1
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Gauttam R, Eng T, Zhao Z, Ul Ain Rana Q, Simmons BA, Yoshikuni Y, Mukhopadhyay A, Singer SW. Development of genetic tools for heterologous protein expression in a pentose-utilizing environmental isolate of Pseudomonas putida. Microb Biotechnol 2023; 16:645-661. [PMID: 36691869 PMCID: PMC9948227 DOI: 10.1111/1751-7915.14205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 01/25/2023] Open
Abstract
Pseudomonas putida has emerged as a promising host for the conversion of biomass-derived sugars and aromatic intermediates into commercially relevant biofuels and bioproducts. Most of the strain development studies previously published have focused on P. putida KT2440, which has been engineered to produce a variety of non-native bioproducts. However, P. putida is not capable of metabolizing pentose sugars, which can constitute up to 25% of biomass hydrolysates. Related P. putida isolates that metabolize a larger fraction of biomass-derived carbon may be attractive as complementary hosts to P. putida KT2440. Here we describe genetic tool development for P. putida M2, a soil isolate that can metabolize pentose sugars. The functionality of five inducible promoter systems and 12 ribosome binding sites was assessed to regulate gene expression. The utility of these expression systems was confirmed by the production of indigoidine from C6 and C5 sugars. Chromosomal integration and expression of non-native genes was achieved by using chassis-independent recombinase-assisted genome engineering (CRAGE) for single-step gene integration of biosynthetic pathways directly into the genome of P. putida M2. These genetic tools provide a foundation to develop hosts complementary to P. putida KT2440 and expand the ability of this versatile microbial group to convert biomass to bioproducts.
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Affiliation(s)
- Rahul Gauttam
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Thomas Eng
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhiying Zhao
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Qurrat Ul Ain Rana
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yasuo Yoshikuni
- Joint Genome Institute, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- The Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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2
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Chang D, Wang C, Ul Islam Z, Yu Z. Omics analysis coupled with gene editing revealed potential transporters and regulators related to levoglucosan metabolism efficiency of the engineered Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:2. [PMID: 35418138 PMCID: PMC8753852 DOI: 10.1186/s13068-022-02102-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/02/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Bioconversion of levoglucosan, a promising sugar derived from the pyrolysis of lignocellulose, into biofuels and chemicals can reduce our dependence on fossil-based raw materials. However, this bioconversion process in microbial strains is challenging due to the lack of catalytic enzyme relevant to levoglucosan metabolism, narrow production ranges of the native strains, poor cellular transport rate of levoglucosan, and inhibition of levoglucosan metabolism by other sugars co-existing in the lignocellulose pyrolysate. The heterologous expression of eukaryotic levoglucosan kinase gene in suitable microbial hosts like Escherichia coli could overcome the first two challenges to some extent; however, no research has been dedicated to resolving the last two issues till now.
Results
Aiming to resolve the two unsolved problems, we revealed that seven ABC transporters (XylF, MalE, UgpB, UgpC, YtfQ, YphF, and MglA), three MFS transporters (KgtP, GntT, and ActP), and seven regulatory proteins (GalS, MhpR, YkgD, Rsd, Ybl162, MalM, and IraP) in the previously engineered levoglucosan-utilizing and ethanol-producing E. coli LGE2 were induced upon exposure to levoglucosan using comparative proteomics technique, indicating these transporters and regulators were involved in the transport and metabolic regulation of levoglucosan. The proteomics results were further verified by transcriptional analysis of 16 randomly selected genes. Subsequent gene knockout and complementation tests revealed that ABC transporter XylF was likely to be a levoglucosan transporter. Molecular docking showed that levoglucosan can bind to the active pocket of XylF by seven H-bonds with relatively strong strength.
Conclusion
This study focusing on the omics discrepancies between the utilization of levoglucosan and non-levoglucosan sugar, could provide better understanding of levoglucosan transport and metabolism mechanisms by identifying the transporters and regulators related to the uptake and regulation of levoglucosan metabolism. The protein database generated from this study could be used for further screening and characterization of the transporter(s) and regulator(s) for downstream enzymatic/genetic engineering work, thereby facilitating more efficient microbial utilization of levoglucosan for biofuels and chemicals production in future.
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3
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Chang D, Wang C, Ndayisenga F, Yu Z. Mutations in adaptively evolved Escherichia coli LGE2 facilitated the cost-effective upgrading of undetoxified bio-oil to bioethanol fuel. BIORESOUR BIOPROCESS 2021; 8:105. [PMID: 38650237 PMCID: PMC10991953 DOI: 10.1186/s40643-021-00459-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Levoglucosan is a promising sugar present in the lignocellulose pyrolysis bio-oil, which is a renewable and environment-friendly source for various value-added productions. Although many microbial catalysts have been engineered to produce biofuels and chemicals from levoglucosan, the demerits that these biocatalysts can only utilize pure levoglucosan while inhibited by the inhibitors co-existing with levoglucosan in the bio-oil have greatly limited the industrial-scale application of these biocatalysts in lignocellulose biorefinery. In this study, the previously engineered Escherichia coli LGE2 was evolved for enhanced inhibitor tolerance using long-term adaptive evolution under the stress of multiple inhibitors and finally, a stable mutant E. coli-H was obtained after ~ 374 generations' evolution. In the bio-oil media with an extremely acidic pH of 3.1, E. coli-H with high inhibitor tolerance exhibited remarkable levoglucosan consumption and ethanol production abilities comparable to the control, while the growth of the non-evolved strain was completely blocked even when the pH was adjusted to 7.0. Finally, 8.4 g/L ethanol was achieved by E. coli-H in the undetoxified bio-oil media with ~ 2.0% (w/v) levoglucosan, reaching 82% of the theoretical yield. Whole-genome re-sequencing to monitor the acquisition of mutations identified 4 new mutations within the globally regulatory genes rssB, yqhA, and basR, and the - 10 box of the putative promoter of yqhD-dgkA operon. Especially, yqhA was the first time to be revealed as a gene responsible for inhibitor tolerance. The mutations were all responsible for improved fitness, while basR mutation greatly contributed to the fitness improvement of E. coli-H. This study, for the first time, generated an inhibitor-tolerant levoglucosan-utilizing strain that could produce cost-effective bioethanol from the toxic bio-oil without detoxification process, and provided important experimental evidence and valuable genetic/proteinic information for the development of other robust microbial platforms involved in lignocellulose biorefining processes.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Cong Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, 100085, People's Republic of China.
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4
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Weimer A, Kohlstedt M, Volke DC, Nikel PI, Wittmann C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl Microbiol Biotechnol 2020; 104:7745-7766. [PMID: 32789744 PMCID: PMC7447670 DOI: 10.1007/s00253-020-10811-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022]
Abstract
Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. KEY POINTS: • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
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5
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Dvořák P, Kováč J, de Lorenzo V. Biotransformation of d-xylose to d-xylonate coupled to medium-chain-length polyhydroxyalkanoate production in cellobiose-grown Pseudomonas putida EM42. Microb Biotechnol 2020; 13:1273-1283. [PMID: 32363744 PMCID: PMC7264884 DOI: 10.1111/1751-7915.13574] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/05/2020] [Accepted: 03/25/2020] [Indexed: 12/23/2022] Open
Abstract
Co-production of two or more desirable compounds from low-cost substrates by a single microbial catalyst could greatly improve the economic competitiveness of many biotechnological processes. However, reports demonstrating the adoption of such co-production strategy are still scarce. In this study, the ability of genome-edited strain Pseudomonas putida EM42 to simultaneously valorize d-xylose and d-cellobiose - two important lignocellulosic carbohydrates - by converting them into the platform chemical d-xylonate and medium-chain-length polyhydroxyalkanoates, respectively, was investigated. Biotransformation experiments performed with P. putida resting cells showed that promiscuous periplasmic glucose oxidation route can efficiently generate extracellular xylonate with a high yield. Xylose oxidation was subsequently coupled to the growth of P. putida with cytoplasmic β-glucosidase BglC from Thermobifida fusca on d-cellobiose. This disaccharide turned out to be a better co-substrate for xylose-to-xylonate biotransformation than monomeric glucose. This was because unlike glucose, cellobiose did not block oxidation of the pentose by periplasmic glucose dehydrogenase Gcd, but, similarly to glucose, it was a suitable substrate for polyhydroxyalkanoate formation in P. putida. Co-production of extracellular xylose-born xylonate and intracellular cellobiose-born medium-chain-length polyhydroxyalkanoates was established in proof-of-concept experiments with P. putida grown on the disaccharide. This study highlights the potential of P. putida EM42 as a microbial platform for the production of xylonate, identifies cellobiose as a new substrate for mcl-PHA production, and proposes a fresh strategy for the simultaneous valorization of xylose and cellobiose.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology)Faculty of ScienceMasaryk UniversityKamenice 753/562500BrnoCzech Republic
| | - Jozef Kováč
- Department of Experimental Biology (Section of Microbiology)Faculty of ScienceMasaryk UniversityKamenice 753/562500BrnoCzech Republic
| | - Víctor de Lorenzo
- Systems and Synthetic Biology ProgramCentro Nacional de Biotecnología CNB‐CSICCantoblancoDarwin 328049MadridSpain
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6
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Williamson JJ, Bahrin N, Hardiman EM, Bugg TDH. Production of Substituted Styrene Bioproducts from Lignin and Lignocellulose Using Engineered Pseudomonas putida KT2440. Biotechnol J 2020; 15:e1900571. [PMID: 32488970 DOI: 10.1002/biot.201900571] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/13/2020] [Indexed: 11/09/2022]
Abstract
Ferulic acid is a renewable chemical found in lignocellulose from grasses such as wheat straw and sugarcane. Pseudomonas putida is able to liberate and metabolize ferulic acid from plant biomass. Deletion of the hydroxycinnamoyl-CoA hydratase-lyase gene (ech) produced a strain of P. putida unable to utilize ferulic and p-coumaric acid, which is able to accumulate ferulic acid and p-coumaric acid from wheat straw or sugar cane bagasse. Further engineering of this strain saw the replacement of ech with the phenolic acid decarboxylase padC, which converts p-coumaric and ferulic acid into 4-vinylphenol and the flavor agent 4-vinylguaiacol, respectively. The engineered strain containing padC is able to generate 4-vinylguaiacol and 4-vinylphenol from media containing lignocellulose or Green Value Protobind lignin as feedstock, and does not require the addition of an exogenous inducer molecule. Biopolymerization of 4-vinylguaiacol and 4-vinylcatechol styrene products is also carried out, using Trametes versicolor laccase, to generate "biopolystyrene" materials on small scale.
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Affiliation(s)
| | - Nurfariza Bahrin
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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7
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Peabody GL, Elmore JR, Martinez-Baird J, Guss AM. Engineered Pseudomonas putida KT2440 co-utilizes galactose and glucose. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:295. [PMID: 31890023 PMCID: PMC6927180 DOI: 10.1186/s13068-019-1627-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/04/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Efficient conversion of plant biomass to commodity chemicals is an important challenge that needs to be solved to enable a sustainable bioeconomy. Deconstruction of biomass to sugars and lignin yields a wide variety of low molecular weight carbon substrates that need to be funneled to product. Pseudomonas putida KT2440 has emerged as a potential platform for bioconversion of lignin and the other components of plant biomass. However, P. putida is unable to natively utilize several of the common sugars in hydrolysate streams, including galactose. RESULTS In this work, we integrated a De Ley-Doudoroff catabolic pathway for galactose catabolism into the chromosome of P. putida KT2440, using genes from several different organisms. We found that the galactonate catabolic pathway alone (DgoKAD) supported slow growth of P. putida on galactose. Further integration of genes to convert galactose to galactonate and to optimize the transporter expression level resulted in a growth rate of 0.371 h-1. Additionally, the best-performing strain was demonstrated to co-utilize galactose with glucose. CONCLUSIONS We have engineered P. putida to catabolize galactose, which will allow future engineered strains to convert more plant biomass carbon to products of interest. Further, by demonstrating co-utilization of glucose and galactose, continuous bioconversion processes for mixed sugar streams are now possible.
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Affiliation(s)
- George L. Peabody
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Joshua R. Elmore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Present Address: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | | | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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8
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Zhao C, Zhang Y, Li Y. Production of fuels and chemicals from renewable resources using engineered Escherichia coli. Biotechnol Adv 2019; 37:107402. [DOI: 10.1016/j.biotechadv.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 05/23/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023]
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9
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Arnold S, Henkel M, Wanger J, Wittgens A, Rosenau F, Hausmann R. Heterologous rhamnolipid biosynthesis by P. putida KT2440 on bio-oil derived small organic acids and fractions. AMB Express 2019; 9:80. [PMID: 31152276 PMCID: PMC6544668 DOI: 10.1186/s13568-019-0804-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 05/25/2019] [Indexed: 11/20/2022] Open
Abstract
In many cases in industrial biotechnology, substrate costs make up a major part of the overall production costs. One strategy to achieve more cost-efficient processes in general is to exploit cheaper sources of substrate. Small organic acids derived from fast pyrolysis of lignocellulosic biomass represent a significant proportion of microbially accessible carbon in bio-oil. However, using bio-oil for microbial cultivation is a highly challenging task due to its strong adverse effects on microbial growth as well as its complex composition. In this study, the suitability of bio-oil as a substrate for industrial biotechnology was investigated with special focus on organic acids. For this purpose, using the example of the genetically engineered, non-pathogenic bacterium Pseudomonas putida KT2440 producing mono-rhamnolipids, cultivation on small organic acids derived from fast pyrolysis of lignocellulosic biomass, as well as on bio-oil fractions, was investigated and evaluated. As biosurfactants, rhamnolipids represent a potential bulk product of industrial biotechnology where substitution of traditional carbon sources is of conceivable interest. Results suggest that maximum achievable productivities as well as substrate-to-biomass yields are in a comparable range for glucose, acetate, as well as the mixture of acetate, formate and propionate. Similar yields were obtained for a pretreated bio-oil fraction, which was used as reference real raw material, although with significantly lower titers. As such, the reported process constitutes a proof-of-principle for using bio-oil as a potential cost-effective alternative carbon source in a future bio-based economy.
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10
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Butt FI, Muhammad N, Hamid A, Moniruzzaman M, Sharif F. Recent progress in the utilization of biosynthesized polyhydroxyalkanoates for biomedical applications – Review. Int J Biol Macromol 2018; 120:1294-1305. [DOI: 10.1016/j.ijbiomac.2018.09.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/20/2018] [Accepted: 09/02/2018] [Indexed: 01/10/2023]
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11
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Ghosh A, Bai X, Brown RC. Solubilized Carbohydrate Production by Acid-Catalyzed Depolymerization of Cellulose in Polar Aprotic Solvents. ChemistrySelect 2018. [DOI: 10.1002/slct.201800764] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Arpa Ghosh
- Department of Chemical and Biological Engineering; Iowa State University, Ames; Iowa USA 50011
- Bioeconomy Institute; Iowa State University, Ames; Iowa USA 50011
| | - Xianglan Bai
- Department of Mechanical Engineering; Iowa State University, Ames; Iowa USA 50011
| | - Robert C. Brown
- Department of Mechanical Engineering; Iowa State University, Ames; Iowa USA 50011
- Bioeconomy Institute; Iowa State University, Ames; Iowa USA 50011
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12
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Liu D, Kim KH, Sun J, Simmons BA, Singh S. Cascade Production of Lactic Acid from Universal Types of Sugars Catalyzed by Lanthanum Triflate. CHEMSUSCHEM 2018; 11:598-604. [PMID: 29178399 DOI: 10.1002/cssc.201701902] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Lignocellulosic biomass conversion into value-added platform chemicals in the non-toxic, water-tolerant Lewis acid, and water solutions bears the hallmark of green chemistry. Lactic acid derived from biomass is an important chemical building block for biodegradable polymers such as polylactide. Herein, a universal method of converting lignocellulosic sugars into lactic acid using catalytic amount of water-stable Lewis acid La(OTf)3 is demonstrated. The lignocellulosic sugars studied in this work include 1) pyrolytic sugars from pyrolysis oil, and 2) sugars derived from ionic liquid (IL)-pretreated biomass. Under moderate conditions (250 °C, 1 h), levoglucosan (major pyrolytic sugar), glucose, and xylose were converted into lactic acid with carbon-based molar yields of 75, 74, and 61 %, respectively. Furthermore, roughly 49 mol % (based on levoglucosan) and 74 wt % (relative to pretreated biomass) of lactic acid were obtained from the conversion of pyrolytic sugars and sugar-rich fraction after lignin removal from switchgrass, respectively. To our knowledge, this is the first reported conversion of pyrolytic sugar into lactic acid by chemocatalysis and also lignocellulosic sugars are converted into lactic acid without hydrolysis. This approach could potentially be extended to other lignocellulosic sugars after simple removal of lignin from biomass pretreatment, rendering moderate to high yields of lactic acid.
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Affiliation(s)
- Dajiang Liu
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Kwang Ho Kim
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Jian Sun
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Seema Singh
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA, 94551, USA
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
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13
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Hemmerich J, Noack S, Wiechert W, Oldiges M. Microbioreactor Systems for Accelerated Bioprocess Development. Biotechnol J 2018; 13:e1700141. [PMID: 29283217 DOI: 10.1002/biot.201700141] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/15/2017] [Indexed: 12/14/2022]
Abstract
In recent years, microbioreactor (MBR) systems have evolved towards versatile bioprocess engineering tools. They provide a unique solution to combine higher experimental throughput with extensive bioprocess monitoring and control, which is indispensable to develop economically and ecologically competitive bioproduction processes. MBR systems are based either on down-scaled stirred tank reactors or on advanced shaken microtiter plate cultivation devices. Importantly, MBR systems make use of optical measurements for non-invasive, online monitoring of important process variables like biomass concentration, dissolved oxygen, pH, and fluorescence. The application range of MBR systems can be further increased by integration into liquid handling robots, enabling automatization and, thus standardization, of various handling and operation procedures. Finally, the tight integration of quantitative strain phenotyping with bioprocess development under industrially relevant conditions greatly increases the probability of finding the right combination of producer strain and bioprocess control strategy. This review will discuss the current state of the art in the field of MBR systems and we can readily conclude that their importance for industrial biotechnology will further increase in the near future.
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Affiliation(s)
- Johannes Hemmerich
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Wiechert
- RWTH Aachen University, Computational Systems Biotechnology (AVT.CSB), Forckenbeckstraße 51, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Marco Oldiges
- Forschungszentrum Jülich, Institute of Bio- and Geosciences - Biotechnology (IBG-1), Wilhelm-Johnen Straße 1, 52425, Jülich, Germany.,RWTH Aachen University, Institute of Biotechnology, Worringer Weg 3, 52074 Aachen, Germany.,Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, 52425 Jülich, Germany
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14
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Arnold S, Moss K, Henkel M, Hausmann R. Biotechnological Perspectives of Pyrolysis Oil for a Bio-Based Economy. Trends Biotechnol 2017; 35:925-936. [DOI: 10.1016/j.tibtech.2017.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/24/2017] [Accepted: 06/06/2017] [Indexed: 12/18/2022]
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15
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Meile K, Zhurinsh A, Viksna A. Comparison of photodiode array, evaporative light scattering, and single-quadrupole mass spectrometric detection methods for the UPLC analysis of pyrolysis liquids. J LIQ CHROMATOGR R T 2017. [DOI: 10.1080/10826076.2017.1308378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Kristine Meile
- Department of Technological Research, Latvian State Institute of Wood Chemistry, Riga, Latvia
- Department of Analytical Chemistry, University of Latvia, Riga, Latvia
| | - Aivars Zhurinsh
- Department of Technological Research, Latvian State Institute of Wood Chemistry, Riga, Latvia
| | - Arturs Viksna
- Department of Analytical Chemistry, University of Latvia, Riga, Latvia
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Guarnieri MT, Ann Franden M, Johnson CW, Beckham GT. Conversion and assimilation of furfural and 5-(hydroxymethyl)furfural by Pseudomonas putida KT2440. Metab Eng Commun 2017; 4:22-28. [PMID: 29468129 PMCID: PMC5779731 DOI: 10.1016/j.meteno.2017.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/28/2016] [Accepted: 02/05/2017] [Indexed: 12/03/2022] Open
Abstract
The sugar dehydration products, furfural and 5-(hydroxymethyl)furfural (HMF), are commonly formed during high-temperature processing of lignocellulose, most often in thermochemical pretreatment, liquefaction, or pyrolysis. Typically, these two aldehydes are considered major inhibitors in microbial conversion processes. Many microbes can convert these compounds to their less toxic, dead-end alcohol counterparts, furfuryl alcohol and 5-(hydroxymethyl)furfuryl alcohol. Recently, the genes responsible for aerobic catabolism of furfural and HMF were discovered in Cupriavidus basilensis HMF14 to enable complete conversion of these compounds to the TCA cycle intermediate, 2-oxo-glutarate. In this work, we engineer the robust soil microbe, Pseudomonas putida KT2440, to utilize furfural and HMF as sole carbon and energy sources via complete genomic integration of the 12 kB hmf gene cluster previously reported from Burkholderia phytofirmans. The common intermediate, 2-furoic acid, is shown to be a bottleneck for both furfural and HMF metabolism. When cultured on biomass hydrolysate containing representative amounts of furfural and HMF from dilute-acid pretreatment, the engineered strain outperforms the wild type microbe in terms of reduced lag time and enhanced growth rates due to catabolism of furfural and HMF. Overall, this study demonstrates that an approach for biological conversion of furfural and HMF, relative to the typical production of dead-end alcohols, enables both enhanced carbon conversion and substantially improves tolerance to hydrolysate inhibitors. This approach should find general utility both in emerging aerobic processes for the production of fuels and chemicals from biomass-derived sugars and in the biological conversion of high-temperature biomass streams from liquefaction or pyrolysis where furfural and HMF are much more abundant than in biomass hydrolysates from pretreatment. HMF and furfural are common microbial inhibitors in biomass conversion. HMF and furfural gene cluster was isolated from Burkholderia phytofirmans.. We heterologously express the HMF/furfural gene cluster in Pseudomonas putida.. Expression enables cultivation on HMF and furfural as a sole carbon source. Expression also enables enhanced conversion on lignocellulosic hydrolysate.
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Affiliation(s)
- Michael T Guarnieri
- National Bioenergy Center, National Renewable Energy Laboratory, Golden CO 80401
| | - Mary Ann Franden
- National Bioenergy Center, National Renewable Energy Laboratory, Golden CO 80401
| | | | - Gregg T Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden CO 80401
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Wendisch VF, Brito LF, Gil Lopez M, Hennig G, Pfeifenschneider J, Sgobba E, Veldmann KH. The flexible feedstock concept in Industrial Biotechnology: Metabolic engineering of Escherichia coli, Corynebacterium glutamicum, Pseudomonas, Bacillus and yeast strains for access to alternative carbon sources. J Biotechnol 2016; 234:139-157. [DOI: 10.1016/j.jbiotec.2016.07.022] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 11/28/2022]
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Xiong X, Lian J, Yu X, Garcia-Perez M, Chen S. Engineering levoglucosan metabolic pathway in Rhodococcus jostii RHA1 for lipid production. J Ind Microbiol Biotechnol 2016; 43:1551-1560. [PMID: 27558782 DOI: 10.1007/s10295-016-1832-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/15/2016] [Indexed: 11/28/2022]
Abstract
Oleaginous strains of Rhodococcus including R. jostii RHA1 have attracted considerable attention due to their ability to accumulate triacylglycerols (TAGs), robust growth properties and genetic tractability. In this study, a novel metabolic pathway was introduced into R. jostii by heterogenous expression of the well-characterized gene, lgk encoding levoglucosan kinase from Lipomyces starkeyi YZ-215. This enables the recombinant R. jostii RHA1 to produce TAGs from the anhydrous sugar, levoglucosan, which can be generated efficiently as the major molecule from the pyrolysis of cellulose. The recombinant R. jostii RHA1 could grow on levoglucosan as the sole carbon source, and the consumption rate of levoglucosan was determined. Furthermore, expression of one more copy of lgk increased the enzymatic activity of LGK in the recombinant. However, the growth performance of the recombinant bearing two copies of lgk on levoglucosan was not improved. Although expression of lgk in the recombinants was not repressed by the glucose present in the media, glucose in the sugar mixture still affected consumption of levoglucosan. Under nitrogen limiting conditions, lipid produced from levoglucosan by the recombinant bearing lgk was up to 43.54 % of the cell dry weight, which was comparable to the content of lipid accumulated from glucose. This work demonstrated the technical feasibility of producing lipid from levoglucosan, an anhydrosugar derived from the pyrolysis of lignocellulosic materials, by the genetically modified rhodococci strains.
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Affiliation(s)
- Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, L. J. Smith Hall, P.O. Box 646120, Pullman, WA, 99164-6120, USA
| | - Jieni Lian
- Department of Biological Systems Engineering, Washington State University, L. J. Smith Hall, P.O. Box 646120, Pullman, WA, 99164-6120, USA.,Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Xiaochen Yu
- Department of Biological Systems Engineering, Washington State University, L. J. Smith Hall, P.O. Box 646120, Pullman, WA, 99164-6120, USA.,Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Manuel Garcia-Perez
- Department of Biological Systems Engineering, Washington State University, L. J. Smith Hall, P.O. Box 646120, Pullman, WA, 99164-6120, USA
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, L. J. Smith Hall, P.O. Box 646120, Pullman, WA, 99164-6120, USA.
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Bacik JP, Jarboe LR. Bioconversion of anhydrosugars: Emerging concepts and strategies. IUBMB Life 2016; 68:700-8. [PMID: 27416973 DOI: 10.1002/iub.1533] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 06/18/2016] [Indexed: 11/12/2022]
Abstract
As methods for the use of anhydrosugars in chemical and biofuel production continue to develop, our collective knowledge of anhydrosugar processing enzymes continues to improve, including their mechanistic details, structural dynamics and modes of substrate binding. Of particular interest, anhydrosugar kinases, such as levoglucosan kinase (LGK) and 1,6-anhydro-N-acetylmuramic acid kinase (AnmK), utilize an unusual mechanism whereby the sugar substrate is both cleaved and phosphorylated. The phosphorylated sugar can then be routed to other metabolic pathways, thereby allowing its further bioconversion. Advanced engineering efforts to improve the catalytic efficiency and stability of LGK have been steadily progressing. Other enzymes that cleave the glycosidic bond of disaccharide sugars containing an anhydrosugar component are also being identified and characterized. Accordingly, the potential future use of these enzymes in large-scale production strategies is becoming increasingly viable. Here, a mini-review of the observed characteristics of anhydrosugar processing enzymes is presented along with recent developments in the bioconversion of these sugars. © 2016 IUBMB Life 68(9):700-708, 2016.
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Affiliation(s)
- John-Paul Bacik
- Department of Chemistry, Princeton University, Princeton, New Jersey, 08544
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011
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