201
|
Schwanemann T, Otto M, Wierckx N, Wynands B. Pseudomonasas Versatile Aromatics Cell Factory. Biotechnol J 2020; 15:e1900569. [DOI: 10.1002/biot.201900569] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/08/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Tobias Schwanemann
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Maike Otto
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Nick Wierckx
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| | - Benedikt Wynands
- Institute of Bio‐ and Geosciences, IBG‐1: Biotechnology Forschungszentrum Jülich, GmbH 52425 Jülich Germany
| |
Collapse
|
202
|
|
203
|
Characterization of alkylguaiacol-degrading cytochromes P450 for the biocatalytic valorization of lignin. Proc Natl Acad Sci U S A 2020; 117:25771-25778. [PMID: 32989155 DOI: 10.1073/pnas.1916349117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cytochrome P450 enzymes have tremendous potential as industrial biocatalysts, including in biological lignin valorization. Here, we describe P450s that catalyze the O-demethylation of lignin-derived guaiacols with different ring substitution patterns. Bacterial strains Rhodococcus rhodochrous EP4 and Rhodococcus jostii RHA1 both utilized alkylguaiacols as sole growth substrates. Transcriptomics of EP4 grown on 4-propylguaiacol (4PG) revealed the up-regulation of agcA, encoding a CYP255A1 family P450, and the aph genes, previously shown to encode a meta-cleavage pathway responsible for 4-alkylphenol catabolism. The function of the homologous pathway in RHA1 was confirmed: Deletion mutants of agcA and aphC, encoding the meta-cleavage alkylcatechol dioxygenase, grew on guaiacol but not 4PG. By contrast, deletion mutants of gcoA and pcaL, encoding a CYP255A2 family P450 and an ortho-cleavage pathway enzyme, respectively, grew on 4-propylguaiacol but not guaiacol. CYP255A1 from EP4 catalyzed the O-demethylation of 4-alkylguaiacols to 4-alkylcatechols with the following apparent specificities (k cat/K M): propyl > ethyl > methyl > guaiacol. This order largely reflected AgcA's binding affinities for the different guaiacols and was the inverse of GcoAEP4's specificities. The biocatalytic potential of AgcA was demonstrated by the ability of EP4 to grow on lignin-derived products obtained from the reductive catalytic fractionation of corn stover, depleting alkylguaiacols and alkylphenols. By identifying related P450s with complementary specificities for lignin-relevant guaiacols, this study facilitates the design of these enzymes for biocatalytic applications. We further demonstrated that the metabolic fate of the guaiacol depends on its substitution pattern, a finding that has significant implications for engineering biocatalysts to valorize lignin.
Collapse
|
204
|
Biggs BW, Bedore SR, Arvay E, Huang S, Subramanian H, McIntyre EA, Duscent-Maitland CV, Neidle EL, Tyo KEJ. Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1. Nucleic Acids Res 2020; 48:5169-5182. [PMID: 32246719 PMCID: PMC7229861 DOI: 10.1093/nar/gkaa167] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/20/2020] [Accepted: 03/04/2020] [Indexed: 01/10/2023] Open
Abstract
One primary objective of synthetic biology is to improve the sustainability of chemical manufacturing. Naturally occurring biological systems can utilize a variety of carbon sources, including waste streams that pose challenges to traditional chemical processing, such as lignin biomass, providing opportunity for remediation and valorization of these materials. Success, however, depends on identifying micro-organisms that are both metabolically versatile and engineerable. Identifying organisms with this combination of traits has been a historic hindrance. Here, we leverage the facile genetics of the metabolically versatile bacterium Acinetobacter baylyi ADP1 to create easy and rapid molecular cloning workflows, including a Cas9-based single-step marker-less and scar-less genomic integration method. In addition, we create a promoter library, ribosomal binding site (RBS) variants and test an unprecedented number of rationally integrated bacterial chromosomal protein expression sites and variants. At last, we demonstrate the utility of these tools by examining ADP1’s catabolic repression regulation, creating a strain with improved potential for lignin bioprocessing. Taken together, this work highlights ADP1 as an ideal host for a variety of sustainability and synthetic biology applications.
Collapse
Affiliation(s)
- Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Biotechnology Training Program, Northwestern University, Evanston, IL 60208, USA
| | - Stacy R Bedore
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Erika Arvay
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.,Biotechnology Training Program, Northwestern University, Evanston, IL 60208, USA
| | - Shu Huang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Harshith Subramanian
- Master of Science in Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Emily A McIntyre
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | | | - Ellen L Neidle
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
205
|
Fed-batch polyhydroxybutyrate production by Paraburkholderia sacchari from a ternary mixture of glucose, xylose and arabinose. Bioprocess Biosyst Eng 2020; 44:185-193. [PMID: 32895870 DOI: 10.1007/s00449-020-02434-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Polyhydroxybutyrate (PHB) is a biodegradable bioplastic that is comparable with many petroleum-based plastics in terms of mechanical properties and is highly biocompatible. Lignocellulosic biomass conversion into PHB can increase profit and add sustainability. Glucose, xylose and arabinose are the main monomer sugars derived from upstream lignocellulosic biomass processing. The sugar mixture ratios may vary greatly depending on the pretreatment and enzymatic hydrolysis conditions. Paraburkholderia sacchari DSM 17165 is a bacterium strain that can convert all three sugars into PHB. In this study, fed-batch mode was applied to produce PHB on three sugar mixtures (glucose:xylose:arabinose = 4:2:1, 2:2:1, 1:2:1). The highest PHB concentration produced was 67 g/L for 4:2:1 mixture at 41 h corresponding to an accumulation of 77% of cell dry weight as PHB. Corresponding sugar conversion efficiency and productivity were 0.33 g PHB/g sugar consumed and 1.6 g/L/h, respectively. The results provide references for process control to maximize PHB production from real sugar streams derived from corn fibre.
Collapse
|
206
|
Park MR, Chen Y, Thompson M, Benites VT, Fong B, Petzold CJ, Baidoo EEK, Gladden JM, Adams PD, Keasling JD, Simmons BA, Singer SW. Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass. CHEMSUSCHEM 2020; 13:4455-4467. [PMID: 32160408 DOI: 10.1002/cssc.202000268] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/11/2020] [Indexed: 06/10/2023]
Abstract
There is strong interest in the valorization of lignin to produce valuable products; however, its structural complexity has been a conversion bottleneck. Chemical pretreatment liberates lignin-derived soluble fractions that may be upgraded by bioconversion. Cholinium ionic liquid pretreatment of sorghum produced soluble, aromatic-rich fractions that were converted by Pseudomonas putida (P. putida), a promising host for aromatic bioconversion. Growth studies and mutational analysis demonstrated that P. putida growth on these fractions was dependent on aromatic monomers but unknown factors also contributed. Proteomic and metabolomic analyses indicated that these unknown factors were amino acids and residual ionic liquid; the oligomeric aromatic fraction derived from lignin was not converted. A cholinium catabolic pathway was identified, and the deletion of the pathway stopped the ability of P. putida to grow on cholinium ionic liquid. This work demonstrates that aromatic-rich fractions obtained through pretreatment contain multiple substrates; conversion strategies should account for this complexity.
Collapse
Affiliation(s)
- Mee-Rye Park
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mitchell Thompson
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Veronica T Benites
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bonnie Fong
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John M Gladden
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biomass Science and Conversion Technology, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, 94551, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technology, Shenzhen, China
| | - Blake A Simmons
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| |
Collapse
|
207
|
Haq I, Mazumder P, Kalamdhad AS. Recent advances in removal of lignin from paper industry wastewater and its industrial applications - A review. BIORESOURCE TECHNOLOGY 2020; 312:123636. [PMID: 32527619 DOI: 10.1016/j.biortech.2020.123636] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 05/12/2023]
Abstract
Pulp and paper mill wastewater contains lignin related synthetic, aromatic and chlorinated chemical compounds. Extracting lignin from pulp and paper mill wastewater is one way of recovering valuable organic material. Due to its complex structure, lignin is difficult to break and provides economical and technical provocations in biomass recovery. The conventional wastewater treatment processes are seldom efficacious for the complete removal of lignin from paper mill effluents. A wide range of thermal, mechanical and physico-chemical methods have been reported for the removal of lignin. Moreover, biological method of lignin removal employed microorganisms including bacteria and fungi as a one-step treatment and/or amalgamation of various physico-chemical techniques. Compared with other methods, biological process for degradation of lignin is regarded as eco-friendly, cost-effective and sustainable. Therefore, this review will provide insight into the recent breakthroughs and future trends in lignin removal with special emphasis on biological treatment and scope of lignin utilization.
Collapse
Affiliation(s)
- Izharul Haq
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Payal Mazumder
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ajay S Kalamdhad
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| |
Collapse
|
208
|
Song Y, Chandra RP, Zhang X, Saddler JN. Non-productive celluase binding onto deep eutectic solvent (DES) extracted lignin from willow and corn stover with inhibitory effects on enzymatic hydrolysis of cellulose. Carbohydr Polym 2020; 250:116956. [PMID: 33049860 DOI: 10.1016/j.carbpol.2020.116956] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
In this work, deep eutectic solvent (DES) was prepared by mixing choline chloride (ChCl) with lactic acid (LA), and effects of cellulase non-productive binding onto DES-extracted lignin from willow and corn stover on enzymatic hydrolysis of cellulose was investigated. The correlation between hydrolysis yield of cellulose and chemical features of lignin was evaluated, and a potential inhibitory mechanism was proposed. Condensation of lignin was observed during DES treatment, and these condensed aromatic structures had an increased tendency to adsorb enzymes through hydrophobic interactions. As well as hydrophobic interactions mediated by lignin condensation, an increase in phenolic hydroxyl groups resulted in a greater amount of hydrogen bonds between cellulases and lignin that appeared to inhibit enzymatic hydrolysis yields of cellulose (39.96-42.86 % to 31.96-32.68 %). Although large amounts of COOHs were generated, the elevated electrostatic repulsion as a result of ionic groups was insufficient to decrease non-productive adsorption.
Collapse
Affiliation(s)
- Yanliang Song
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Richard P Chandra
- Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Xu Zhang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Jack N Saddler
- Forest Products Biotechnology/Bioenergy Group, Department of Wood Science, Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| |
Collapse
|
209
|
Khan TS, Gupta S, Ahmad M, Alam MI, Haider MA. Effect of substituents and promoters on the Diels-Alder cycloaddition reaction in the biorenewable synthesis of trimellitic acid. RSC Adv 2020; 10:30656-30670. [PMID: 35516025 PMCID: PMC9056362 DOI: 10.1039/d0ra04318d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/11/2020] [Indexed: 11/21/2022] Open
Abstract
An efficient route to produce oxanorbornene, a precursor for the production of bio-based trimellitic acid (TMLA) via the Diels-Alder (DA) reaction of biomass-derived dienes and dienophiles has been proposed by utilizing density functional theory (DFT) simulations. It has been suggested that DA reaction of dienes such as 5-hydroxymethyl furfural (HMF), 2,5-dimethylfuran (DMF), furan dicarboxylic acid (FDCA) and biomass-derived dienophiles (ethylene derivatives e.g., acrolein, acrylic acid, etc.) leads to the formation of an intermediate product oxanorbornene, a precursor for the production of TMLA. The activation barriers for the DA reaction were correlated to the type of substituent present on the dienes and dienophiles. Among the dienophiles, acrolein was found to be the best candidate showing a low activation energy (<40 kJ mol-1) for the cycloaddition reaction with dienes DMF, HMF and hydroxy methyl furoic acid (HMFA). The FMO gap and (IPdiene + EAdienophile)/2 were both suggested to be suitable descriptors for the DA reaction of electron-rich diene and electron-deficient dienophile. Further solvents did not have a significant effect on the activation barrier for DA reaction. In contrast, the presence of a Lewis acid was seen to lower the activation barrier due to the reduction in the FMO gap.
Collapse
Affiliation(s)
- Tuhin Suvra Khan
- Nanocatalysis Area, Light Stock Processing Division, CSIR-Indian Institute of Petroleum Dehradun 248005 Uttarakhand India +91-135-2525915
| | - Shelaka Gupta
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad Kandi Sangareddy 502205 India
| | - Maaz Ahmad
- Renewable Energy and Chemicals Laboratory, Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas Delhi 110016 India +91-11-2658-2037 +91-11-26591016
| | - Md Imteyaz Alam
- Renewable Energy and Chemicals Laboratory, Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas Delhi 110016 India +91-11-2658-2037 +91-11-26591016
| | - M Ali Haider
- Renewable Energy and Chemicals Laboratory, Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas Delhi 110016 India +91-11-2658-2037 +91-11-26591016
| |
Collapse
|
210
|
Singhvi M, Kim BS. Lignin valorization using biological approach. Biotechnol Appl Biochem 2020; 68:459-468. [PMID: 32725827 DOI: 10.1002/bab.1995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 11/06/2022]
Abstract
Due to the structural complexity and recalcitrance nature of lignin, its depolymerization into monomeric units becomes one of the biggest challenges in the bioconversion of lignin into value-added products. Depolymerization of lignin produces a blend of many compounds that are problematic for isolating components in a cost-effective way. Lignin valorization using a biological approach facilitates sustainable and commercially viable biorefineries. The use of microbes for the conversion of depolymerized lignin compounds into target products can be a solution to the heterogeneity issue. Several studies have been carried out to develop robust strains that can utilize all relevant lignin-derived compounds, but constructing these strains is difficult. As an alternative, designing multiple microbes to convert a mixture of various compounds into the desired product seems realistic. This review provides an overview of lignin bioconversion using various approaches such as metabolic engineering and synthetic biology. Ligninolytic strains have a broad enzymatic machine for depolymerization of lignin and its conversion into intermediates such as catechol or protocatechuate. These intermediates can be further converted to metabolite products such as polyhydroxyalkanoates and triacylglycerol. Synthetic biology offers encouraging methodologies to construct pathways for lignin conversion and to engineer ligninolytic microbes as prospective strains for lignin bioconversion.
Collapse
Affiliation(s)
- Mamata Singhvi
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Beom Soo Kim
- Department of Chemical Engineering, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| |
Collapse
|
211
|
|
212
|
Mendonca CM, Wilkes RA, Aristilde L. Advancements in 13C isotope tracking of synergistic substrate co-utilization in Pseudomonas species and implications for biotechnology applications. Curr Opin Biotechnol 2020; 64:124-133. [DOI: 10.1016/j.copbio.2020.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/16/2022]
|
213
|
Zhang J, Feng E, Li W, Sheng H, Milton JR, Easterling LF, Nash JJ, Kenttämaa HI. Studies of the Fragmentation Mechanisms of Deprotonated Lignin Model Compounds in Tandem Mass Spectrometry. Anal Chem 2020; 92:11895-11903. [PMID: 32786494 DOI: 10.1021/acs.analchem.0c02275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jifa Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Erlu Feng
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Wanru Li
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Huaming Sheng
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Jacob R. Milton
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Leah F. Easterling
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - John J. Nash
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hilkka I. Kenttämaa
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| |
Collapse
|
214
|
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.
Collapse
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
| |
Collapse
|
215
|
Valderrama-Gómez MÁ, Lomnitz JG, Fasani RA, Savageau MA. Mechanistic Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0. iScience 2020; 23:101200. [PMID: 32531747 PMCID: PMC7287267 DOI: 10.1016/j.isci.2020.101200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/04/2020] [Accepted: 05/21/2020] [Indexed: 01/24/2023] Open
Abstract
Mechanistic models of biochemical systems provide a rigorous description of biological phenomena. They are indispensable for making predictions and elucidating biological design principles. To date, mathematical analysis and characterization of these models encounter a bottleneck consisting of large numbers of unknown parameter values. Here, we introduce the Design Space Toolbox v.3.0 (DST3), a software implementation of the Design Space formalism enabling mechanistic modeling without requiring previous knowledge of parameter values. This is achieved by using a phenotype-centric modeling approach, in which the system is first decomposed into a series of biochemical phenotypes. Parameter values realizing phenotypes of interest are subsequently predicted. DST3 represents the most generally applicable implementation of the Design Space formalism and offers unique advantages over earlier versions. By expanding the Design Space formalism and streamlining its distribution, DST3 represents a valuable tool for elucidating biological design principles and designing novel synthetic circuits. DST3 extends the Design Space formalism by identifying additional phenotypes Additional phenotypes arise from cycles, conservations, and metabolic imbalances DST3 enables mechanistic modeling without previous knowledge of parameter values It fully unlocks the potential of the novel phenotype-centric modeling strategy
Collapse
Affiliation(s)
| | | | | | - Michael A Savageau
- Department of Microbiology & Molecular Genetics, University of California, Davis, CA 95616, USA; Department of Biomedical Engineering, University of California, Davis, CA 95616, USA.
| |
Collapse
|
216
|
Zhu D, Adebisi WA, Ahmad F, Sethupathy S, Danso B, Sun J. Recent Development of Extremophilic Bacteria and Their Application in Biorefinery. Front Bioeng Biotechnol 2020; 8:483. [PMID: 32596215 PMCID: PMC7303364 DOI: 10.3389/fbioe.2020.00483] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.
Collapse
Affiliation(s)
- Daochen Zhu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
| | - Wasiu Adewale Adebisi
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Fiaz Ahmad
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Blessing Danso
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| |
Collapse
|
217
|
Gonçalves CC, Bruce T, Silva CDOG, Fillho EXF, Noronha EF, Carlquist M, Parachin NS. Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods. Front Microbiol 2020; 11:1081. [PMID: 32582068 PMCID: PMC7295907 DOI: 10.3389/fmicb.2020.01081] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 01/02/2023] Open
Abstract
Lignin is an abundant cell wall component, and it has been used mainly for generating steam and electricity. Nevertheless, lignin valorization, i.e. the conversion of lignin into high value-added fuels, chemicals, or materials, is crucial for the full implementation of cost-effective lignocellulosic biorefineries. From this perspective, rapid screening methods are crucial for time- and resource-efficient development of novel microbial strains and enzymes with applications in the lignin biorefinery. The present review gives an overview of recent developments and applications of a vast arsenal of activity and sequence-based methodologies for uncovering novel microbial strains with ligninolytic potential, novel enzymes for lignin depolymerization and for unraveling the main metabolic routes during growth on lignin. Finally, perspectives on the use of each of the presented methods and their respective advantages and disadvantages are discussed.
Collapse
Affiliation(s)
- Carolyne Caetano Gonçalves
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| | - Thiago Bruce
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| | | | | | - Eliane Ferreira Noronha
- Laboratory of Enzymology, Department of Cellular Biology, University of Brasília, Brasília, Brazil
| | - Magnus Carlquist
- Division of Applied Microbiology, Department of Chemistry, Faculty of Engineering, Lund University, Lund, Sweden
| | - Nádia Skorupa Parachin
- Department of Genomic Science and Biotechnology, Universidade Católica de Brasília - UCB, Brasília, Brazil
| |
Collapse
|
218
|
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.
Collapse
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
| |
Collapse
|
219
|
Incha MR, Thompson MG, Blake-Hedges JM, Liu Y, Pearson AN, Schmidt M, Gin JW, Petzold CJ, Deutschbauer AM, Keasling JD. Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida. Metab Eng Commun 2020; 10:e00119. [PMID: 32280587 PMCID: PMC7136493 DOI: 10.1016/j.mec.2019.e00119] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas putida is a saprophytic bacterium with robust metabolisms and strong solvent tolerance making it an attractive host for metabolic engineering and bioremediation. Due to its diverse carbon metabolisms, its genome encodes an array of proteins and enzymes that can be readily applied to produce valuable products. In this work we sought to identify design principles and bottlenecks in the production of type III polyketide synthase (T3PKS)-derived compounds in P. putida. T3PKS products are widely used as nutraceuticals and medicines and often require aromatic starter units, such as coumaroyl-CoA, which is also an intermediate in the native coumarate catabolic pathway of P. putida. Using a randomly barcoded transposon mutant (RB-TnSeq) library, we assayed gene functions for a large portion of aromatic catabolism, confirmed known pathways, and proposed new annotations for two aromatic transporters. The 1,3,6,8-tetrahydroxynapthalene synthase of Streptomyces coelicolor (RppA), a microbial T3PKS, was then used to rapidly assay growth conditions for increased T3PKS product accumulation. The feruloyl/coumaroyl CoA synthetase (Fcs) of P. putida was used to supply coumaroyl-CoA for the curcuminoid synthase (CUS) of Oryza sativa, a plant T3PKS. We identified that accumulation of coumaroyl-CoA in this pathway results in extended growth lag times in P. putida. Deletion of the second step in coumarate catabolism, the enoyl-CoA hydratase-lyase (Ech), resulted in increased production of the type III polyketide bisdemethoxycurcumin.
Collapse
Affiliation(s)
- Matthew R. Incha
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jacquelyn M. Blake-Hedges
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Allison N. Pearson
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Matthias Schmidt
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer W. Gin
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam M. Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D. Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 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, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| |
Collapse
|
220
|
Giannì P, Lange H, Crestini C. Functionalized Organosolv Lignins Suitable for Modifications of Hard Surfaces. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2020; 8:7628-7638. [PMID: 33828929 PMCID: PMC8016396 DOI: 10.1021/acssuschemeng.0c00886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/12/2020] [Indexed: 05/08/2023]
Abstract
Two different organosolv lignins (OSLs), that is, wheat straw and corn stover OSLs, were chemically and enzymatically functionalized. Functional groups were attached via the formation of stable ether bonds exploiting the reactivity of free phenolic OH groups along the lignin backbone. The functional groups introduced a range from compact charged and chargeable building blocks for the generation of surface-active lignins to oligomeric and polymeric species used in lignin block-copolymer productions. Combination of selected functions led to novel charged or chargeable polymeric lignin-based materials. Products could be realized with different degrees of technical loadings in terms of introduced functional groups.
Collapse
Affiliation(s)
- Paola Giannì
- Department
of Chemical Sciences and Technologies, University
of Rome “Tor Vergata”, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Heiko Lange
- Department
of Pharmacy, University of Naples “Federico
II”, V ia Domenico
Montesano 49, 80131 Naples, Italy
- CSGI—Center
for Colloid and Surface Science, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudia Crestini
- CSGI—Center
for Colloid and Surface Science, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Department
of Molecular Science and Nanosystems, University
of Venice Ca’ Foscari, Via Torino 155, 30170 Venice Mestre, Italy
| |
Collapse
|
221
|
Wang J, Yan K, Wang W, Zhou Y. A method for high-throughput screening hydrolase of lignin β-aryl ether linkage from directed evolution by glutathione (GSH) assay. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00317-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Lignin’s valorization plays a critical role in refining the bioresource. Considering that the β-aryl ether linkage (β-O-4 bond) accounts for 50–70% of lignin chemical linkage between aromatic rings, the hydrolase of lignin β-aryl ether linkage, especially the β-etherase, provided a promising way for the lignin depolymerization and valorization. As a result, it is essential to develop the effective high-throughput methods for screening the mutant library of β-etherase from directed evolution.
Results
Based on the enzymatic mechanism of β-O-4 bond’s cleavage by β-etherase, the LigF was selected as the model to study high-throughput method by GSH assay for screening the mutant library of β-etherase from directed evolution. After the primary study with purified LigF and cell lysate, the GSH assay was used to screen mutant library of β-etherase. The study on screening the mutant library with about 600 colonies indicated that the selected transformants all have one or two mutated sites in the gene sequence of LigF, and the activities from GSH assay of most selected transformants were the same as their activities from HPLC assay.
Conclusions
The results from the high-throughput screening of mutant library demonstrated that GSH assay could be applied to screen β-etherase mutant from directed evolution.
Collapse
|
222
|
Xu L, Zhang SJ, Zhong C, Li BZ, Yuan YJ. Alkali-Based Pretreatment-Facilitated Lignin Valorization: A Review. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c01456] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Li Xu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China
| | - Sen-Jia Zhang
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Cheng Zhong
- Key Laboratory of Industrial Fermentation Microbiology (Ministry of Education), Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China
| |
Collapse
|
223
|
Weiss R, Guebitz GM, Pellis A, Nyanhongo GS. Harnessing the Power of Enzymes for Tailoring and Valorizing Lignin. Trends Biotechnol 2020; 38:1215-1231. [PMID: 32423726 DOI: 10.1016/j.tibtech.2020.03.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Lignin, a structural component of lignocellulosic plants, is an alternative raw material with enormous potential to replace diminishing fossil-based resources for the sustainable production of many chemicals and materials. Unfortunately, lignin's heterogeneity, low reactivity, and strong intra- and intermolecular hydrogen interactions and modifications introduced during the pulping process present significant technical challenges. However, the increasing ability to tailor lignin biosynthesis pathways by targeting enzymes and the continued discovery of more robust biocatalysts are enabling the synthesis of novel valuable products. This review summarizes how enzymes involved in lignin biosynthesis pathways and microbial enzymes are being harnessed to produce chemicals and materials and to upgrade lignin properties for the synthesis of a variety of value-added lignin industrial products.
Collapse
Affiliation(s)
- Renate Weiss
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Georg M Guebitz
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria; Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria
| | - Alessandro Pellis
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria
| | - Gibson S Nyanhongo
- University of Natural Resources and Life Sciences, Vienna, Institute of Environmental Biotechnology, Konrad Lorenz Straße 20, 3430, Tulln an der Donau, Austria; Austrian Centre for Industrial Biotechnology (ACIB), Konrad Lorenz Strasse 20, 3430, Tulln an der Donau, Austria.
| |
Collapse
|
224
|
Tailoring microbes to upgrade lignin. Curr Opin Chem Biol 2020; 59:23-29. [PMID: 32388219 DOI: 10.1016/j.cbpa.2020.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022]
Abstract
Lignin depolymerization generates a mixture of numerous compounds that are difficult to separate cost-effectively. To address this heterogeneity issue, microbes have been employed to 'biologically funnel' a broad range of compounds present in depolymerized lignin into common central metabolites that can be converted into a single desirable product. Because the composition of depolymerized lignin varies significantly with the type of biomass and the depolymerization method, microbes should be selected and engineered by considering this compositional variation. An ideal microbe must efficiently metabolize all relevant lignin-derived compounds regardless of the compositional variation of feedstocks, but discovering or developing such a perfect microbe is very challenging. Instead, developing multiple tailored microbes to tolerate a given mixture of lignin-derived compounds and to convert most of these into a target product is more practical. This review summarizes recent progress toward the development of such microbes for lignin valorization and offers future directions.
Collapse
|
225
|
Lin L, Wang X, Cao L, Xu M. Lignin catabolic pathways reveal unique characteristics of dye-decolorizing peroxidases in Pseudomonas putida. Environ Microbiol 2020; 21:1847-1863. [PMID: 30882973 DOI: 10.1111/1462-2920.14593] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 11/28/2022]
Abstract
Lignin is one of the largest carbon reservoirs in the environment, playing an important role in the global carbon cycle. However, lignin degradation in bacteria, especially non-model organisms, has not been well characterized either enzymatically or genetically. Here, a lignin-degrading bacterial strain, Pseudomonas putida A514, was used as the research model. Genomic and proteomic analyses suggested that two B subfamily dye-decolorizing peroxidases (DypBs) were prominent in lignin depolymerization, while the classic O2 -dependent ring cleavage strategy was utilized in central pathways to catabolize lignin-derived aromatic compounds that were funnelled by peripheral pathways. These enzymes, together with a range of transporters, sequential and expression-dose dependent regulation and stress response systems coordinated for lignin metabolism. Catalytic assays indicated these DypBs show unique Mn2+ independent lignin depolymerization activity, while Mn2+ oxidation activity is absent. Furthermore, a high synergy between DypB enzymes and A514 cells was observed to promote cell growth (5 × 1012 cfus/ml) and lignin degradation (27%). This suggested DypBs are competitive lignin biocatalysts and pinpointed limited extracellular secretion capacity as the rate-limiting factor in bacterial lignin degradation. DypB production was, therefore, optimized in recombinant strains and a 14,141-fold increase in DypB activity (56,565 U/l) was achieved, providing novel insights for lignin bioconversion.
Collapse
Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Jinan, China.,Ocean College, Zhejiang University, Hangzhou, China
| | | | - Lanfang Cao
- Ocean College, Zhejiang University, Hangzhou, China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou, China
| |
Collapse
|
226
|
Karlen SD, Fasahati P, Mazaheri M, Serate J, Smith RA, Sirobhushanam S, Chen M, Tymokhin VI, Cass CL, Liu S, Padmakshan D, Xie D, Zhang Y, McGee MA, Russell JD, Coon JJ, Kaeppler HF, de Leon N, Maravelias CT, Runge TM, Kaeppler SM, Sedbrook JC, Ralph J. Assessing the Viability of Recovery of Hydroxycinnamic Acids from Lignocellulosic Biorefinery Alkaline Pretreatment Waste Streams. CHEMSUSCHEM 2020; 13:2012-2024. [PMID: 31984673 PMCID: PMC7217007 DOI: 10.1002/cssc.201903345] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Indexed: 05/03/2023]
Abstract
The hydroxycinnamic acids p-coumaric acid (pCA) and ferulic acid (FA) add diversity to the portfolio of products produced by using grass-fed lignocellulosic biorefineries. The level of lignin-bound pCA in Zea mays was modified by the alteration of p-coumaroyl-CoA monolignol transferase expression. The biomass was processed in a lab-scale alkaline-pretreatment biorefinery process and the data were used for a baseline technoeconomic analysis to determine where to direct future research efforts to couple plant design to biomass utilization processes. It is concluded that future plant engineering efforts should focus on strategies that ramp up accumulation of one type of hydroxycinnamate (pCA or FA) predominantly and suppress that of the other. Technoeconomic analysis indicates that target extraction titers of one hydroxycinnamic acid need to be >50 g kg-1 biomass, at least five times higher than observed titers for the impure pCA/FA product mixture from wild-type maize. The technical challenge for process engineers is to develop a viable process that requires more than 80 % reduction of the isolation costs.
Collapse
|
227
|
Recent advances in polyhydroxyalkanoate production: Feedstocks, strains and process developments. Int J Biol Macromol 2020; 156:691-703. [PMID: 32315680 DOI: 10.1016/j.ijbiomac.2020.04.082] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 11/20/2022]
Abstract
Polyhydroxyalkanoates (PHAs) have been actively studied in academia and industry for their properties comparable to petroleum-derived plastics and high biocompatibility. However, the major limitation for commercialization is their high cost. Feedstock costs, especially carbon costs, account for the majority of the final cost. Finding cheap feedstocks for PHA production and associated process development are critical for a cost-effective PHA production. In this study, waste materials from different sources, particularly lignocellulosic biomass, were proposed as suitable feedstocks for PHA production. Strains involved in the conversion of these feedstocks into PHA were reviewed. Newly isolated strains were emphasized. Related process development, including the factors that affect PHA production, fermentation modes and downstream processing, was elaborated upon.
Collapse
|
228
|
Lin CY, Eudes A. Strategies for the production of biochemicals in bioenergy crops. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:71. [PMID: 32318116 PMCID: PMC7158082 DOI: 10.1186/s13068-020-01707-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/02/2020] [Indexed: 05/12/2023]
Abstract
Industrial crops are grown to produce goods for manufacturing. Rather than food and feed, they supply raw materials for making biofuels, pharmaceuticals, and specialty chemicals, as well as feedstocks for fabricating fiber, biopolymer, and construction materials. Therefore, such crops offer the potential to reduce our dependency on petrochemicals that currently serve as building blocks for manufacturing the majority of our industrial and consumer products. In this review, we are providing examples of metabolites synthesized in plants that can be used as bio-based platform chemicals for partial replacement of their petroleum-derived counterparts. Plant metabolic engineering approaches aiming at increasing the content of these metabolites in biomass are presented. In particular, we emphasize on recent advances in the manipulation of the shikimate and isoprenoid biosynthetic pathways, both of which being the source of multiple valuable compounds. Implementing and optimizing engineered metabolic pathways for accumulation of coproducts in bioenergy crops may represent a valuable option for enhancing the commercial value of biomass and attaining sustainable lignocellulosic biorefineries.
Collapse
Affiliation(s)
- Chien-Yuan Lin
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| |
Collapse
|
229
|
Accumulation of high-value bioproducts in planta can improve the economics of advanced biofuels. Proc Natl Acad Sci U S A 2020; 117:8639-8648. [PMID: 32220956 PMCID: PMC7165473 DOI: 10.1073/pnas.2000053117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cellulosic biofuels have not yet reached cost parity with conventional petroleum fuels. One strategy to address this challenge is to generate valuable coproducts alongside biofuels. Engineering bioenergy crops to generate value-added bioproducts in planta can reduce input requirements relative to microbial chassis and skip costly deconstruction and conversion steps. Although rapid progress has been made in plant metabolic engineering, there has been no systematic analysis devoted to quantifying the impact of such engineered bioenergy crops on biorefinery economics. Here, we provide new insights into how bioproduct accumulation in planta affects biofuel selling prices. We present the range of bioproduct selling prices and accumulation rates needed to compensate for additional extraction steps and reach a target $2.50/gal minimum biofuel selling price. Coproduction of high-value bioproducts at biorefineries is a key factor in making biofuels more cost-competitive. One strategy for generating coproducts is to directly engineer bioenergy crops to accumulate bioproducts in planta that can be fractionated and recovered at biorefineries. Here, we develop quantitative insights into the relationship between bioproduct market value and target accumulation rates by investigating a set of industrially relevant compounds already extracted from plant sources with a wide range of market prices and applications, including <$10/kg (limonene, latex, and polyhydroxybutyrate [PHB]), $10 to $100/kg (cannabidiol), and >$100/kg (artemisinin). These compounds are used to identify a range of mass fraction thresholds required to achieve net economic benefits for biorefineries and the additional amounts needed to reach a target $2.50/gal biofuel selling price, using cellulosic ethanol production as a test case. Bioproduct market prices and recovery costs determine the accumulation threshold; we find that moderate- to high-value compounds (i.e., cannabidiol and artemisinin) offer net economic benefits at accumulation rates of just 0.01% dry weight (dwt) to 0.02 dwt%. Lower-value compounds, including limonene, latex, and PHB, require at least an order-of-magnitude greater accumulation to overcome additional extraction and recovery costs (0.3 to 1.2 dwt%). We also find that a diversified approach is critical. For example, global artemisinin demand could be met with fewer than 10 biorefineries, while global demand for latex is equivalent to nearly 180 facilities. Our results provide a roadmap for future plant metabolic engineering efforts aimed at increasing the value derived from bioenergy crops.
Collapse
|
230
|
Huo J, Shanks BH. Bioprivileged Molecules: Integrating Biological and Chemical Catalysis for Biomass Conversion. Annu Rev Chem Biomol Eng 2020; 11:63-85. [PMID: 32155351 DOI: 10.1146/annurev-chembioeng-101519-121127] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Further development of biomass conversions to viable chemicals and fuels will require improved atom utilization, process efficiency, and synergistic allocation of carbon feedstock into diverse products, as is the case in the well-developed petroleum industry. The integration of biological and chemical processes, which harnesses the strength of each type of process, can lead to advantaged processes over processes limited to one or the other. This synergy can be achieved through bioprivileged molecules that can be leveraged to produce a diversity of products, including both replacement molecules and novel molecules with enhanced performance properties. However, important challenges arise in the development of bioprivileged molecules. This review discusses the integration of biological and chemical processes and its use in the development of bioprivileged molecules, with a further focus on key hurdles that must be overcome for successful implementation.
Collapse
Affiliation(s)
- Jiajie Huo
- Center for Biorenewable Chemicals and Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA;
| | - Brent H Shanks
- Center for Biorenewable Chemicals and Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA;
| |
Collapse
|
231
|
Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion. Commun Biol 2020; 3:98. [PMID: 32139868 PMCID: PMC7058019 DOI: 10.1038/s42003-020-0824-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/12/2020] [Indexed: 12/18/2022] Open
Abstract
Ferulic acid is a ubiquitous phenolic compound in lignocellulose, which is recognized for its role in the microbial carbon catabolism and industrial value. However, its recalcitrance and toxicity poses a challenge for ferulic acid-to-bioproducts bioconversion. Here, we develop a genome editing strategy for Pseudomonas putida KT2440 using an integrated CRISPR/Cas9n-λ-Red system with pyrF as a selection marker, which maintains cell viability and genetic stability, increases mutation efficiency, and simplifies genetic manipulation. Via this method, four functional modules, comprised of nine genes involved in ferulic acid catabolism and polyhydroxyalkanoate biosynthesis, were integrated into the genome, generating the KTc9n20 strain. After metabolic engineering and optimization of C/N ratio, polyhydroxyalkanoate production was increased to ~270 mg/L, coupled with ~20 mM ferulic acid consumption. This study not only establishes a simple and efficient genome editing strategy, but also offers an encouraging example of how to apply this method to improve microbial aromatic compound bioconversion. Yueyue Zhou et al. develop a genetic engineering method that increases the production of polyhydroxyalkanoate from ferulic acid, which is toxic at high concentrations. This study provides insight into the bioconversion of the aromatic compound in Pseudomonas.
Collapse
|
232
|
|
233
|
Vanillin Production in Pseudomonas: Whole-Genome Sequencing of Pseudomonas sp. Strain 9.1 and Reannotation of Pseudomonas putida CalA as a Vanillin Reductase. Appl Environ Microbiol 2020; 86:AEM.02442-19. [PMID: 31924622 PMCID: PMC7054097 DOI: 10.1128/aem.02442-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Microbial degradation of lignin and its related aromatic compounds has great potential for the sustainable production of chemicals and bioremediation of contaminated soils. We previously isolated Pseudomonas sp. strain 9.1 from historical waste deposits (forming so-called fiber banks) released from pulp and paper mills along the Baltic Sea coast. The strain accumulated vanillyl alcohol during growth on vanillin, and while reported in other microbes, this phenotype is less common in wild-type pseudomonads. As the reduction of vanillin to vanillyl alcohol is an undesired trait in Pseudomonas strains engineered to accumulate vanillin, connecting the strain 9.1 phenotype with a genotype would increase the fundamental understanding and genetic engineering potential of microbial vanillin metabolism. The genome of Pseudomonas sp. 9.1 was sequenced and assembled. Annotation identified oxidoreductases with homology to Saccharomyces cerevisiae alcohol dehydrogenase ScADH6p, known to reduce vanillin to vanillyl alcohol, in both the 9.1 genome and the model strain Pseudomonas putida KT2440. Recombinant expression of the Pseudomonas sp. 9.1 FEZ21_09870 and P. putida KT2440 PP_2426 (calA) genes in Escherichia coli revealed that these open reading frames encode aldehyde reductases that convert vanillin to vanillyl alcohol, and that P. putida KT2440 PP_3839 encodes a coniferyl alcohol dehydrogenase that oxidizes coniferyl alcohol to coniferyl aldehyde (i.e., the function previously assigned to calA). The deletion of PP_2426 in P. putida GN442 engineered to accumulate vanillin resulted in a decrease in by-product (vanillyl alcohol) yield from 17% to ∼1%. Based on these results, we propose the reannotation of PP_2426 and FEZ21_09870 as areA and PP_3839 as calA-II IMPORTANCE Valorization of lignocellulose (nonedible plant matter) is of key interest for the sustainable production of chemicals from renewable resources. Lignin, one of the main constituents of lignocellulose, is a heterogeneous aromatic biopolymer that can be chemically depolymerized into a heterogeneous mixture of aromatic building blocks; those can be further converted by certain microbes into value-added aromatic chemicals, e.g., the flavoring agent vanillin. We previously isolated a Pseudomonas sp. strain with the (for the genus) unusual trait of vanillyl alcohol production during growth on vanillin. Whole-genome sequencing of the isolate led to the identification of a vanillin reductase candidate gene whose deletion in a recombinant vanillin-accumulating P. putida strain almost completely alleviated the undesired vanillyl alcohol by-product yield. These results represent an important step toward biotechnological production of vanillin from lignin using bacterial cell factories.
Collapse
|
234
|
Li X, Li M, Pu Y, Ragauskas AJ, Zheng Y. Simultaneous depolymerization and fermentation of lignin into value-added products by the marine protist, Thraustochytrium striatum. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
235
|
Li M, Wilkins M. Fed-batch cultivation and adding supplements to increase yields of polyhydroxybutyrate production by Cupriavidus necator from corn stover alkaline pretreatment liquor. BIORESOURCE TECHNOLOGY 2020; 299:122676. [PMID: 31924491 DOI: 10.1016/j.biortech.2019.122676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 06/10/2023]
Abstract
The aim of this study was to evaluate polyhydroxybutyrate (PHB) production and productivity with supplements under fed-batch cultivation at bioreactor scale (1.3 L). In this study, multiple supplements including oxidative enzyme, mediators, surfactants and silicon nanoparticles were added to Cupriavidus necator culture growing on alkaline pretreatment liquor (APL). At 1.3 L bioreactor scale, PHB production reached 3.3 g/L. To further enhance PHB production, fed-batch cultivation with two different feeding strategies were applied. Under single pulse feeding of 300 mL medium, PHB production reached 4.0 g/L. Under 4 pulses feeding of 75 mL medium each time, PHB production reached 4.5 g/L. This is the highest PHB production from lignin that the authors are aware of in literature.
Collapse
Affiliation(s)
- Mengxing Li
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln 68583 USA; Department of Statistics, The University of Nebraska-Lincoln, Lincoln 68583 USA
| | - Mark Wilkins
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln 68583 USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588 USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln 68583 USA.
| |
Collapse
|
236
|
Granja-Travez RS, Persinoti GF, Squina FM, Bugg TDH. Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism. Appl Microbiol Biotechnol 2020; 104:3305-3320. [PMID: 32088760 DOI: 10.1007/s00253-019-10318-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/06/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023]
Abstract
Although several bacterial lignin-oxidising enzymes have been discovered in recent years, it is not yet clear whether different lignin-degrading bacteria use similar mechanisms for lignin oxidation and degradation of lignin fragments. Genome sequences of 13 bacterial lignin-oxidising bacteria, including new genome sequences for Microbacterium phyllosphaerae and Agrobacterium sp., were analysed for the presence of lignin-oxidising enzymes and aromatic degradation gene clusters that could be used to metabolise the products of lignin degradation. Ten bacterial genomes contain DyP-type peroxidases, and ten bacterial strains contain putative multi-copper oxidases (MCOs), both known to have activity for lignin oxidation. Only one strain lacks both MCOs and DyP-type peroxidase genes. Eleven bacterial genomes contain aromatic degradation gene clusters, of which ten contain the central β-ketoadipate pathway, with variable numbers and types of degradation clusters for other aromatic substrates. Hence, there appear to be diverse metabolic strategies used for lignin oxidation in bacteria, while the β-ketoadipate pathway appears to be the most common route for aromatic metabolism in lignin-degrading bacteria.
Collapse
Affiliation(s)
- Rommel Santiago Granja-Travez
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
| | | | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| |
Collapse
|
237
|
Liao Y, Koelewijn SF, Van den Bossche G, Van Aelst J, Van den Bosch S, Renders T, Navare K, Nicolaï T, Van Aelst K, Maesen M, Matsushima H, Thevelein JM, Van Acker K, Lagrain B, Verboekend D, Sels BF. A sustainable wood biorefinery for low–carbon footprint chemicals production. Science 2020; 367:1385-1390. [DOI: 10.1126/science.aau1567] [Citation(s) in RCA: 354] [Impact Index Per Article: 88.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/17/2019] [Accepted: 02/04/2020] [Indexed: 01/05/2023]
Abstract
The profitability and sustainability of future biorefineries are dependent on efficient feedstock use. Therefore, it is essential to valorize lignin when using wood. We have developed an integrated biorefinery that converts 78 weight % (wt %) of birch into xylochemicals. Reductive catalytic fractionation of the wood produces a carbohydrate pulp amenable to bioethanol production and a lignin oil. After extraction of the lignin oil, the crude, unseparated mixture of phenolic monomers is catalytically funneled into 20 wt % of phenol and 9 wt % of propylene (on the basis of lignin weight) by gas-phase hydroprocessing and dealkylation; the residual phenolic oligomers (30 wt %) are used in printing ink as replacements for controversial para-nonylphenol. A techno-economic analysis predicts an economically competitive production process, and a life-cycle assessment estimates a lower carbon dioxide footprint relative to that of fossil-based production.
Collapse
Affiliation(s)
- Yuhe Liao
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Steven-Friso Koelewijn
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Gil Van den Bossche
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Joost Van Aelst
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Sander Van den Bosch
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Tom Renders
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Kranti Navare
- Department of Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
| | - Thomas Nicolaï
- Laboratory of Molecular Cell Biology, KU Leuven, and Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Korneel Van Aelst
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Maarten Maesen
- Lawter bvba, Ketenislaan 1C, Haven 1520, 9130 Kallo, Belgium
| | | | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, KU Leuven, and Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Karel Van Acker
- Department of Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
- Center for Economics and Corporate Sustainability, KU Leuven, Warmoesberg 26, 1000 Brussels, Belgium
| | - Bert Lagrain
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Danny Verboekend
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Bert F. Sels
- Center for Sustainable Catalysis and Engineering, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| |
Collapse
|
238
|
Visible/near infrared spectroscopy and machine learning for predicting polyhydroxybutyrate production cultured on alkaline pretreated liquor from corn stover. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100386] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
239
|
Huang K, Fasahati P, Maravelias CT. System-Level Analysis of Lignin Valorization in Lignocellulosic Biorefineries. iScience 2020; 23:100751. [PMID: 31884163 PMCID: PMC6941866 DOI: 10.1016/j.isci.2019.100751] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/15/2019] [Accepted: 11/23/2019] [Indexed: 12/02/2022] Open
Abstract
We study the economics and energy efficiency of biorefineries employing lignin valorization. We use superstructure-based process synthesis to study different configurations under different types of constraints. Using optimization, we examine the impact of various parameters for lignin valorization such as bioproduct selling price, production cost, conversion coefficient, and energy requirement. The results show that the optimal strategy leading to a minimum ethanol selling price (MESP) of $3.44/GGE does not include lignin valorization. Results indicate that under certain scenarios, the optimal biorefinery strategies with lignin valorization tend to be energy deficient, and thus the optimal pretreatment technology may switch from γ-valerolactone-based deconstruction to ammonia fiber expansion. Further analysis is performed to study how improvements in combinations of selected parameters can lead to lower cost for a thermal-neural biorefinery. Developed optimization model to evaluate biorefinery with lignin valorization Studied impact of technical, economic, and energy parameters on economics Lignin utilization is optimized to achieve a thermal-neutral biorefinery Established technology targets for economic and energetic feasibility
Collapse
Affiliation(s)
- Kefeng Huang
- Department of Chemical and Biological Engineering and DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, USA
| | - Peyman Fasahati
- Department of Chemical and Biological Engineering and DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, USA
| | - Christos T Maravelias
- Department of Chemical and Biological Engineering and DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706, USA.
| |
Collapse
|
240
|
Engineering glucose metabolism for enhanced muconic acid production in Pseudomonas putida KT2440. Metab Eng 2020; 59:64-75. [PMID: 31931111 DOI: 10.1016/j.ymben.2020.01.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/01/2020] [Accepted: 01/04/2020] [Indexed: 12/24/2022]
Abstract
Pseudomonas putida KT2440 has received increasing attention as an important biocatalyst for the conversion of diverse carbon sources to multiple products, including the olefinic diacid, cis,cis-muconic acid (muconate). P. putida has been previously engineered to produce muconate from glucose; however, periplasmic oxidation of glucose causes substantial 2-ketogluconate accumulation, reducing product yield and selectivity. Deletion of the glucose dehydrogenase gene (gcd) prevents 2-ketogluconate accumulation, but dramatically slows growth and muconate production. In this work, we employed adaptive laboratory evolution to improve muconate production in strains incapable of producing 2-ketogluconate. Growth-based selection improved growth, but reduced muconate titer. A new muconate-responsive biosensor was therefore developed to enable muconate-based screening using fluorescence activated cell sorting. Sorted clones demonstrated both improved growth and muconate production. Mutations identified by whole genome resequencing of these isolates indicated that glucose metabolism may be dysregulated in strains lacking gcd. Using this information, we used targeted engineering to recapitulate improvements achieved by evolution. Deletion of the transcriptional repressor gene hexR improved strain growth and increased the muconate production rate, and the impact of this deletion was investigated using transcriptomics. The genes gntZ and gacS were also disrupted in several evolved clones, and deletion of these genes further improved strain growth and muconate production. Together, these targets provide a suite of modifications that improve glucose conversion to muconate by P. putida in the context of gcd deletion. Prior to this work, our engineered strain lacking gcd generated 7.0 g/L muconate at a productivity of 0.07 g/L/h and a 38% yield (mol/mol) in a fed-batch bioreactor. Here, the resulting strain with the deletion of hexR, gntZ, and gacS achieved 22.0 g/L at 0.21 g/L/h and a 35.6% yield (mol/mol) from glucose in similar conditions. These strategies enabled enhanced muconic acid production and may also improve production of other target molecules from glucose in P. putida.
Collapse
|
241
|
Ghosh A, Haverly MR, Lindstrom JK, Johnston PA, Brown RC. Tetrahydrofuran-based two-step solvent liquefaction process for production of lignocellulosic sugars. REACT CHEM ENG 2020. [DOI: 10.1039/d0re00192a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
THF-based solvent liquefaction demonstrates a new economic and sustainable approach for fractionating, saccharifying biomass with simple and efficient solvent recovery.
Collapse
Affiliation(s)
- Arpa Ghosh
- Bioeconomy Institute
- Iowa State University
- Ames
- USA
| | | | | | | | - Robert C. Brown
- Bioeconomy Institute
- Iowa State University
- Ames
- USA
- Department of Mechanical Engineering
| |
Collapse
|
242
|
Gabirondo E, Sangroniz A, Etxeberria A, Torres-Giner S, Sardon H. Poly(hydroxy acids) derived from the self-condensation of hydroxy acids: from polymerization to end-of-life options. Polym Chem 2020. [DOI: 10.1039/d0py00088d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Poly(hydroxy acids) derived from the self-condensation of hydroxy acid are biodegradable and can be fully recycled in a Circular Economy approach.
Collapse
Affiliation(s)
- Elena Gabirondo
- Department of Polymer Science and Technology
- Institute for Polymer Materials (POLYMAT)
- Faculty of Chemistry
- University of the Basque Country (UPV/EHU)
- 20018 Donostia
| | - Ainara Sangroniz
- Department of Polymer Science and Technology
- Institute for Polymer Materials (POLYMAT)
- Faculty of Chemistry
- University of the Basque Country (UPV/EHU)
- 20018 Donostia
| | - Agustin Etxeberria
- Department of Polymer Science and Technology
- Institute for Polymer Materials (POLYMAT)
- Faculty of Chemistry
- University of the Basque Country (UPV/EHU)
- 20018 Donostia
| | - Sergio Torres-Giner
- Novel Materials and Nanotechnology Group
- Institute of Agrochemistry and Food Technology (IATA)
- Spanish National Research Council (CSIC)
- 46980 Paterna
- Spain
| | - Haritz Sardon
- Department of Polymer Science and Technology
- Institute for Polymer Materials (POLYMAT)
- Faculty of Chemistry
- University of the Basque Country (UPV/EHU)
- 20018 Donostia
| |
Collapse
|
243
|
Zhu S, Chen Y, Gao X, Lv Z, He Y, Wang J, Fan W. Kraft lignin derived S and O co-doped porous graphene for metal-free benzylic alcohol oxidation. Catal Sci Technol 2020. [DOI: 10.1039/c9cy02476j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
S and O co-doped graphene derived from lignin carbonization achieved 95.9% yield of benzaldehyde in metal-free oxidation of benzyl alcohol.
Collapse
Affiliation(s)
- Shanhui Zhu
- State Key Laboratory of Coal Conversion
- Institute of Coal Chemistry
- Chinese Academy of Sciences
- Taiyuan 030001
- PR China
| | - Yanyan Chen
- State Key Laboratory of Coal Conversion
- Institute of Coal Chemistry
- Chinese Academy of Sciences
- Taiyuan 030001
- PR China
| | - Xiaoqing Gao
- State Key Laboratory of Coal Conversion
- Institute of Coal Chemistry
- Chinese Academy of Sciences
- Taiyuan 030001
- PR China
| | - Zexiang Lv
- State Key Laboratory of Coal Conversion
- Institute of Coal Chemistry
- Chinese Academy of Sciences
- Taiyuan 030001
- PR China
| | - Yue He
- State Key Laboratory of Coal Conversion
- Institute of Coal Chemistry
- Chinese Academy of Sciences
- Taiyuan 030001
- PR China
| | - Jianguo Wang
- State Key Laboratory of Coal Conversion
- Institute of Coal Chemistry
- Chinese Academy of Sciences
- Taiyuan 030001
- PR China
| | - Weibin Fan
- State Key Laboratory of Coal Conversion
- Institute of Coal Chemistry
- Chinese Academy of Sciences
- Taiyuan 030001
- PR China
| |
Collapse
|
244
|
Li M, Wilkins M. Flow cytometry for quantitation of polyhydroxybutyrate production by Cupriavidus necator using alkaline pretreated liquor from corn stover. BIORESOURCE TECHNOLOGY 2020; 295:122254. [PMID: 31629285 DOI: 10.1016/j.biortech.2019.122254] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
Alkaline pretreated liquor (APL) from lignocellulosic feedstock pretreatment is a lignin-rich stream. Polyhydroxybutyrate (PHB), a biodegradable polymer, has been previously synthesized from APL. It is of interest to monitor PHB production and cell number from APL rapidly for process control. However, APL has insoluble substances and is dark, which makes quantitation of cells by visible light absorbance difficult. A sample preparation method was developed using Nile Red staining and flow cytometry to quantify bacterial cells and PHB concentration. A linear model with good fitness (R2 = 0.9939) was constructed to predict PHB concentration (0.2-2.1 g/L) based on fluorescence intensity acquired from a flow cytometer. A linear model (R2 = 0.8614) to predict cell number based on fluorescence intensity was also established. The good correlation between PHB concentration and fluorescence intensity indicates the potential of applying flow cytometry for quantitation of PHB from APL and other media that is dark and/or contains insoluble particles.
Collapse
Affiliation(s)
- Mengxing Li
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Statistics, The University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Mark Wilkins
- Department of Biological Systems Engineering, The University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| |
Collapse
|
245
|
Nguyen ST, Murray PRD, Knowles RR. Light-Driven Depolymerization of Native Lignin Enabled by Proton-Coupled Electron Transfer. ACS Catal 2019. [DOI: 10.1021/acscatal.9b04813] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Suong T. Nguyen
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Philip R. D. Murray
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert R. Knowles
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
246
|
Chan JC, Paice M, Zhang X. Enzymatic Oxidation of Lignin: Challenges and Barriers Toward Practical Applications. ChemCatChem 2019. [DOI: 10.1002/cctc.201901480] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jou C. Chan
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
| | - Michael Paice
- FPInnovations Pulp Paper & Bioproducts 2665 East Mall Vancouver BC V6T 1Z4 Canada
| | - Xiao Zhang
- Voiland School of Chemical Engineering and Bioengineering Washington State University 2710 Crimson Way Richland WA-99354 USA
- Pacific Northwest National Laboratory 520 Battelle Boulevard P.O. Box 999, MSIN P8-60 Richland WA-99352 USA
| |
Collapse
|
247
|
Stevens JC, Shi J. Biocatalysis in ionic liquids for lignin valorization: Opportunities and recent developments. Biotechnol Adv 2019; 37:107418. [DOI: 10.1016/j.biotechadv.2019.107418] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/13/2019] [Accepted: 07/15/2019] [Indexed: 01/11/2023]
|
248
|
Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO. High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. Environ Microbiol 2019; 22:255-269. [PMID: 31657101 PMCID: PMC7078882 DOI: 10.1111/1462-2920.14843] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/27/2019] [Accepted: 10/23/2019] [Indexed: 12/19/2022]
Abstract
Genome-scale reconstructions of metabolism are computational species-specific knowledge bases able to compute systemic metabolic properties. We present a comprehensive and validated reconstruction of the biotechnologically relevant bacterium Pseudomonas putida KT2440 that greatly expands computable predictions of its metabolic states. The reconstruction represents a significant reactome expansion over available reconstructed bacterial metabolic networks. Specifically, iJN1462 (i) incorporates several hundred additional genes and associated reactions resulting in new predictive capabilities, including new nutrients supporting growth; (ii) was validated by in vivo growth screens that included previously untested carbon (48) and nitrogen (41) sources; (iii) yielded gene essentiality predictions showing large accuracy when compared with a knock-out library and Bar-seq data; and (iv) allowed mapping of its network to 82 P. putida sequenced strains revealing functional core that reflect the large metabolic versatility of this species, including aromatic compounds derived from lignin. Thus, this study provides a thoroughly updated metabolic reconstruction and new computable phenotypes for P. putida, which can be leveraged as a first step toward understanding the pan metabolic capabilities of Pseudomonas.
Collapse
Affiliation(s)
- Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Joshua Mueller
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Francisco J Canalejo
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Estrella Duque
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Jonathan Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Juan Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Wei Niu
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| |
Collapse
|
249
|
Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
|
250
|
Promoting microbial utilization of phenolic substrates from bio-oil. ACTA ACUST UNITED AC 2019; 46:1531-1545. [DOI: 10.1007/s10295-019-02208-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/21/2019] [Indexed: 10/26/2022]
Abstract
Abstract
The economic viability of the biorefinery concept is limited by the valorization of lignin. One possible method of lignin valorization is biological upgrading with aromatic-catabolic microbes. In conjunction, lignin monomers can be produced by fast pyrolysis and fractionation. However, biological upgrading of these lignin monomers is limited by low water solubility. Here, we address the problem of low water solubility with an emulsifier blend containing approximately 70 wt% Tween® 20 and 30 wt% Span® 80. Pseudomonas putida KT2440 grew to an optical density (OD600) of 1.0 ± 0.2 when supplied with 1.6 wt% emulsified phenolic monomer-rich product produced by fast pyrolysis of red oak using an emulsifier dose of 0.076 ± 0.002 g emulsifier blend per g of phenolic monomer-rich product. This approach partially mitigated the toxicity of the model phenolic monomer p-coumarate to the microbe, but not benzoate or vanillin. This study provides a proof of concept that processing of biomass-derived phenolics to increase aqueous availability can enhance microbial utilization.
Collapse
|