 94550, USA.
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12
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Wehrs M, Prahl JP, Moon J, Li Y, Tanjore D, Keasling JD, Pray T, Mukhopadhyay A. Correction to: Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae. Microb Cell Fact 2019; 18:218. [PMID: 31884968 PMCID: PMC6936116 DOI: 10.1186/s12934-019-1262-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 11/24/2022] Open
Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Institut für Genetik, Technische Universität Braunschweig, Brunswick, Germany.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jadie Moon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Yuchen Li
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.,Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Todd Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA. .,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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13
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Wehrs M, Tanjore D, Eng T, Lievense J, Pray TR, Mukhopadhyay A. Engineering Robust Production Microbes for Large-Scale Cultivation. Trends Microbiol 2019; 27:524-537. [PMID: 30819548 DOI: 10.1016/j.tim.2019.01.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/11/2019] [Accepted: 01/23/2019] [Indexed: 11/27/2022]
Abstract
Systems biology and synthetic biology are increasingly used to examine and modulate complex biological systems. As such, many issues arising during scaling-up microbial production processes can be addressed using these approaches. We review differences between laboratory-scale cultures and larger-scale processes to provide a perspective on those strain characteristics that are especially important during scaling. Systems biology has been used to examine a range of microbial systems for their response in bioreactors to fluctuations in nutrients, dissolved gases, and other stresses. Synthetic biology has been used both to assess and modulate strain response, and to engineer strains to improve production. We discuss these approaches and tools in the context of their use in engineering robust microbes for applications in large-scale production.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA
| | | | - Todd R Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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14
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Narani A, Konda NVSNM, Chen CS, Tachea F, Coffman P, Gardner J, Li C, Ray AE, Hartley DS, Simmons B, Pray TR, Tanjore D. Simultaneous application of predictive model and least cost formulation can substantially benefit biorefineries outside Corn Belt in United States: A case study in Florida. Bioresour Technol 2019; 271:218-227. [PMID: 30273825 DOI: 10.1016/j.biortech.2018.09.103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Previously, a predictive model was developed to identify optimal blends of expensive high-quality and cheaper low-quality feedstocks for a given geographical location that can deliver high sugar yields. In this study, the optimal process conditions were tested for application at commercially-relevant higher biomass loadings. We observed lower sugar yields but 100% conversion to ethanol from a blend that contained only 20% high-quality feedstock. The impact of applying this predictive model simultaneously with least cost formulation model for a biorefinery location outside of the US Corn Belt in Lee County, Florida was investigated. A blend ratio of 0.30 EC, 0.45 SG, and 0.25 CS in Lee County was necessary to produce sugars at high yields and ethanol at a capacity of 50 MMGY. This work demonstrates utility in applying predictive model and LCF to reduce feedstock costs and supply chain risks while optimizing for product yields.
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Affiliation(s)
- Akash Narani
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - N V S N Murthy Konda
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chyi-Shin Chen
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Firehiwot Tachea
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Phil Coffman
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - James Gardner
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chenlin Li
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Energy and Environment Science and Technology, Idaho National Laboratory, Idaho Falls, ID, United States
| | - Allison E Ray
- Energy and Environment Science and Technology, Idaho National Laboratory, Idaho Falls, ID, United States
| | - Damon S Hartley
- Energy and Environment Science and Technology, Idaho National Laboratory, Idaho Falls, ID, United States
| | - Blake Simmons
- Biofuels and Biomaterials Science and Technology, Sandia National Laboratory, Livermore, CA, United States
| | - Todd R Pray
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Deepti Tanjore
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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15
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Wehrs M, Prahl JP, Moon J, Li Y, Tanjore D, Keasling JD, Pray T, Mukhopadhyay A. Production efficiency of the bacterial non-ribosomal peptide indigoidine relies on the respiratory metabolic state in S. cerevisiae. Microb Cell Fact 2018; 17:193. [PMID: 30545355 PMCID: PMC6293659 DOI: 10.1186/s12934-018-1045-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/11/2018] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Beyond pathway engineering, the metabolic state of the production host is critical in maintaining the efficiency of cellular production. The biotechnologically important yeast Saccharomyces cerevisiae adjusts its energy metabolism based on the availability of oxygen and carbon sources. This transition between respiratory and non-respiratory metabolic state is accompanied by substantial modifications of central carbon metabolism, which impact the efficiency of metabolic pathways and the corresponding final product titers. Non-ribosomal peptide synthetases (NRPS) are an important class of biocatalysts that provide access to a wide array of secondary metabolites. Indigoidine, a blue pigment, is a representative NRP that is valuable by itself as a renewably produced pigment. RESULTS Saccharomyces cerevisiae was engineered to express a bacterial NRPS that converts glutamine to indigoidine. We characterize carbon source use and production dynamics, and demonstrate that indigoidine is solely produced during respiratory cell growth. Production of indigoidine is abolished during non-respiratory growth even under aerobic conditions. By promoting respiratory conditions via controlled feeding, we scaled the production to a 2 L bioreactor scale, reaching a maximum titer of 980 mg/L. CONCLUSIONS This study represents the first use of the Streptomyces lavendulae NRPS (BpsA) in a fungal host and its scale-up. The final product indigoidine is linked to the activity of the TCA cycle and serves as a reporter for the respiratory state of S. cerevisiae. Our approach can be broadly applied to investigate diversion of flux from central carbon metabolism for NRPS and other heterologous pathway engineering, or to follow a population switch between respiratory and non-respiratory modes.
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Affiliation(s)
- Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Institut für Genetik, Technische Universität Braunschweig, Brunswick, Germany
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jadie Moon
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Yuchen Li
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Todd Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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16
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Yuzawa S, Mirsiaghi M, Jocic R, Fujii T, Masson F, Benites VT, Baidoo EEK, Sundstrom E, Tanjore D, Pray TR, George A, Davis RW, Gladden JM, Simmons BA, Katz L, Keasling JD. Short-chain ketone production by engineered polyketide synthases in Streptomyces albus. Nat Commun 2018; 9:4569. [PMID: 30385744 PMCID: PMC6212451 DOI: 10.1038/s41467-018-07040-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [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: 04/03/2018] [Accepted: 09/26/2018] [Indexed: 01/14/2023] Open
Abstract
Microbial production of fuels and commodity chemicals has been performed primarily using natural or slightly modified enzymes, which inherently limits the types of molecules that can be produced. Type I modular polyketide synthases (PKSs) are multi-domain enzymes that can produce unique and diverse molecular structures by combining particular types of catalytic domains in a specific order. This catalytic mechanism offers a wealth of engineering opportunities. Here we report engineered microbes that produce various short-chain (C5-C7) ketones using hybrid PKSs. Introduction of the genes into the chromosome of Streptomyces albus enables it to produce >1 g · l-1 of C6 and C7 ethyl ketones and several hundred mg · l-1 of C5 and C6 methyl ketones from plant biomass hydrolysates. Engine tests indicate these short-chain ketones can be added to gasoline as oxygenates to increase the octane of gasoline. Together, it demonstrates the efficient and renewable microbial production of biogasolines by hybrid enzymes.
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Affiliation(s)
- Satoshi Yuzawa
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States. .,Joint BioEnegy Institute, Emeryville, California, 94608, United States. .,Biotechnology Research Center, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Mona Mirsiaghi
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States.,Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States
| | - Renee Jocic
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States
| | - Tatsuya Fujii
- Joint BioEnegy Institute, Emeryville, California, 94608, United States.,Research Institute for Sustainable Chemistry, Institute for Synthetic Biology, National Institute of Advanced Industrial Science and Technology, Higashi-hiroshima, Hiroshima, 739-0046, Japan
| | - Fabrice Masson
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States.,Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States
| | - Veronica T Benites
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States.,Joint BioEnegy Institute, Emeryville, California, 94608, United States
| | - Edward E K Baidoo
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States.,Joint BioEnegy Institute, Emeryville, California, 94608, United States
| | - Eric Sundstrom
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States.,Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States
| | - Deepti Tanjore
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States.,Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States
| | - Todd R Pray
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States.,Advanced Biofuels & Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States
| | - Anthe George
- Joint BioEnegy Institute, Emeryville, California, 94608, United States.,Department of Biomass Science and Conversion Technologies, Sandia National Laboratory, Livermore, California, 94551, United States
| | - Ryan W Davis
- Department of Biomass Science and Conversion Technologies, Sandia National Laboratory, Livermore, California, 94551, United States
| | - John M Gladden
- Joint BioEnegy Institute, Emeryville, California, 94608, United States.,Department of Biomass Science and Conversion Technologies, Sandia National Laboratory, Livermore, California, 94551, United States
| | - Blake A Simmons
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States.,Joint BioEnegy Institute, Emeryville, California, 94608, United States
| | - Leonard Katz
- Joint BioEnegy Institute, Emeryville, California, 94608, United States.,QB3 Institute, University of California, Berkeley, California, 94720, United States
| | - Jay D Keasling
- Biogical Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States. .,Joint BioEnegy Institute, Emeryville, California, 94608, United States. .,QB3 Institute, University of California, Berkeley, California, 94720, United States. .,Department of Bioengineering, University of California, Berkeley, California, 94720, United States. .,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, 94720, United States. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, DK-2800, Kgs, Lyngby, Denmark. .,Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, Guangdong, 518055, China.
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17
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Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW. A bacterial pioneer produces cellulase complexes that persist through community succession. Nat Microbiol 2017; 3:99-107. [PMID: 29109478 PMCID: PMC6794216 DOI: 10.1038/s41564-017-0052-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 01/26/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022]
Abstract
Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, ‘Candidatus Reconcilibacillus cellulovorans’, possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the ‘Ca. Reconcilibacillus cellulovorans’ multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology. Cultivation of a cellulolytic consortium reveals successional community dynamics and the presence of multidomain glycoside hydrolases assembled into stable complexes distinct from cellulosomes, which are produced by a potential pioneer population.
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Affiliation(s)
- Sebastian Kolinko
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Evelyn Denzel
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Jennifer Hiras
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Corning Incorporated, Corning, NY, USA
| | - Raphael Gabriel
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Bäcker
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephanie A Eichorst
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network "Chemistry meets Microbiology", University of Vienna, Vienna, Austria
| | - Dario Frey
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Qiushi Chen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Todd R Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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18
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Narani A, Coffman P, Gardner J, Li C, Ray AE, Hartley DS, Stettler A, Konda NVSNM, Simmons B, Pray TR, Tanjore D. Predictive modeling to de-risk bio-based manufacturing by adapting to variability in lignocellulosic biomass supply. Bioresour Technol 2017; 243:676-685. [PMID: 28709073 DOI: 10.1016/j.biortech.2017.06.156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
Commercial-scale bio-refineries are designed to process 2000tons/day of single lignocellulosic biomass. Several geographical areas in the United States generate diverse feedstocks that, when combined, can be substantial for bio-based manufacturing. Blending multiple feedstocks is a strategy being investigated to expand bio-based manufacturing outside Corn Belt. In this study, we developed a model to predict continuous envelopes of biomass blends that are optimal for a given pretreatment condition to achieve a predetermined sugar yield or vice versa. For example, our model predicted more than 60% glucose yield can be achieved by treating an equal part blend of energy cane, corn stover, and switchgrass with alkali pretreatment at 120°C for 14.8h. By using ionic liquid to pretreat an equal part blend of the biomass feedstocks at 160°C for 2.2h, we achieved 87.6% glucose yield. Such a predictive model can potentially overcome dependence on a single feedstock.
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Affiliation(s)
- Akash Narani
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Phil Coffman
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - James Gardner
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Chenlin Li
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Energy and Environmental Science and Technology, Idaho National Laboratory, Idaho Falls, ID, United States
| | - Allison E Ray
- Energy and Environmental Science and Technology, Idaho National Laboratory, Idaho Falls, ID, United States
| | - Damon S Hartley
- Energy and Environmental Science and Technology, Idaho National Laboratory, Idaho Falls, ID, United States
| | - Allison Stettler
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - N V S N Murthy Konda
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Blake Simmons
- Biofuels and Biomaterials Science and Technology, Sandia National Laboratory, Livermore, CA, United States
| | - Todd R Pray
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Deepti Tanjore
- Advanced Biofuels Process Demonstration Unit (AB-PDU), Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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19
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Li C, Liang L, Sun N, Thompson VS, Xu F, Narani A, He Q, Tanjore D, Pray TR, Simmons BA, Singh S. Scale-up and process integration of sugar production by acidolysis of municipal solid waste/corn stover blends in ionic liquids. Biotechnol Biofuels 2017; 10:13. [PMID: 28070222 PMCID: PMC5217572 DOI: 10.1186/s13068-016-0694-8] [Citation(s) in RCA: 5] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Lignocellulosic biorefineries have tonnage and throughput requirements that must be met year round and there is no single feedstock available in any given region that is capable of meeting the price and availability demands of the biorefineries scheduled for deployment. Significant attention has been historically given to agriculturally derived feedstocks; however, a diverse range of wastes, including municipal solid wastes (MSW), also have the potential to serve as feedstocks for the production of advanced biofuels and have not been extensively studied. In addition, ionic liquid (IL) pretreatment with certain ILs is receiving great interest as a potential process that enables fractionation of a wide range of feedstocks. Acid catalysts have been used previously to hydrolyze polysaccharides into fermentable sugars following IL pretreatment, which could potentially provide a means of liberating fermentable sugars from lignocellulose without the use of costly enzymes. However, successful optimization and scale-up of the one-pot acid-assisted IL deconstruction for further commercialization involve challenges such as reactor compatibility, mixing at high solid loading, sugar recovery, and IL recycling, which have not been effectively resolved during the development stages at bench scale. RESULTS Here, we present the successful scale-up demonstration of the acid-assisted IL deconstruction on feedstock blends of municipal solid wastes and agricultural residues (corn stover) by 30-fold, relative to the bench scale (6 vs 0.2 L), at 10% solid loading. By integrating IL pretreatment and acid hydrolysis with subsequent centrifugation and extraction, the sugar and lignin products can be further recovered efficiently. This scale-up development at Advanced Biofuels/Bioproducts Process Demonstration Unit (ABPDU) will leverage the opportunity and synergistic efforts toward developing a cost-effective IL-based deconstruction technology by drastically eliminating enzyme, reducing water usage, and simplifying the downstream sugar/lignin recovery and IL recycling. CONCLUSION Results indicate that MSW blends are viable and valuable resource to consider when assessing biomass availability and affordability for lignocellulosic biorefineries. This scale-up evaluation demonstrates that the acid-assisted IL deconstruction technology can be effectively scaled up to larger operations and the current study established the baseline of scaling parameters for this process.
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Affiliation(s)
- Chenlin Li
- Advanced Biofuels (and BioProducts) Process Demonstration Unit, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Energy and Environmental Science and Technology, Idaho National Laboratory, 2525 North Fremont Ave, Idaho Falls, ID 83415 USA
| | - Ling Liang
- Advanced Biofuels (and BioProducts) Process Demonstration Unit, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Ning Sun
- Advanced Biofuels (and BioProducts) Process Demonstration Unit, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Vicki S. Thompson
- Energy and Environmental Science and Technology, Idaho National Laboratory, 2525 North Fremont Ave, Idaho Falls, ID 83415 USA
| | - Feng Xu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551 USA
| | - Akash Narani
- Advanced Biofuels (and BioProducts) Process Demonstration Unit, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Qian He
- Advanced Biofuels (and BioProducts) Process Demonstration Unit, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Deepti Tanjore
- Advanced Biofuels (and BioProducts) Process Demonstration Unit, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Todd R. Pray
- Advanced Biofuels (and BioProducts) Process Demonstration Unit, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Blake A. Simmons
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Seema Singh
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, 7011 East Avenue, Livermore, CA 94551 USA
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20
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Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons BA, Singer SW, Magnuson JK, Arkin AP, Skerker JM, Gladden JM. Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts. Biotechnol Biofuels 2017; 10:241. [PMID: 29075325 PMCID: PMC5651578 DOI: 10.1186/s13068-017-0927-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/10/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND Economical conversion of lignocellulosic biomass into biofuels and bioproducts is central to the establishment of a robust bioeconomy. This requires a conversion host that is able to both efficiently assimilate the major lignocellulose-derived carbon sources and divert their metabolites toward specific bioproducts. RESULTS In this study, the carotenogenic yeast Rhodosporidium toruloides was examined for its ability to convert lignocellulose into two non-native sesquiterpenes with biofuel (bisabolene) and pharmaceutical (amorphadiene) applications. We found that R. toruloides can efficiently convert a mixture of glucose and xylose from hydrolyzed lignocellulose into these bioproducts, and unlike many conventional production hosts, its growth and productivity were enhanced in lignocellulosic hydrolysates relative to purified substrates. This organism was demonstrated to have superior growth in corn stover hydrolysates prepared by two different pretreatment methods, one using a novel biocompatible ionic liquid (IL) choline α-ketoglutarate, which produced 261 mg/L of bisabolene at bench scale, and the other using an alkaline pretreatment, which produced 680 mg/L of bisabolene in a high-gravity fed-batch bioreactor. Interestingly, R. toruloides was also observed to assimilate p-coumaric acid liberated from acylated grass lignin in the IL hydrolysate, a finding we verified with purified substrates. R. toruloides was also able to consume several additional compounds with aromatic motifs similar to lignin monomers, suggesting that this organism may have the metabolic potential to convert depolymerized lignin streams alongside lignocellulosic sugars. CONCLUSIONS This study highlights the natural compatibility of R. toruloides with bioprocess conditions relevant to lignocellulosic biorefineries and demonstrates its ability to produce non-native terpenes.
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Affiliation(s)
- Junko Yaegashi
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354 USA
| | - James Kirby
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720 USA
| | - Masakazu Ito
- Energy Biosciences Institute, 2151 Berkeley Way, Berkeley, CA 94704 USA
| | - Jian Sun
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551 USA
| | - Tanmoy Dutta
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551 USA
| | - Mona Mirsiaghi
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - Eric R. Sundstrom
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - Alberto Rodriguez
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551 USA
| | - Edward Baidoo
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - Deepti Tanjore
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - Todd Pray
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - Kenneth Sale
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551 USA
| | - Seema Singh
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551 USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720 USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - Steven W. Singer
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - Jon K. Magnuson
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354 USA
| | - Adam P. Arkin
- Energy Biosciences Institute, 2151 Berkeley Way, Berkeley, CA 94704 USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Jeffrey M. Skerker
- Energy Biosciences Institute, 2151 Berkeley Way, Berkeley, CA 94704 USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720 USA
| | - John M. Gladden
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608 USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551 USA
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Schuerg T, Prahl JP, Gabriel R, Harth S, Tachea F, Chen CS, Miller M, Masson F, He Q, Brown S, Mirshiaghi M, Liang L, Tom LM, Tanjore D, Sun N, Pray TR, Singer SW. Xylose induces cellulase production in Thermoascus aurantiacus. Biotechnol Biofuels 2017; 10:271. [PMID: 29167701 PMCID: PMC5688616 DOI: 10.1186/s13068-017-0965-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/07/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Lignocellulosic biomass is an important resource for renewable production of biofuels and bioproducts. Enzymes that deconstruct this biomass are critical for the viability of biomass-based biofuel production processes. Current commercial enzyme mixtures have limited thermotolerance. Thermophilic fungi may provide enzyme mixtures with greater thermal stability leading to more robust processes. Understanding the induction of biomass-deconstructing enzymes in thermophilic fungi will provide the foundation for strategies to construct hyper-production strains. RESULTS Induction of cellulases using xylan was demonstrated during cultivation of the thermophilic fungus Thermoascus aurantiacus. Simulated fed-batch conditions with xylose induced comparable levels of cellulases. These fed-batch conditions were adapted to produce enzymes in 2 and 19 L bioreactors using xylose and xylose-rich hydrolysate from dilute acid pretreatment of corn stover. Enzymes from T. aurantiacus that were produced in the xylose-fed bioreactor demonstrated comparable performance in the saccharification of deacetylated, dilute acid-pretreated corn stover when compared to a commercial enzyme mixture at 50 °C. The T. aurantiacus enzymes retained this activity at of 60 °C while the commercial enzyme mixture was largely inactivated. CONCLUSIONS Xylose induces both cellulase and xylanase production in T. aurantiacus and was used to produce enzymes at up to the 19 L bioreactor scale. The demonstration of induction by xylose-rich hydrolysate and saccharification of deacetylated, dilute acid-pretreated corn stover suggests a scenario to couple biomass pretreatment with onsite enzyme production in a biorefinery. This work further demonstrates the potential for T. aurantiacus as a thermophilic platform for cellulase development.
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Affiliation(s)
- Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Chyi-Shin Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Matthew Miller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Fabrice Masson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Qian He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Sarah Brown
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Mona Mirshiaghi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ling Liang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Lauren M. Tom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ning Sun
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Todd R. Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
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Sun N, Xu F, Sathitsuksanoh N, Thompson VS, Cafferty K, Li C, Tanjore D, Narani A, Pray TR, Simmons BA, Singh S. Blending municipal solid waste with corn stover for sugar production using ionic liquid process. Bioresour Technol 2015; 186:200-206. [PMID: 25817030 DOI: 10.1016/j.biortech.2015.02.087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/20/2015] [Accepted: 02/21/2015] [Indexed: 06/04/2023]
Abstract
Municipal solid waste (MSW) represents an attractive cellulosic resource for sustainable fuel production. However, its heterogeneity is the major barrier to efficient conversion to biofuels. MSW paper mix was generated and blended with corn stover (CS). It has been shown that both of them can be efficiently pretreated in certain ionic liquids (ILs) with high yields of fermentable sugars. After pretreatment in 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]), over 80% glucose has been released with enzymatic saccharification. We have also applied an enzyme-free process by adding mineral acid and water directly into the IL/biomass slurry to induce hydrolysis. With the acidolysis process in 1-ethyl-3-methylimidazolium chloride ([C2C1Im]Cl), up to 80% glucose and 90% xylose are released. There is a correlation between the viscosity profile and hydrolysis efficiency; low viscosity of the hydrolysate generally corresponds to high sugar yields. Overall, the results indicate the feasibility of incorporating MSW as a robust blending agent for biorefineries.
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Affiliation(s)
- Ning Sun
- Deconstruction Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Feng Xu
- Deconstruction Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Biological and Materials Sciences Center, Sandia National Laboratories, Livermore, CA, USA
| | - Noppadon Sathitsuksanoh
- Deconstruction Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vicki S Thompson
- Idaho National Laboratory, Biological and Chemical Processing Department, Idaho Falls, ID, USA
| | - Kara Cafferty
- Idaho National Laboratory, Environmental Engineering and Technology, Idaho Falls, ID, USA
| | - Chenlin Li
- Advanced Biofuel Process Demonstration Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Deepti Tanjore
- Advanced Biofuel Process Demonstration Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Akash Narani
- Advanced Biofuel Process Demonstration Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Todd R Pray
- Advanced Biofuel Process Demonstration Unit, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Biological and Materials Sciences Center, Sandia National Laboratories, Livermore, CA, USA
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Biological and Materials Sciences Center, Sandia National Laboratories, Livermore, CA, USA
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23
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Gardner JL, He W, Li C, Wong J, Sale KL, Simmons BA, Singh S, Tanjore D. Calorimetric evaluation indicates that lignin conversion to advanced biofuels is vital to improving energy yields. RSC Adv 2015. [DOI: 10.1039/c5ra01503k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Energy density measurements using bomb calorimetry were applied along with mass yields to calculate energy yields from and lignocellulosic feedstocks conversion processes.
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Affiliation(s)
- James L. Gardner
- Advanced Biofuels Process Demonstration Unit
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - Wei He
- Advanced Biofuels Process Demonstration Unit
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - Chenlin Li
- Advanced Biofuels Process Demonstration Unit
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - Jessica Wong
- Advanced Biofuels Process Demonstration Unit
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
| | - Kenneth L. Sale
- Deconstruction Division
- Joint BioEnergy Institute
- Emeryville
- USA
- Biological and Material Science Center
| | - Blake A. Simmons
- Deconstruction Division
- Joint BioEnergy Institute
- Emeryville
- USA
- Biological and Material Science Center
| | - Seema Singh
- Deconstruction Division
- Joint BioEnergy Institute
- Emeryville
- USA
- Biological and Material Science Center
| | - Deepti Tanjore
- Advanced Biofuels Process Demonstration Unit
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
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24
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Li C, Tanjore D, He W, Wong J, Gardner JL, Sale KL, Simmons BA, Singh S. Scale-up and evaluation of high solid ionic liquid pretreatment and enzymatic hydrolysis of switchgrass. Biotechnol Biofuels 2013; 6:154. [PMID: 24160440 PMCID: PMC3817576 DOI: 10.1186/1754-6834-6-154] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 10/07/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND Ionic liquid (IL) pretreatment is receiving significant attention as a potential process that enables fractionation of lignocellulosic biomass and produces high yields of fermentable sugars suitable for the production of renewable fuels. However, successful optimization and scale up of IL pretreatment involves challenges, such as high solids loading, biomass handling and transfer, washing of pretreated solids and formation of inhibitors, which are not addressed during the development stages at the small scale in a laboratory environment. As a first in the research community, the Joint BioEnergy Institute, in collaboration with the Advanced Biofuels Process Demonstration Unit, a Department of Energy funded facility that supports academic and industrial entities in scaling their novel biofuels enabling technologies, have performed benchmark studies to identify key challenges associated with IL pretreatment using 1-ethyl-3-methylimidazolium acetate and subsequent enzymatic saccharification beyond bench scale. RESULTS Using switchgrass as the model feedstock, we have successfully executed 600-fold, relative to the bench scale (6 L vs 0.01 L), scale-up of IL pretreatment at 15% (w/w) biomass loading. Results show that IL pretreatment at 15% biomass generates a product containing 87.5% of glucan, 42.6% of xylan and only 22.8% of lignin relative to the starting material. The pretreated biomass is efficiently converted into monosaccharides during subsequent enzymatic hydrolysis at 10% loading over a 150-fold scale of operations (1.5 L vs 0.01 L) with 99.8% fermentable sugar conversion. The yield of glucose and xylose in the liquid streams were 94.8% and 62.2%, respectively, and the hydrolysate generated contains high titers of fermentable sugars (62.1 g/L of glucose and 5.4 g/L cellobiose). The overall glucan and xylan balance from pretreatment and saccharification were 95.0% and 77.1%, respectively. Enzymatic inhibition by [C2mim][OAc] at high solids loadings requires further process optimization to obtain higher yields of fermentable sugars. CONCLUSION Results from this initial scale up evaluation indicate that the IL-based conversion technology can be effectively scaled to larger operations and the current study establishes the first scaling parameters for this conversion pathway but several issues must be addressed before a commercially viable technology can be realized, most notably reduction in water consumption and efficient IL recycle.
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Affiliation(s)
- Chenlin Li
- Advanced Biofuels Process Demonstration Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Deepti Tanjore
- Advanced Biofuels Process Demonstration Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Wei He
- Advanced Biofuels Process Demonstration Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Jessica Wong
- Advanced Biofuels Process Demonstration Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - James L Gardner
- Advanced Biofuels Process Demonstration Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Kenneth L Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA, USA
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA, USA
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