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Meriläinen E, Efimova E, Santala V, Santala S. Carbon-wise utilization of lignin-related compounds by synergistically employing anaerobic and aerobic bacteria. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:78. [PMID: 38851749 PMCID: PMC11161944 DOI: 10.1186/s13068-024-02526-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Lignin is a highly abundant but strongly underutilized natural resource that could serve as a sustainable feedstock for producing chemicals by microbial cell factories. Because of the heterogeneous nature of the lignin feedstocks, the biological upgrading of lignin relying on the metabolic routes of aerobic bacteria is currently considered as the most promising approach. However, the limited substrate range and the inefficient catabolism of the production hosts hinder the upgrading of lignin-related aromatics. Particularly, the aerobic O-demethylation of the methoxyl groups in aromatic substrates is energy-limited, inhibits growth, and results in carbon loss in the form of CO2. RESULTS In this study, we present a novel approach for carbon-wise utilization of lignin-related aromatics by the integration of anaerobic and aerobic metabolisms. In practice, we employed an acetogenic bacterium Acetobacterium woodii for anaerobic O-demethylation of aromatic compounds, which distinctively differs from the aerobic O-demethylation; in the process, the carbon from the methoxyl groups is fixed together with CO2 to form acetate, while the aromatic ring remains unchanged. These accessible end-metabolites were then utilized by an aerobic bacterium Acinetobacter baylyi ADP1. By utilizing this cocultivation approach, we demonstrated an upgrading of guaiacol, an abundant but inaccessible substrate to most microbes, into a plastic precursor muconate, with a nearly equimolar yields (0.9 mol/mol in a small-scale cultivation and 1.0 mol/mol in a one-pot bioreactor cultivation). The process required only a minor genetic engineering, namely a single gene knock-out. Noticeably, by employing a metabolic integration of the two bacteria, it was possible to produce biomass and muconate by utilizing only CO2 and guaiacol as carbon sources. CONCLUSIONS By the novel approach, we were able to overcome the issues related to aerobic O-demethylation of methoxylated aromatic substrates and demonstrated carbon-wise conversion of lignin-related aromatics to products with yields unattainable by aerobic processes. This study highlights the power of synergistic integration of distinctive metabolic features of bacteria, thus unlocking new opportunities for harnessing microbial cocultures in upgrading challenging feedstocks.
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Affiliation(s)
- Ella Meriläinen
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Elena Efimova
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Ville Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Suvi Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta Campus, Korkeakoulunkatu 8, 33720, Tampere, Finland.
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Shrestha S, Awasthi D, Chen Y, Gin J, Petzold CJ, Adams PD, Simmons BA, Singer SW. Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2. Appl Environ Microbiol 2023; 89:e0085223. [PMID: 37724856 PMCID: PMC10617552 DOI: 10.1128/aem.00852-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in P. putida M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds (p-coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis revealed that glucose exerted stronger repression than xylose on the aromatic catabolic proteins. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during cultivation with aromatic compounds implying simultaneous catabolite repression by sugars and aromatic compounds. Reduction of crc expression via CRISPRi led to faster growth and glucose and p-coumarate uptake in the CRISPRi strains compared to the control, while no difference was observed on xylose+p-coumarate. The increased abundances of Eda and amino acid biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that CrcY and CrcZ homologues levels in M2, previously identified in P. putida strains, were lower under strong CCR (glucose+p-coumarate) condition compared to when repression was absent (p-coumarate or glucose only).IMPORTANCEA newly isolated Pseudomonas putida strain, P. putida M2, can utilize both hexose and pentose sugars as well as aromatic compounds making it a promising host for the valorization of lignocellulosic biomass. Pseudomonads have developed a regulatory strategy, carbon catabolite repression, to control the assimilation of carbon sources in the environment. Carbon catabolite repression may impede the simultaneous and complete metabolism of sugars and aromatic compounds present in lignocellulosic biomass and hinder the development of an efficient industrial biocatalyst. This study provides insight into the cellular physiology and proteome during mixed-substrate utilization in P. putida M2. The phenotypic and proteomics results demonstrated simultaneous catabolite repression in the sugar-aromatic mixtures, while the CRISPRi and sRNA sequencing demonstrated the potential role of the crc gene and small RNAs in carbon catabolite repression.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jennifer Gin
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W. Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Wu X, De Bruyn M, Barta K. Deriving high value products from depolymerized lignin oil, aided by (bio)catalytic funneling strategies. Chem Commun (Camb) 2023; 59:9929-9951. [PMID: 37526604 DOI: 10.1039/d3cc01555f] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Lignin holds tremendous and versatile possibilities to produce value-added chemicals and high performing polymeric materials. Over the years, different cutting-edge lignin depolymerization methodologies have been developed, mainly focusing on achieving excellent yields of mono-phenolic products, some even approaching the theoretical maximum. However, due to lignin's inherent heterogeneity and recalcitrance, its depolymerization leads to relatively complex product streams, also containing dimers, and higher molecular weight fragments in substantial quantities. The subsequent chemo-catalytic valorization of these higher molecular weight streams, containing difficult-to-break, mainly C-C covalent bonds, is tremendously challenging, and has consequently received much less attention. In this minireview, we present an overview of recent advances on the development of sustainable biorefinery strategies aimed at the production of well-defined chemicals and polymeric materials, the prime focus being on depolymerized lignin oils, containing high molecular weight fractions. The key central unit operation to achieve this is (bio)catalytic funneling, which holds great potential to overcome separation and purification challenges.
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Affiliation(s)
- Xianyuan Wu
- University of Groningen, Stratingh Institute for Chemistry, Nijenborgh 4, Groningen, The Netherlands
| | - Mario De Bruyn
- University of Graz, Department of Chemistry, Organic and Bioorganic Chemistry, Heinrichstrasse 28/II, 8010 Graz, Austria.
| | - Katalin Barta
- University of Groningen, Stratingh Institute for Chemistry, Nijenborgh 4, Groningen, The Netherlands
- University of Graz, Department of Chemistry, Organic and Bioorganic Chemistry, Heinrichstrasse 28/II, 8010 Graz, Austria.
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Lignin Valorization: Production of High Value-Added Compounds by Engineered Microorganisms. Catalysts 2023. [DOI: 10.3390/catal13030555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Lignin is the second most abundant polymer in nature, which is also widely generated during biomass fractionation in lignocellulose biorefineries. At present, most of technical lignin is simply burnt for energy supply although it represents the richest natural source of aromatics, and thus it is a promising feedstock for generation of value-added compounds. Lignin is heterogeneous in composition and recalcitrant to degradation, with this substantially hampering its use. Notably, microbes have evolved particular enzymes and specialized metabolic pathways to degrade this polymer and metabolize its various aromatic components. In recent years, novel pathways have been designed allowing to establish engineered microbial cell factories able to efficiently funnel the lignin degradation products into few metabolic intermediates, representing suitable starting points for the synthesis of a variety of valuable molecules. This review focuses on recent success cases (at the laboratory/pilot scale) based on systems metabolic engineering studies aimed at generating value-added and specialty chemicals, with much emphasis on the production of cis,cis-muconic acid, a building block of recognized industrial value for the synthesis of plastic materials. The upgrade of this global waste stream promises a sustainable product portfolio, which will become an industrial reality when economic issues related to process scale up will be tackled.
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Son J, Lim SH, Kim YJ, Lim HJ, Lee JY, Jeong S, Park C, Park SJ. Customized valorization of waste streams by Pseudomonas putida: State-of-the-art, challenges, and future trends. BIORESOURCE TECHNOLOGY 2023; 371:128607. [PMID: 36638894 DOI: 10.1016/j.biortech.2023.128607] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Preventing catastrophic climate events warrants prompt action to delay global warming, which threatens health and food security. In this context, waste management using engineered microbes has emerged as a long-term eco-friendly solution for addressing the global climate crisis and transitioning to clean energy. Notably, Pseudomonas putida can valorize industry-derived synthetic wastes including plastics, oils, food, and agricultural waste into products of interest, and it has been extensively explored for establishing a fully circular bioeconomy through the conversion of waste into bio-based products, including platform chemicals (e.g., cis,cis-muconic and adipic acid) and biopolymers (e.g., medium-chain length polyhydroxyalkanoate). However, the efficiency of waste pretreatment technologies, capability of microbial cell factories, and practicability of synthetic biology tools remain low, posing a challenge to the industrial application of P. putida. The present review discusses the state-of-the-art, challenges, and future prospects for divergent biosynthesis of versatile products from waste-derived feedstocks using P. putida.
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Affiliation(s)
- Jina Son
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seo Hyun Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yu Jin Kim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hye Jin Lim
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ji Yeon Lee
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seona Jeong
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Chulhwan Park
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Si Jae Park
- Department of Chemical Engineering and Materials Science, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea.
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Kohlstedt M, Weimer A, Weiland F, Stolzenberger J, Selzer M, Sanz M, Kramps L, Wittmann C. Biobased PET from lignin using an engineered cis, cis-muconate-producing Pseudomonas putida strain with superior robustness, energy and redox properties. Metab Eng 2022; 72:337-352. [DOI: 10.1016/j.ymben.2022.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/18/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022]
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Weiland F, Kohlstedt M, Wittmann C. Guiding stars to the field of dreams: Metabolically engineered pathways and microbial platforms for a sustainable lignin-based industry. Metab Eng 2021; 71:13-41. [PMID: 34864214 DOI: 10.1016/j.ymben.2021.11.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 12/19/2022]
Abstract
Lignin is an important structural component of terrestrial plants and is readily generated during biomass fractionation in lignocellulose processing facilities. Due to lacking alternatives the majority of technical lignins is industrially simply burned into heat and energy. However, regarding its vast abundance and a chemically interesting richness in aromatics, lignin is presently regarded as the most under-utilized and promising feedstock for value-added applications. Notably, microbes have evolved powerful enzymes and pathways that break down lignin and metabolize its various aromatic components. This natural pathway atlas meanwhile serves as a guiding star for metabolic engineers to breed designed cell factories and efficiently upgrade this global waste stream. The metabolism of aromatic compounds, in combination with success stories from systems metabolic engineering, as reviewed here, promises a sustainable product portfolio from lignin, comprising bulk and specialty chemicals, biomaterials, and fuels.
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Affiliation(s)
- Fabia Weiland
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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8
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Wirth NT, Nikel PI. Combinatorial pathway balancing provides biosynthetic access to 2-fluoro- cis, cis-muconate in engineered Pseudomonas putida. CHEM CATALYSIS 2021; 1:1234-1259. [PMID: 34977847 PMCID: PMC8711041 DOI: 10.1016/j.checat.2021.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/15/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022]
Abstract
The wealth of bio-based building blocks produced by engineered microorganisms seldom include halogen atoms. Muconate is a platform chemical with a number of industrial applications that could be broadened by introducing fluorine atoms to tune its physicochemical properties. The soil bacterium Pseudomonas putida naturally assimilates benzoate via the ortho-cleavage pathway with cis,cis-muconate as intermediate. Here, we harnessed the native enzymatic machinery (encoded within the ben and cat gene clusters) to provide catalytic access to 2-fluoro-cis,cis-muconate (2-FMA) from fluorinated benzoates. The reactions in this pathway are highly imbalanced, leading to accumulation of toxic intermediates and limited substrate conversion. By disentangling regulatory patterns of ben and cat in response to fluorinated effectors, metabolic activities were adjusted to favor 2-FMA biosynthesis. After implementing this combinatorial approach, engineered P. putida converted 3-fluorobenzoate to 2-FMA at the maximum theoretical yield. Hence, this study illustrates how synthetic biology can expand the diversity of nature's biochemical catalysis.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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9
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Characterization of highly ferulate-tolerant Acinetobacter baylyi ADP1 isolates by a rapid reverse-engineering method. Appl Environ Microbiol 2021; 88:e0178021. [PMID: 34788063 DOI: 10.1128/aem.01780-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptive laboratory evolution (ALE) is a powerful approach for improving phenotypes of microbial hosts. Evolved strains typically contain numerous mutations that can be revealed by whole-genome sequencing. However, determining the contribution of specific mutations to new phenotypes is typically challenging and laborious. This task is complicated by factors such as the mutation type, the genomic context, and the interplay between different mutations. Here, a novel approach was developed to identify the significance of mutations in strains evolved from Acinetobacter baylyi ADP1. This method, termed Rapid Advantageous Mutation ScrEening and Selection (RAMSES), was used to analyze mutants that emerged from stepwise adaptation to, and consumption of, high levels of ferulate, a common lignin-derived aromatic compound. After whole-genome sequence analysis, RAMSES allowed rapid determination of effective mutations and seamless introduction of the beneficial mutations into the chromosomes of new strains with different genetic backgrounds. This simple approach to reverse-engineering exploits the natural competence and high recombination efficiency of ADP1. Mutated DNA, added directly to growing cells, replaces homologous chromosomal regions to generate transformants that will become enriched if there is selective benefit. Thus, advantageous mutations can be rapidly identified. Here, the growth advantage of transformants under selective pressure revealed key mutations in genes related to aromatic transport, including hcaE, hcaK, and vanK, and a gene, ACIAD0482, which is associated with lipopolysaccharide synthesis. This study provides insights into enhanced utilization of industrially relevant aromatic substrates and demonstrates the use of A. baylyi ADP1 as a convenient platform for strain development and evolution studies. Importance Microbial conversion of lignin-enriched streams is a promising approach for lignin valorization. However, the lignin-derived aromatic compounds are toxic to cells at relevant concentrations. Although adaptive laboratory evolution (ALE) is a powerful approach to develop more tolerant strains, it is typically laborious to identify the mechanisms underlying phenotypic improvement. We employed Acinetobacter baylyi ADP1, an aromatic compound degrading strain that may be useful for biotechnology. The natural competence and high recombination efficiency of this strain can be exploited for critical applications such as the breakdown of lignin and plastics, abundant polymers composed of aromatic subunits. The natural transformability of this bacterium enabled us to develop a novel approach for rapid screening of advantageous mutations from ALE-derived aromatic-tolerant ADP1-derived strains. We clarified the mechanisms and genetic targets for improved tolerance towards common lignin-derived aromatic compounds. This study facilitates metabolic engineering for lignin valorization.
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10
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A Review on the Utilization of Lignin as a Fermentation Substrate to Produce Lignin-Modifying Enzymes and Other Value-Added Products. Molecules 2021; 26:molecules26102960. [PMID: 34065753 PMCID: PMC8156730 DOI: 10.3390/molecules26102960] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/11/2022] Open
Abstract
The lignocellulosic biomass is comprised of three major components: cellulose, hemicellulose, and lignin. Among these three, cellulose and hemicellulose were already used for the generation of simple sugars and subsequent value-added products. However, lignin is the least applied material in this regard because of its complex and highly variable nature. Regardless, lignin is the most abundant material, and it can be used to produce value-added products such as lignin-modifying enzymes (LMEs), polyhydroxyalkanoates (PHAs), microbial lipids, vanillin, muconic acid, and many others. This review explores the potential of lignin as the microbial substrate to produce such products. A special focus was given to the different types of lignin and how each one can be used in different microbial and biochemical pathways to produce intermediate products, which can then be used as the value-added products or base to make other products. This review paper will summarize the effectiveness of lignin as a microbial substrate to produce value-added products through microbial fermentations. First, basic structures of lignin along with its types and chemistry are discussed. The subsequent sections highlight LMEs and how such enzymes can enhance the value of lignin by microbial degradation. A major focus was also given to the value-added products that can be produced from lignin.
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Kumar M, You S, Beiyuan J, Luo G, Gupta J, Kumar S, Singh L, Zhang S, Tsang DCW. Lignin valorization by bacterial genus Pseudomonas: State-of-the-art review and prospects. BIORESOURCE TECHNOLOGY 2021; 320:124412. [PMID: 33249259 DOI: 10.1016/j.biortech.2020.124412] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
The most prominent aromatic feedstock on Earth is lignin, however, lignin valorization is still an underrated subject. The principal preparatory strategies for lignin valorization are fragmentation and depolymerization which help in the production of fuels and chemicals. Owing to lignin's structural heterogeneity, these strategies result in product generation which requires tedious separation and purification to extract target products. The bacterial genus Pseudomonas has been dominant for its lignin valorization potency, owing to a robust enzymatic machinery that is used to funnel variable lignin derivatives into certain target products such as polyhydroxyalkanotes (PHAs) and cis, cis-muconic acid (MA). In this review, the potential of genus Pseudomonas in lignin valorization is critically reviewed along with the advanced genetic techniques and tools to ease the use of lignin/lignin-model compounds for the synthesis of bioproducts. This review also highlights the research gaps in lignin biovalorization and discuss the challenges and possibilities for future research.
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Affiliation(s)
- Manish Kumar
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Siming You
- University of Glasgow, James Watt School of Engineering, Glasgow G12 8 QQ, United Kingdom
| | - Jingzi Beiyuan
- Biochar Engineering Technology Research Center of Guangdong Province, School of Environment and Chemical Engineering, Foshan University, Foshan 528000, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sunil Kumar
- CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Lal Singh
- CSIR - National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440 020, India
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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12
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Wang S, Cui J, Bilal M, Hu H, Wang W, Zhang X. Pseudomonas spp. as cell factories (MCFs) for value-added products: from rational design to industrial applications. Crit Rev Biotechnol 2020; 40:1232-1249. [PMID: 32907412 DOI: 10.1080/07388551.2020.1809990] [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: 10/23/2022]
Abstract
In recent years, there has been increasing interest in microbial biotechnology for the production of value-added compounds from renewable resources. Pseudomonas species have been proposed as a suitable workhorse for high-value secondary metabolite production because of their unique characteristics for fast growth on sustainable carbon sources, a clear inherited background, versatile intrinsic metabolism with diverse enzymatic capacities, and their robustness in an extreme environment. It has also been demonstrated that metabolically engineered Pseudomonas strains can produce several industrially valuable aromatic chemicals and natural products such as phenazines, polyhydroxyalkanoates, rhamnolipids, and insecticidal proteins from renewable feedstocks with remarkably high yields suitable for commercial application. In this review, we summarize cell factory construction in Pseudomonas for the biosynthesis of native and non-native bioactive compounds in P. putida, P. chlororaphis, P. aeruginosa, as well as pharmaceutical proteins production by P. fluorescens. Additionally, some novel strategies together with metabolic engineering strategies in order to improve the biosynthetic abilities of Pseudomonas as an ideal chassis are discussed. Finally, we proposed emerging opportunities, challenges, and essential strategies to enable the successful development of Pseudomonas as versatile microbial cell factories for the bioproduction of diverse bioactive compounds.
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Affiliation(s)
- Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiajia Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Weimer A, Kohlstedt M, Volke DC, Nikel PI, Wittmann C. Industrial biotechnology of Pseudomonas putida: advances and prospects. Appl Microbiol Biotechnol 2020; 104:7745-7766. [PMID: 32789744 PMCID: PMC7447670 DOI: 10.1007/s00253-020-10811-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 11/17/2022]
Abstract
Pseudomonas putida is a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications of P. putida as a cell factory. KEY POINTS: • Pseudomonas putida advances to a global industrial cell factory. • Novel tools enable system-wide understanding and streamlined genomic engineering. • Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, 66123, Saarbrücken, Germany.
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Choi S, Lee HN, Park E, Lee SJ, Kim ES. Recent Advances in Microbial Production of cis,cis-Muconic Acid. Biomolecules 2020; 10:biom10091238. [PMID: 32854378 PMCID: PMC7564838 DOI: 10.3390/biom10091238] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
cis,cis-Muconic acid (MA) is a valuable C6 dicarboxylic acid platform chemical that is used as a starting material for the production of various valuable polymers and drugs, including adipic acid and terephthalic acid. As an alternative to traditional chemical processes, bio-based MA production has progressed to the establishment of de novo MA pathways in several microorganisms, such as Escherichia coli, Corynebacterium glutamicum, Pseudomonas putida, and Saccharomyces cerevisiae. Redesign of the metabolic pathway, intermediate flux control, and culture process optimization were all pursued to maximize the microbial MA production yield. Recently, MA production from biomass, such as the aromatic polymer lignin, has also attracted attention from researchers focusing on microbes that are tolerant to aromatic compounds. This paper summarizes recent microbial MA production strategies that involve engineering the metabolic pathway genes as well as the heterologous expression of some foreign genes involved in MA biosynthesis. Microbial MA production will continue to play a vital role in the field of bio-refineries and a feasible way to complement various petrochemical-based chemical processes.
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Affiliation(s)
- Sisun Choi
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
| | - Han-Na Lee
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
- STR Biotech Co., Ltd., Chuncheon-si, Gangwon-do 24232, Korea;
| | - Eunhwi Park
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
| | - Sang-Jong Lee
- STR Biotech Co., Ltd., Chuncheon-si, Gangwon-do 24232, Korea;
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
- Correspondence: ; Tel.: +82-32-860-8318; Fax: +82-32-872-4046
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15
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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]
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16
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Duuren JBJH, Wild PJ, Starck S, Bradtmöller C, Selzer M, Mehlmann K, Schneider R, Kohlstedt M, Poblete‐Castro I, Stolzenberger J, Barton N, Fritz M, Scholl S, Venus J, Wittmann C. Limited life cycle and cost assessment for the bioconversion of lignin‐derived aromatics into adipic acid. Biotechnol Bioeng 2020; 117:1381-1393. [DOI: 10.1002/bit.27299] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/03/2020] [Indexed: 01/20/2023]
Affiliation(s)
| | - Paul J. Wild
- Biomass & Energy Efficiency, TNOPetten The Netherlands
| | - Sören Starck
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Christian Bradtmöller
- Institute for Chemical and Thermal Process EngineeringTechnische Universität BraunschweigBraunschweig Germany
| | - Mirjam Selzer
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Kerstin Mehlmann
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Roland Schneider
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Michael Kohlstedt
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Ignacio Poblete‐Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural SciencesUniversidad Andres BelloSantiago de Chile Chile
| | | | - Nadja Barton
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Michel Fritz
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
| | - Stephan Scholl
- Institute for Chemical and Thermal Process EngineeringTechnische Universität BraunschweigBraunschweig Germany
| | - Joachim Venus
- Department of BioengineeringLeibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Potsdam Germany
| | - Christoph Wittmann
- Institute of Systems BiotechnologySaarland UniversitySaarbrücken Germany
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17
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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]
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18
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Li X, Zheng Y. Biotransformation of lignin: Mechanisms, applications and future work. Biotechnol Prog 2019; 36:e2922. [PMID: 31587530 DOI: 10.1002/btpr.2922] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 01/04/2023]
Abstract
As one of the most abundant polymers in biosphere, lignin has attracted extensive attention as a kind of promising feedstock for biofuel and bio-based products. However, the utilization of lignin presents various challenges in that its complex composition and structure and high resistance to degradation. Lignin conversion through biological platform harnesses the catalytic power of microorganisms to decompose complex lignin molecules and obtain value-added products through biosynthesis. Given the heterogeneity of lignin, various microbial metabolic pathways are involved in lignin bioconversion processes, which has been characterized in extensive research work. With different types of lignin substrates (e.g., model compounds, technical lignin, and lignocellulosic biomass), several bacterial and fungal species have been proved to own lignin-degrading abilities and accumulate microbial products (e.g., lipid and polyhydroxyalkanoates), while the lignin conversion efficiencies are still relatively low. Genetic and metabolic strategies have been developed to enhance lignin biodegradation by reprogramming microbial metabolism, and diverse products, such as vanillin and dicarboxylic acids were also produced from lignin. This article aims at presenting a comprehensive review on lignin bioconversion including lignin degradation mechanisms, metabolic pathways, and applications for the production of value-added bioproducts. Advanced techniques on genetic and metabolic engineering are also covered in the recent development of biological platforms for lignin utilization. To conclude this article, the existing challenges for efficient lignin bioprocessing are analyzed and possible directions for future work are proposed.
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Affiliation(s)
- Xiang Li
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas
| | - Yi Zheng
- Department of Grain Science and Industry, Kansas State University, Manhattan, Kansas
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19
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Pleissner D, Dietz D, van Duuren JBJH, Wittmann C, Yang X, Lin CSK, Venus J. Biotechnological Production of Organic Acids from Renewable Resources. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 166:373-410. [PMID: 28265703 DOI: 10.1007/10_2016_73] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Biotechnological processes are promising alternatives to petrochemical routes for overcoming the challenges of resource depletion in the future in a sustainable way. The strategies of white biotechnology allow the utilization of inexpensive and renewable resources for the production of a broad range of bio-based compounds. Renewable resources, such as agricultural residues or residues from food production, are produced in large amounts have been shown to be promising carbon and/or nitrogen sources. This chapter focuses on the biotechnological production of lactic acid, acrylic acid, succinic acid, muconic acid, and lactobionic acid from renewable residues, these products being used as monomers for bio-based material and/or as food supplements. These five acids have high economic values and the potential to overcome the "valley of death" between laboratory/pilot scale and commercial/industrial scale. This chapter also provides an overview of the production strategies, including microbial strain development, used to convert renewable resources into value-added products.
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Affiliation(s)
- Daniel Pleissner
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Donna Dietz
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Xiaofeng Yang
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Joachim Venus
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany.
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20
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Kukurugya MA, Mendonca CM, Solhtalab M, Wilkes RA, Thannhauser TW, Aristilde L. Multi-omics analysis unravels a segregated metabolic flux network that tunes co-utilization of sugar and aromatic carbons in Pseudomonas putida. J Biol Chem 2019; 294:8464-8479. [PMID: 30936206 DOI: 10.1074/jbc.ra119.007885] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/26/2019] [Indexed: 11/06/2022] Open
Abstract
Pseudomonas species thrive in different nutritional environments and can catabolize divergent carbon substrates. These capabilities have important implications for the role of these species in natural and engineered carbon processing. However, the metabolic phenotypes enabling Pseudomonas to utilize mixed substrates remain poorly understood. Here, we employed a multi-omics approach involving stable isotope tracers, metabolomics, fluxomics, and proteomics in Pseudomonas putida KT2440 to investigate the constitutive metabolic network that achieves co-utilization of glucose and benzoate, respectively a monomer of carbohydrate polymers and a derivative of lignin monomers. Despite nearly equal consumption of both substrates, metabolite isotopologues revealed nonuniform assimilation throughout the metabolic network. Gluconeogenic flux of benzoate-derived carbons from the tricarboxylic acid cycle did not reach the upper Embden-Meyerhof-Parnas pathway nor the pentose-phosphate pathway. These latter two pathways were populated exclusively by glucose-derived carbons through a cyclic connection with the Entner-Doudoroff pathway. We integrated the 13C-metabolomics data with physiological parameters for quantitative flux analysis, demonstrating that the metabolic segregation of the substrate carbons optimally sustained biosynthetic flux demands and redox balance. Changes in protein abundance partially predicted the metabolic flux changes in cells grown on the glucose:benzoate mixture versus on glucose alone. Notably, flux magnitude and directionality were also maintained by metabolite levels and regulation of phosphorylation of key metabolic enzymes. These findings provide new insights into the metabolic architecture that affords adaptability of P. putida to divergent carbon substrates and highlight regulatory points at different metabolic nodes that may underlie the high nutritional flexibility of Pseudomonas species.
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Affiliation(s)
- Matthew A Kukurugya
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Caroll M Mendonca
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Mina Solhtalab
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Rebecca A Wilkes
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
| | | | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States.
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Huccetogullari D, Luo ZW, Lee SY. Metabolic engineering of microorganisms for production of aromatic compounds. Microb Cell Fact 2019; 18:41. [PMID: 30808357 PMCID: PMC6390333 DOI: 10.1186/s12934-019-1090-4] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/19/2019] [Indexed: 01/09/2023] Open
Abstract
Metabolic engineering has been enabling development of high performance microbial strains for the efficient production of natural and non-natural compounds from renewable non-food biomass. Even though microbial production of various chemicals has successfully been conducted and commercialized, there are still numerous chemicals and materials that await their efficient bio-based production. Aromatic chemicals, which are typically derived from benzene, toluene and xylene in petroleum industry, have been used in large amounts in various industries. Over the last three decades, many metabolically engineered microorganisms have been developed for the bio-based production of aromatic chemicals, many of which are derived from aromatic amino acid pathways. This review highlights the latest metabolic engineering strategies and tools applied to the biosynthesis of aromatic chemicals, many derived from shikimate and aromatic amino acids, including L-phenylalanine, L-tyrosine and L-tryptophan. It is expected that more and more engineered microorganisms capable of efficiently producing aromatic chemicals will be developed toward their industrial-scale production from renewable biomass.
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Affiliation(s)
- Damla Huccetogullari
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Zi Wei Luo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea.
- BioProcess Engineering Research Center and Bioinformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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22
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Calero P, Nikel PI. Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms. Microb Biotechnol 2019; 12:98-124. [PMID: 29926529 PMCID: PMC6302729 DOI: 10.1111/1751-7915.13292] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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23
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Becker J, Kuhl M, Kohlstedt M, Starck S, Wittmann C. Metabolic engineering of Corynebacterium glutamicum for the production of cis, cis-muconic acid from lignin. Microb Cell Fact 2018; 17:115. [PMID: 30029656 PMCID: PMC6054733 DOI: 10.1186/s12934-018-0963-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/13/2018] [Indexed: 11/25/2022] Open
Abstract
Background Cis, cis-muconic acid (MA) is a dicarboxylic acid of recognized industrial value. It provides direct access to adipic acid and terephthalic acid, prominent monomers of commercial plastics. Results In the present work, we engineered the soil bacterium Corynebacterium glutamicum into a stable genome-based cell factory for high-level production of bio-based MA from aromatics and lignin hydrolysates. The elimination of muconate cycloisomerase (catB) in the catechol branch of the β-ketoadipate pathway provided a mutant, which accumulated MA at 100% molar yield from catechol, phenol, and benzoic acid, using glucose as additional growth substrate. The production of MA was optimized by constitutive overexpression of catA, which increased the activity of the encoded catechol 1,2-dioxygenase, forming MA from catechol, tenfold. Intracellular levels of catechol were more than 30-fold lower than extracellular levels, minimizing toxicity, but still saturating the high affinity CatA enzyme. In a fed-batch process, the created strain C. glutamicum MA-2 accumulated 85 g L−1 MA from catechol in 60 h and achieved a maximum volumetric productivity of 2.4 g L−1 h−1. The strain was furthermore used to demonstrate the production of MA from lignin in a cascade process. Following hydrothermal depolymerization of softwood lignin into small aromatics, the MA-2 strain accumulated 1.8 g L−1 MA from the obtained hydrolysate. Conclusions Our findings open the door to valorize lignin, the second most abundant polymer on earth, by metabolically engineered C. glutamicum for industrial production of MA and potentially other chemicals. Electronic supplementary material The online version of this article (10.1186/s12934-018-0963-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Judith Becker
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sören Starck
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany.
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Kohlstedt M, Starck S, Barton N, Stolzenberger J, Selzer M, Mehlmann K, Schneider R, Pleissner D, Rinkel J, Dickschat JS, Venus J, B.J.H. van Duuren J, Wittmann C. From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida. Metab Eng 2018; 47:279-293. [DOI: 10.1016/j.ymben.2018.03.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 12/31/2022]
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Ravi K, García-Hidalgo J, Nöbel M, Gorwa-Grauslund MF, Lidén G. Biological conversion of aromatic monolignol compounds by a Pseudomonas isolate from sediments of the Baltic Sea. AMB Express 2018; 8:32. [PMID: 29500726 PMCID: PMC5834416 DOI: 10.1186/s13568-018-0563-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 02/22/2018] [Indexed: 11/10/2022] Open
Abstract
Bacterial strains were isolated from the sediments of the Baltic Sea using ferulic acid, guaiacol or a lignin-rich softwood waste stream as substrate. In total nine isolates were obtained, five on ferulic acid, two on guaiacol and two on a lignin-rich softwood stream as a carbon source. Three of the isolates were found to be Pseudomonas sp. based on 16S rRNA sequencing. Among them, isolate 9.1, which showed the fastest growth in defined M9 medium, was tentatively identified as a Pseudomonas deceptionensis strain based on the gyrB sequencing. The growth of isolate 9.1 was further examined on six selected lignin model compounds (ferulate, p-coumarate, benzoate, syringate, vanillin and guaiacol) from different upper funneling aromatic pathways and was found able to grow on four out of these six compounds. No growth was detected on syringate and guaiacol. The highest specific growth and uptake rates were observed for benzoate (0.3 h-1 and 4.2 mmol g CDW-1 h-1) whereas the lowest were for the compounds from the coniferyl branch. Interestingly, several pathway intermediates were excreted during batch growth. Vanillyl alcohol was found to be excreted during growth on vanillin. Several other intermediates like cis,cis-muconate, catechol, vanillate and 4-hydroxybenzoate from the known bacterial catabolic pathways were excreted during growth on the model compounds.
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Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Matthias Nöbel
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Marie F. Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, 221 00 Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00 Lund, Sweden
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Pleissner D, Kümmerer K. Green Chemistry and Its Contribution to Industrial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 173:281-298. [PMID: 30270411 DOI: 10.1007/10_2018_73] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sustainable chemistry is a broad framework that starts with the function that a chemical product is offering. Not only chemical but also economic and ethical aspects come into focus throughout the complete lifecycle of chemical products. Green chemistry is an important building block for sustainable chemistry and addresses the issue of greener synthesis and, to a certain degree, the more benign properties of chemicals. The principles of green chemistry clearly aim at making chemical reactions and processes more environmentally friendly. Aspects such as atom efficiency, energy efficiency, harmless reactants, renewable resources, and pollution prevention are considered. Despite the progress made toward a "greener" chemistry, biotechnological processes, as processes for the conversion of biomass into value-added products, have not been properly adapted to new developments. Processes used in industrial biotechnology are predominantly linear. This review elaborates on the potential contributions of green chemistry to industrial biotechnology and vice versa. Examples are presented of how green chemistry and biotechnology can be connected to make substrate supply, upstream and downstream processing, and product formation more sustainable. The chapter ends with a case study of adipic acid production from lignin to illustrate the importance of a strong connection between green chemistry and biotechnology.
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Affiliation(s)
- Daniel Pleissner
- Institute of Sustainable and Environmental Chemistry, Leuphana University of Lüneburg, Lüneburg, Germany.
| | - Klaus Kümmerer
- Institute of Sustainable and Environmental Chemistry, Leuphana University of Lüneburg, Lüneburg, Germany
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27
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Enabling the valorization of guaiacol-based lignin: Integrated chemical and biochemical production of cis,cis-muconic acid using metabolically engineered Amycolatopsis sp ATCC 39116. Metab Eng 2017; 45:200-210. [PMID: 29246517 DOI: 10.1016/j.ymben.2017.12.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/18/2017] [Accepted: 12/01/2017] [Indexed: 01/20/2023]
Abstract
Lignin is nature's second most abundant polymer and displays a largely unexploited renewable resource for value-added bio-production. None of the lignin-based fermentation processes so far managed to use guaiacol (2-methoxy phenol), the predominant aromatic monomer in depolymerized lignin. In this work, we describe metabolic engineering of Amycolatopsis sp. ATCC 39116 to produce cis,cis-muconic acid (MA), a precursor of recognized industrial value for commercial plastics, from guaiacol. The microbe utilized a very broad spectrum of lignin-based aromatics, such as catechol, guaiacol, phenol, toluene, p-coumarate, and benzoate, tolerated them in elevated amounts and even preferred them over sugars. As a next step, we developed a novel approach for genomic engineering of this challenging, GC-rich actinomycete. The successful introduction of conjugation and blue-white screening, using β-glucuronidase, enabled tailored genomic modifications within ten days. Successive deletion of two putative muconate cycloisomerases from the genome provided the mutant Amycolatopsis sp. ATCC 39116 MA-2, which accumulated 3.1gL-1 MA from guaiacol within 24h, achieving a yield of 96%. The mutant was found also capable to produce MA from a guaiacol-rich true lignin hydrolysate, obtained from pine through hydrothermal conversion. This provides an important proof-of-concept to successfully coupling chemical and biochemical process steps into a value chain from the lignin polymer to an industrial chemical. In addition, Amycolatopsis sp. ATCC 39116 MA-2 was able to produce 2-methyl MA from o-cresol (2-methyl phenol), which opens possibilities towards polymers with novel architecture and properties.
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28
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Wang W, Zhang C, Sun X, Su S, Li Q, Linhardt RJ. Efficient, environmentally-friendly and specific valorization of lignin: promising role of non-radical lignolytic enzymes. World J Microbiol Biotechnol 2017; 33:125. [DOI: 10.1007/s11274-017-2286-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022]
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29
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Metabolic engineering strategies to bio-adipic acid production. Curr Opin Biotechnol 2017; 45:136-143. [PMID: 28365404 DOI: 10.1016/j.copbio.2017.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 11/21/2022]
Abstract
Adipic acid is the most industrially important dicarboxylic acid as it is a key monomer in the synthesis of nylon. Today, adipic acid is obtained via a chemical process that relies on petrochemical precursors and releases large quantities of greenhouse gases. In the last two years, significant progress has been made in engineering microbes for the production of adipic acid and its immediate precursors, muconic acid and glucaric acid. Not only have the microbial substrates expanded beyond glucose and glycerol to include lignin monomers and hemicellulose components, but the number of microbial chassis now goes further than Escherichia coli and Saccharomyces cerevisiae to include microbes proficient in aromatic degradation, cellulose secretion and degradation of multiple carbon sources. Here, we review the metabolic engineering and nascent protein engineering strategies undertaken in each of these chassis to convert different feedstocks to adipic, muconic and glucaric acid. We also highlight near term prospects and challenges for each of the metabolic routes discussed.
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Opportunities and challenges in biological lignin valorization. Curr Opin Biotechnol 2016; 42:40-53. [DOI: 10.1016/j.copbio.2016.02.030] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/24/2016] [Indexed: 02/08/2023]
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Poblete-Castro I, Borrero-de Acuña JM, Nikel PI, Kohlstedt M, Wittmann C. Host Organism: Pseudomonas putida. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ignacio Poblete-Castro
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - José M. Borrero-de Acuña
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program; National Spanish Center for Biotechnology (CNB-CSIC); Calle Darwin, 3 28049 Madrid, Spain
| | - Michael Kohlstedt
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
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Deng Y, Ma L, Mao Y. Biological production of adipic acid from renewable substrates: Current and future methods. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.08.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Top value platform chemicals: bio-based production of organic acids. Curr Opin Biotechnol 2015; 36:168-75. [DOI: 10.1016/j.copbio.2015.08.022] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/11/2015] [Accepted: 08/18/2015] [Indexed: 11/19/2022]
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Sonoki T, Morooka M, Sakamoto K, Otsuka Y, Nakamura M, Jellison J, Goodell B. Enhancement of protocatechuate decarboxylase activity for the effective production of muconate from lignin-related aromatic compounds. J Biotechnol 2015; 192 Pt A:71-7. [PMID: 25449108 DOI: 10.1016/j.jbiotec.2014.10.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 10/24/2022]
Abstract
The decarboxylation reaction of protocatechuate has been described as a bottleneck and a rate-limiting step in cis,cis-muconate (ccMA) bioproduction from renewable feedstocks such as sugar. Because sugars are already in high demand in the development of many bio-based products, our work focuses on improving protocatechuate decarboxylase (Pdc) activity and ccMA production in particular, from lignin-related aromatic compounds. We previously had transformed an Escherichia coli strain using aroY, which had been used as a protocatechuate decarboxylase encoding gene from Klebsiella pneumoniae subsp. pneumoniae A170-40, and inserted other required genes from Pseudomonas putida KT2440, to allow the production of ccMA from vanillin. This recombinant strain produced ccMA from vanillin, however the Pdc reaction step remained a bottleneck during incubation. In the current study, we identify a way to increase protocatechuate decarboxylase activity in E. coli through enzyme production involving both aroY and kpdB; the latter which encodes for the B subunit of 4-hydroxybenzoate decarboxylase. This permits expression of Pdc activity at a level approximately 14-fold greater than the strain with aroY only. The expression level of AroY increased, apparently as a function of the co-expression of AroY and KpdB. Our results also imply that ccMA may inhibit vanillate demethylation, a reaction step that is rate limiting for efficient ccMA production from lignin-related aromatic compounds, so even though ccMA production may be enhanced, other challenges to overcome vanilate demethylation inhibition still remain.
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Han L, Liu P, Sun J, Wu Y, Zhang Y, Chen W, Lin J, Wang Q, Ma Y. Engineering catechol 1, 2-dioxygenase by design for improving the performance of the cis, cis-muconic acid synthetic pathway in Escherichia coli. Sci Rep 2015; 5:13435. [PMID: 26306712 PMCID: PMC4549619 DOI: 10.1038/srep13435] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/27/2015] [Indexed: 11/09/2022] Open
Abstract
Regulating and ameliorating enzyme expression and activity greatly affects the performance of a given synthetic pathway. In this study, a new synthetic pathway for cis, cis-muconic acid (ccMA) production was reconstructed without exogenous induction by regulating the constitutive expression of the important enzyme catechol 1,2-dioxygenase (CatA). Next, new CatAs with significantly improved activities were developed to enhance ccMA production using structure-assisted protein design. Nine mutations were designed, simulated and constructed based on the analysis of the CatA crystal structure. These results showed that mutations at Gly72, Leu73 and/or Pro76 in CatA could improve enzyme activity, and the activity of the most effective mutant was 10-fold greater than that of the wild-type CatA from Acinetobacter sp. ADP1. The most productive synthetic pathway with a mutated CatA increased the titer of ccMA by more than 25%. Molecular dynamic simulation results showed that enlarging the entrance of the substrate-binding pocket in the mutants contributed to their increased enzyme activities and thus improved the performance of the synthetic pathway.
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Affiliation(s)
- Li Han
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Yuanqing Wu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuanyuan Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wujiu Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jianping Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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Johnson CW, Beckham GT. Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin. Metab Eng 2015; 28:240-247. [DOI: 10.1016/j.ymben.2015.01.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/08/2015] [Accepted: 01/13/2015] [Indexed: 10/24/2022]
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Xie NZ, Liang H, Huang RB, Xu P. Biotechnological production of muconic acid: current status and future prospects. Biotechnol Adv 2014; 32:615-22. [PMID: 24751381 DOI: 10.1016/j.biotechadv.2014.04.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/23/2014] [Accepted: 04/07/2014] [Indexed: 11/17/2022]
Abstract
Muconic acid (MA), a high value-added bio-product with reactive dicarboxylic groups and conjugated double bonds, has garnered increasing interest owing to its potential applications in the manufacture of new functional resins, bio-plastics, food additives, agrochemicals, and pharmaceuticals. At the very least, MA can be used to produce commercially important bulk chemicals such as adipic acid, terephthalic acid and trimellitic acid. Recently, great progress has been made in the development of biotechnological routes for MA production. This present review provides a comprehensive and systematic overview of recent advances and challenges in biotechnological production of MA. Various biological methods are summarized and compared, and their constraints and possible solutions are also described. Finally, the future prospects are discussed with respect to the current state, challenges, and trends in this field, and the guidelines to develop high-performance microbial cell factories are also proposed for the MA production by systems metabolic engineering.
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Affiliation(s)
- Neng-Zhong Xie
- State Key Laboratory of Non-Food Biomass Energy and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, People's Republic of China
| | - Hong Liang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Ri-Bo Huang
- State Key Laboratory of Non-Food Biomass Energy and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, People's Republic of China.
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
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A microrespirometric method for the determination of stoichiometric and kinetic parameters of heterotrophic and autotrophic cultures. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Quitmann H, Fan R, Czermak P. Acidic organic compounds in beverage, food, and feed production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 143:91-141. [PMID: 24275825 DOI: 10.1007/10_2013_262] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Organic acids and their derivatives are frequently used in beverage, food, and feed production. Acidic additives may act as buffers to regulate acidity, antioxidants, preservatives, flavor enhancers, and sequestrants. Beneficial effects on animal health and growth performance have been observed when using acidic substances as feed additives. Organic acids could be classified in groups according to their chemical structure. Each group of organic acids has its own specific properties and is used for different applications. Organic acids with low molecular weight (e.g. acetic acid, lactic acid, and citric acid), which are part of the primary metabolism, are often produced by fermentation. Others are produced more economically by chemical synthesis based on petrochemical raw materials on an industrial scale (e.g. formic acid, propionic and benzoic acid). Biotechnology-based production is of interest due to legislation, consumer demand for natural ingredients, and increasing environmental awareness. In the United States, for example, biocatalytically produced esters for food applications can be labeled as "natural," whereas identical conventional acid catalyst-based molecules cannot. Natural esters command a price several times that of non-natural esters. Biotechnological routes need to be optimized regarding raw materials and yield, microorganisms, and recovery methods. New bioprocesses are being developed for organic acids, which are at this time commercially produced by chemical synthesis. Moreover, new organic acids that could be produced with biotechnological methods are under investigation for food applications.
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Affiliation(s)
- Hendrich Quitmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Science Mittelhessen, Wiesenstrasse 14, 35390, Giessen, Germany
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Guazzaroni ME, Morgante V, Mirete S, González-Pastor JE. Novel acid resistance genes from the metagenome of the Tinto River, an extremely acidic environment. Environ Microbiol 2012; 15:1088-102. [PMID: 23145860 DOI: 10.1111/1462-2920.12021] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/03/2012] [Accepted: 10/06/2012] [Indexed: 11/28/2022]
Abstract
Microorganisms that thrive in acidic environments are endowed with specialized molecular mechanisms to survive under this extremely harsh condition. In this work, we performed functional screening of six metagenomic libraries from planktonic and rhizosphere microbial communities of the Tinto River, an extremely acidic environment, to identify genes involved in acid resistance. This approach has revealed 15 different genes conferring acid resistance to Escherichia coli, most of which encoding putative proteins of unknown function or previously described proteins not known to be related to acid resistance. Moreover, we were able to assign function to one unknown and three hypothetical proteins. Among the recovered genes were the ClpXP protease, the transcriptional repressor LexA and nucleic acid-binding proteins such as an RNA-binding protein, HU and Dps. Furthermore, nine of the retrieved genes were cloned and expressed in Pseudomonas putida and Bacillus subtilis and, remarkably, most of them were able to expand the capability of these bacteria to survive under severe acid stress. From this set of genes, four presented a broad-host range as they enhance the acid resistance of the three different organisms tested. These results expand our knowledge about the different strategies used by microorganisms to survive under extremely acid conditions.
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Affiliation(s)
- María-Eugenia Guazzaroni
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
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Poblete-Castro I, Becker J, Dohnt K, dos Santos VM, Wittmann C. Industrial biotechnology of Pseudomonas putida and related species. Appl Microbiol Biotechnol 2012; 93:2279-90. [DOI: 10.1007/s00253-012-3928-0] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/29/2022]
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