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Shimizu T, Suzuki K, Inui M. A mycofactocin-associated dehydrogenase is essential for ethylene glycol metabolism by Rhodococcus jostii RHA1. Appl Microbiol Biotechnol 2024; 108:58. [PMID: 38175243 DOI: 10.1007/s00253-023-12966-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
Ethylene glycol is an industrially important diol in many manufacturing processes and a building block of polymers, such as poly(ethylene terephthalate). In this study, we found that a mycolic acid-containing bacterium Rhodococcus jostii RHA1 can grow with ethylene glycol as a sole source of carbon and energy. Deletion of a putative glycolate dehydrogenase gene (RHA1_ro03227) abolished growth with ethylene glycol, indicating that ethylene glycol is assimilated via glycolate in R. jostii RHA1. Transcriptome sequencing and gene deletion analyses revealed that a gene homologous to mycofactocin (MFT)-associated dehydrogenase (RHA1_ro06057), hereafter referred to as EgaA, is essential for ethylene glycol assimilation. Furthermore, egaA deletion also negatively affected the utilization of ethanol, 1-propanol, propylene glycol, and 1-butanol, suggesting that EgaA is involved in the utilization of various alcohols in R. jostii RHA1. Deletion of MFT biosynthetic genes abolished growth with ethylene glycol, indicating that MFT is the physiological electron acceptor of EgaA. Further genetic studies revealed that a putative aldehyde dehydrogenase (RHA1_ro06081) is a major aldehyde dehydrogenase in ethylene glycol metabolism by R. jostii RHA1. KEY POINTS: • Rhodococcus jostii RHA1 can assimilate ethylene glycol via glycolate • A mycofactocin-associated dehydrogenase is involved in the oxidation of ethylene glycol • An aldehyde dehydrogenase gene is important for the ethylene glycol assimilation.
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Affiliation(s)
- Tetsu Shimizu
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa-Shi, Kyoto, 619-0292, Japan
| | - Kai Suzuki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, 630-0192, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa-Shi, Kyoto, 619-0292, Japan.
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, 630-0192, Japan.
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2
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Roccor R, Wolf ME, Liu J, Eltis LD. The catabolism of ethylene glycol by Rhodococcus jostii RHA1 and its dependence on mycofactocin. Appl Environ Microbiol 2024; 90:e0041624. [PMID: 38837369 PMCID: PMC11267921 DOI: 10.1128/aem.00416-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024] Open
Abstract
Ethylene glycol (EG) is a widely used industrial chemical with manifold applications and also generated in the degradation of plastics such as polyethylene terephthalate. Rhodococcus jostii RHA1 (RHA1), a potential biocatalytic chassis, grows on EG. Transcriptomic analyses revealed four clusters of genes potentially involved in EG catabolism: the mad locus, predicted to encode mycofactocin-dependent alcohol degradation, including the catabolism of EG to glycolate; two GCL clusters, predicted to encode glycolate and glyoxylate catabolism; and the mft genes, predicted to specify mycofactocin biosynthesis. Bioinformatic analyses further revealed that the mad and mft genes are widely distributed in mycolic acid-producing bacteria such as RHA1. Neither ΔmadA nor ΔmftC RHA1 mutant strains grew on EG but grew on acetate. In resting cell assays, the ΔmadA mutant depleted glycolaldehyde but not EG from culture media. These results indicate that madA encodes a mycofactocin-dependent alcohol dehydrogenase that initiates EG catabolism. In contrast to some mycobacterial strains, the mad genes did not appear to enable RHA1 to grow on methanol as sole substrate. Finally, a strain of RHA1 adapted to grow ~3× faster on EG contained an overexpressed gene, aldA2, predicted to encode an aldehyde dehydrogenase. When incubated with EG, this strain accumulated lower concentrations of glycolaldehyde than RHA1. Moreover, ecotopically expressed aldA2 increased RHA1's tolerance for EG further suggesting that glycolaldehyde accumulation limits growth of RHA1 on EG. Overall, this study provides insights into the bacterial catabolism of small alcohols and aldehydes and facilitates the engineering of Rhodococcus for the upgrading of plastic waste streams.IMPORTANCEEthylene glycol (EG), a two-carbon (C2) alcohol, is produced in high volumes for use in a wide variety of applications. There is burgeoning interest in understanding and engineering the bacterial catabolism of EG, in part to establish circular economic routes for its use. This study identifies an EG catabolic pathway in Rhodococcus, a genus of bacteria well suited for biocatalysis. This pathway is responsible for the catabolism of methanol, a C1 feedstock, in related bacteria. Finally, we describe strategies to increase the rate of degradation of EG by increasing the transformation of glycolaldehyde, a toxic metabolic intermediate. This work advances the development of biocatalytic strategies to transform C2 feedstocks.
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Affiliation(s)
- Raphael Roccor
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Megan E. Wolf
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jie Liu
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
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3
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Dank A, Liu Y, Wen X, Lin F, Wiersma A, Boeren S, Smid EJ, Notebaart RA, Abee T. Ethylene glycol is metabolized to ethanol and acetate and induces expression of bacterial microcompartments in Propionibacterium freudenreichii. Heliyon 2024; 10:e33444. [PMID: 39027605 PMCID: PMC11255663 DOI: 10.1016/j.heliyon.2024.e33444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024] Open
Abstract
Ethylene glycol (EG, 1,2-ethanediol) is a two-carbon dihydroxy alcohol that can be derived from fermentation of plant-derived xylose and arabinose and which can be formed during food fermentations. Here we show that Propionibacterium freudenreichii DSM 20271 is able to convert EG in anaerobic conditions to ethanol and acetate in almost equimolar amounts. The metabolism of EG led to a moderate increase of biomass, indicating its metabolism is energetically favourable. A proteomic analysis revealed EG induced expression of the pdu-cluster, which encodes a functional bacterial microcompartment (BMC) involved in the degradation of 1,2-propanediol, with the presence of BMCs confirmed using transmission electron microscopy. Cross-examination of the proteomes of 1,2-propanediol and EG grown cells revealed PDU BMC-expressing cells have elevated levels of DNA repair proteins and cysteine biosynthesis proteins. Cells grown in 1,2-propanediol and EG also showed enhanced resistance against acid and bile salt-induced stresses compared to lactate-grown cells. Our analysis of whole genome sequences of selected genomes of BMC-encoding microorganisms able to metabolize EG with acetaldehyde as intermediate indicate a potentially broad-distributed role of the pdu operon in metabolism of EG. Based on our results we conclude EG is metabolized to acetate and ethanol with acetaldehyde as intermediate within BMCs in P. freudenreichii.
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Affiliation(s)
- Alexander Dank
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Yue Liu
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Xin Wen
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Fan Lin
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Anne Wiersma
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, Netherlands
| | - Eddy J. Smid
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
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4
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Satta A, Ghiotto G, Santinello D, Giangeri G, Bergantino E, Modesti M, Raga R, Treu L, Campanaro S, Zampieri G. Synergistic functional activity of a landfill microbial consortium in a microplastic-enriched environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174696. [PMID: 38997032 DOI: 10.1016/j.scitotenv.2024.174696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Plastic pollution of the soil is a global issue of increasing concern, with far-reaching impact on the environment and human health. To fully understand the medium- and long-term impact of plastic dispersal in the environment, it is necessary to define its interaction with the residing microbial communities and the biochemical routes of its degradation and metabolization. However, despite recent attention on this problem, research has largely focussed on microbial functional potential, failing to clearly identify collective adaptation strategies of these communities. Our study combines genome-centric metagenomics and metatranscriptomics to characterise soil microbial communities adapting to high polyethylene and polyethylene terephthalate concentration. The microbiota were sampled from a landfill subject to decades-old plastic contamination and enriched through prolonged cultivation using these microplastics as the only carbon source. This approach aimed to select the microorganisms that best adapt to these specific substrates. As a result, we obtained simplified communities where multiple plastic metabolization pathways are widespread across abundant and rare microbial taxa. Major differences were found in terms of expression, which on average was higher in planktonic microbes than those firmly adhered to plastic, indicating complementary metabolic roles in potential microplastic assimilation. Moreover, metatranscriptomic patterns indicate a high transcriptional level of numerous genes in emerging taxa characterised by a marked accumulation of genomic variants, supporting the hypothesis that plastic metabolization requires an extensive rewiring in energy metabolism and thus provides a strong selective pressure. Altogether, our results provide an improved characterisation of the impact of microplastics derived from common plastics types on terrestrial microbial communities and suggest biotic responses investing contaminated sites as well as potential biotechnological targets for cooperative plastic upcycling.
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Affiliation(s)
- Alessandro Satta
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Gabriele Ghiotto
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Davide Santinello
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Ginevra Giangeri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy; Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, 227, 220, 2800 Kgs. Lyngby, Denmark
| | | | - Michele Modesti
- Department of Industrial Engineering, University of Padua, Via Gradenigo, 6/a, 35131 Padova, Italy
| | - Roberto Raga
- Department of Civil, Environmental and Architectural Engineering, University of Padua, via Marzolo 9, 35131 Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, via U. Bassi 58/b, 35131 Padova, Italy
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5
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Moon J, Poehlein A, Daniel R, Müller V. Redirecting electron flow in Acetobacterium woodii enables growth on CO and improves growth on formate. Nat Commun 2024; 15:5424. [PMID: 38926344 PMCID: PMC11208171 DOI: 10.1038/s41467-024-49680-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Anaerobic, acetogenic bacteria are well known for their ability to convert various one-carbon compounds, promising feedstocks for a future, sustainable biotechnology, to products such as acetate and biofuels. The model acetogen Acetobacterium woodii can grow on CO2, formate or methanol, but not on carbon monoxide, an important industrial waste product. Since hydrogenases are targets of CO inhibition, here, we genetically delete the two [FeFe] hydrogenases HydA2 and HydBA in A. woodii. We show that the ∆hydBA/hydA2 mutant indeed grows on CO and produces acetate, but only after a long adaptation period. SNP analyzes of CO-adapted cells reveal a mutation in the HycB2 subunit of the HydA2/HydB2/HydB3/Fdh-containing hydrogen-dependent CO2 reductase (HDCR). We observe an increase in ferredoxin-dependent CO2 reduction and vice versa by the HDCR in the absence of the HydA2 module and speculate that this is caused by the mutation in HycB2. In addition, the CO-adapted ∆hydBA/hydA2 mutant growing on formate has a final biomass twice of that of the wild type.
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Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, Göttingen, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, Germany.
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6
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Shimizu T, Inui M. Novel aspects of ethylene glycol catabolism. Appl Microbiol Biotechnol 2024; 108:369. [PMID: 38861200 PMCID: PMC11166783 DOI: 10.1007/s00253-024-13179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/12/2024]
Abstract
Ethylene glycol (EG) is an industrially important two-carbon diol used as a solvent, antifreeze agent, and building block of polymers such as poly(ethylene terephthalate) (PET). Recently, the use of EG as a starting material for the production of bio-fuels or bio-chemicals is gaining attention as a sustainable process since EG can be derived from materials not competing with human food stocks including CO2, syngas, lignocellulolytic biomass, and PET waste. In order to design and construct microbial process for the conversion of EG to value-added chemicals, microbes capable of catabolizing EG such as Escherichia coli, Pseudomonas putida, Rhodococcus jostii, Ideonella sakaiensis, Paracoccus denitrificans, and Acetobacterium woodii are candidates of chassis for the construction of synthetic pathways. In this mini-review, we describe EG catabolic pathways and catabolic enzymes in these microbes, and further review recent advances in microbial conversion of EG to value-added chemicals by means of metabolic engineering. KEY POINTS: • Ethylene glycol is a potential next-generation feedstock for sustainable industry. • Microbial conversion of ethylene glycol to value-added chemicals is gaining attention. • Ethylene glycol-utilizing microbes are useful as chassis for synthetic pathways.
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Affiliation(s)
- Tetsu Shimizu
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto, 619-0292, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa-shi, Kyoto, 619-0292, Japan.
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan.
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7
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Sun X, Li Y, Giller K, Kunz C, Terranova M, Niu M. Comparative assessment of emulsifiers for in vitro ruminal gas production and fermentation measurements: Tween 80 is a suitable emulsifier. J Anim Physiol Anim Nutr (Berl) 2024; 108:680-690. [PMID: 38223976 DOI: 10.1111/jpn.13924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/16/2024]
Abstract
Emulsifiers are essential for achieving a homogenous distribution of lipophilic supplements in in vitro rumen fluid incubations. Since emulsifiers can alter rumen fermentation, it is crucial to select one that minimally impacts fermentation parameters to reduce potential biases. This study aimed to evaluate seven emulsifiers' impact on in vitro ruminal fermentation using the Hohenheim Gas Test in order to identify the most inert emulsifier. Rumen fluids were collected from three non-lactating Original Brown-Swiss cannulated cows before morning feeding and incubated for 24 h with a basal diet in triplicates. The emulsifiers tested were ethanol, ethyl acetate, propylene glycol, glycerol, ethylene glycol, soy lecithin, and Tween® 80, each in two dosages (0.5% or 1% v/v). The untreated basal diet served as control. Compared to control, in vitro organic matter digestibility was enhanced by ethyl acetate (by 36.9 and 48.2%), ethylene glycol (by 20.6 and 20.1%), glycerol (by 46.9 and 56.8%) and soy lecithin (by 19.7 and 26.8%) at 0.5 and 1% dosage, respectively. Additionally, the 24-h methane production increased for ethanol (by 41.9 and 46.2%), ethylene glycol (by 50.5 and 51.5%), and glycerol (by 63.1 and 65.4%) for the 0.5 and 1% dosage, respectively, and 0.5% dosage for ethyl acetate (by 31.6%). The acetate molar proportion was 17.2%pt higher for ethyl acetate, and 25.5%pt lower for glycerol at 1% dosage, compared to the control. The propionate concentration was 22.1%pt higher 1% glycerol, and 15.2%pt and 15.1%pt higher for 0.5 and 1% propylene glycol, respectively, compared to the control. In summary, Tween® 80 did not significantly affect in vitro rumen fermentation parameters, making it the most suitable choice for in vitro incubations involving lipophilic substances in rumen fluid. Ethanol may be considered as an alternative emulsifier if methane production is not the variable of interest.
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Affiliation(s)
- Xiaoge Sun
- Department of Environmental Systems Science, ETH Zürich, Institute of Agricultural Sciences, Zürich, Switzerland
| | - Yang Li
- Department of Environmental Systems Science, ETH Zürich, Institute of Agricultural Sciences, Zürich, Switzerland
| | - Katrin Giller
- Department of Environmental Systems Science, ETH Zürich, Institute of Agricultural Sciences, Zürich, Switzerland
| | - Carmen Kunz
- Department of Environmental Systems Science, ETH Zürich, Institute of Agricultural Sciences, Zürich, Switzerland
| | | | - Mutian Niu
- Department of Environmental Systems Science, ETH Zürich, Institute of Agricultural Sciences, Zürich, Switzerland
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8
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Senatore VG, Milanesi R, Masotti F, Maestroni L, Pagliari S, Cannavacciuolo C, Campone L, Serra I, Branduardi P. Exploring yeast biodiversity and process conditions for optimizing ethylene glycol conversion into glycolic acid. FEMS Yeast Res 2024; 24:foae024. [PMID: 39104224 PMCID: PMC11344169 DOI: 10.1093/femsyr/foae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024] Open
Abstract
Plastics have become an indispensable material in many fields of human activities, with production increasing every year; however, most of the plastic waste is still incinerated or landfilled, and only 10% of the new plastic is recycled even once. Among all plastics, polyethylene terephthalate (PET) is the most produced polyester worldwide; ethylene glycol (EG) is one of the two monomers released by the biorecycling of PET. While most research focuses on bacterial EG metabolism, this work reports the ability of Saccharomyces cerevisiae and nine other common laboratory yeast species not only to consume EG, but also to produce glycolic acid (GA) as the main by-product. A two-step bioconversion of EG to GA by S. cerevisiae was optimized by a design of experiment approach, obtaining 4.51 ± 0.12 g l-1 of GA with a conversion of 94.25 ± 1.74% from 6.21 ± 0.04 g l-1 EG. To improve the titer, screening of yeast biodiversity identified Scheffersomyces stipitis as the best GA producer, obtaining 23.79 ± 1.19 g l-1 of GA (yield 76.68%) in bioreactor fermentation, with a single-step bioprocess. Our findings contribute in laying the ground for EG upcycling strategies with yeasts.
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Affiliation(s)
- Vittorio Giorgio Senatore
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Riccardo Milanesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Fiorella Masotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Letizia Maestroni
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Pagliari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Ciro Cannavacciuolo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Luca Campone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Immacolata Serra
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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9
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Re A. Translational efficiency in gas-fermenting bacteria: Adding a new layer of regulation to gene expression in acetogens. iScience 2023; 26:108383. [PMID: 38034355 PMCID: PMC10684804 DOI: 10.1016/j.isci.2023.108383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
Major advances in mastering metabolism of single carbon (C1) gaseous feedstocks in acetogenic microorganisms are primed to fuel the transition toward environmentally sustainable and cost-efficient production schemes of biofuels and value-added biochemicals. Since acetogens grow under autotrophic energy-limited conditions, protein synthesis is expected to be controlled. This survey integrated publicly available RNA sequencing and ribosome profiling studies of several acetogens, providing data on genome-scale transcriptional and translational responses of A. woodii, E. limosum, C. drakei, and C. ljungdahlii to autotrophic and heterotrophic growth conditions. The extent of translational efficiency turned out to vary across key functional modules in acetogens' metabolism. Translational control was confirmed to support stoichiometric protein production in multimeric complexes. Comparing the autotrophic to the heterotrophic growth condition revealed growth-dependent regulation of translational efficiency, pointing at translational buffering as a widespread phenomenon shared by acetogens.
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Affiliation(s)
- Angela Re
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
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10
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Wagner N, Wen L, Frazão CJR, Walther T. Next-generation feedstocks methanol and ethylene glycol and their potential in industrial biotechnology. Biotechnol Adv 2023; 69:108276. [PMID: 37918546 DOI: 10.1016/j.biotechadv.2023.108276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/13/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023]
Abstract
Microbial fermentation processes are expected to play an important role in reducing dependence on fossil-based raw materials for the production of everyday chemicals. In order to meet the growing demand for biotechnological products in the future, alternative carbon sources that do not compete with human nutrition must be exploited. The chemical conversion of the industrially emitted greenhouse gas CO2 into microbially utilizable platform chemicals such as methanol represents a sustainable strategy for the utilization of an abundant carbon source and has attracted enormous scientific interest in recent years. A relatively new approach is the microbial synthesis of products from the C2-compound ethylene glycol, which can also be synthesized from CO2 and non-edible biomass and, in addition, can be recovered from plastic waste. Here we summarize the main chemical routes for the synthesis of methanol and ethylene glycol from sustainable resources and give an overview of recent metabolic engineering work for establishing natural and synthetic microbial assimilation pathways. The different metabolic routes for C1 and C2 alcohol-dependent bioconversions were compared in terms of their theoretical maximum yields and their oxygen requirements for a wide range of value-added products. Assessment of the process engineering challenges for methanol and ethylene glycol-based fermentations underscores the theoretical advantages of new synthetic metabolic routes and advocates greater consideration of ethylene glycol, a C2 substrate that has received comparatively little attention to date.
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Affiliation(s)
- Nils Wagner
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Linxuan Wen
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Cláudio J R Frazão
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany
| | - Thomas Walther
- TU Dresden, Institute of Natural Materials Technology, Bergstraße 120, 01062 Dresden, Germany.
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11
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Schaerer L, Putman L, Bigcraft I, Byrne E, Kulas D, Zolghadr A, Aloba S, Ong R, Shonnard D, Techtmann S. Coexistence of specialist and generalist species within mixed plastic derivative-utilizing microbial communities. MICROBIOME 2023; 11:224. [PMID: 37838714 PMCID: PMC10576394 DOI: 10.1186/s40168-023-01645-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/09/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Plastic-degrading microbial isolates offer great potential to degrade, transform, and upcycle plastic waste. Tandem chemical and biological processing of plastic wastes has been shown to substantially increase the rates of plastic degradation; however, the focus of this work has been almost entirely on microbial isolates (either bioengineered or naturally occurring). We propose that a microbial community has even greater potential for plastic upcycling. A microbial community has greater metabolic diversity to process mixed plastic waste streams and has built-in functional redundancy for optimal resilience. RESULTS Here, we used two plastic-derivative degrading communities as a model system to investigate the roles of specialist and generalist species within the microbial communities. These communities were grown on five plastic-derived substrates: pyrolysis treated high-density polyethylene, chemically deconstructed polyethylene terephthalate, disodium terephthalate, terephthalamide, and ethylene glycol. Short-read metagenomic and metatranscriptomic sequencing were performed to evaluate activity of microorganisms in each treatment. Long-read metagenomic sequencing was performed to obtain high-quality metagenome assembled genomes and evaluate division of labor. CONCLUSIONS Data presented here show that the communities are primarily dominated by Rhodococcus generalists and lower abundance specialists for each of the plastic-derived substrates investigated here, supporting previous research that generalist species dominate batch culture. Additionally, division of labor may be present between Hydrogenophaga terephthalate degrading specialists and lower abundance protocatechuate degrading specialists. Video Abstract.
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Affiliation(s)
- Laura Schaerer
- Department of Biological Sciences, Michigan Technological University, 740 Dow ESE Building, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Lindsay Putman
- Department of Biological Sciences, Michigan Technological University, 740 Dow ESE Building, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Isaac Bigcraft
- Department of Biological Sciences, Michigan Technological University, 740 Dow ESE Building, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Emma Byrne
- Department of Biological Sciences, Michigan Technological University, 740 Dow ESE Building, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Daniel Kulas
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Ali Zolghadr
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Sulihat Aloba
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Rebecca Ong
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - David Shonnard
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Stephen Techtmann
- Department of Biological Sciences, Michigan Technological University, 740 Dow ESE Building, 1400 Townsend Drive, Houghton, MI, 49931, USA.
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12
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Moon J, Schubert A, Poehlein A, Daniel R, Müller V. A new metabolic trait in an acetogen: Mixed acid fermentation of fructose in a methylene-tetrahydrofolate reductase mutant of Acetobacterium woodii. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:339-351. [PMID: 37150590 PMCID: PMC10472528 DOI: 10.1111/1758-2229.13160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/20/2023] [Indexed: 05/09/2023]
Abstract
To inactivate the Wood-Ljungdahl pathway in the acetogenic model bacterium Acetobacterium woodii, the genes metVF encoding two of the subunits of the methylene-tetrahydrofolate reductase were deleted. As expected, the mutant did not grow on C1 compounds and also not on lactate, ethanol or butanediol. In contrast to a mutant in which the first enzyme of the pathway (hydrogen-dependent CO2 reductase) had been genetically deleted, cells were able to grow on fructose, albeit with lower rates and yields than the wild-type. Growth was restored by addition of an external electron sink, glycine betaine + CO2 or caffeate. Resting cells pre-grown on fructose plus an external electron acceptor fermented fructose to two acetate and four hydrogen, that is, performed hydrogenogenesis. Cells pre-grown under fermentative conditions on fructose alone redirected carbon and electrons to form lactate, formate, ethanol as well as hydrogen. Apparently, growth on fructose alone induced enzymes for mixed acid fermentation (MAF). Transcriptome analyses revealed enzymes potentially involved in MAF and a quantitative model for MAF from fructose in A. woodii is presented.
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Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Schubert
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and GeneticsGeorg August UniversityGöttingenGermany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular BiosciencesJohann Wolfgang Goethe UniversityFrankfurtGermany
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13
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Moon J, Waschinger LM, Müller V. Lactate formation from fructose or C1 compounds in the acetogen Acetobacterium woodii by metabolic engineering. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12637-7. [PMID: 37417977 PMCID: PMC10390620 DOI: 10.1007/s00253-023-12637-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023]
Abstract
Anaerobic, acetogenic bacteria are promising biocatalysts for a sustainable bioeconomy since they capture and convert carbon dioxide to acetic acid. Hydrogen is an intermediate in acetate formation from organic as well as C1 substrates. Here, we analyzed mutants of the model acetogen Acetobacterium woodii in which either one of the two hydrogenases or both together were genetically deleted. In resting cells of the double mutant, hydrogen formation from fructose was completely abolished and carbon was redirected largely to lactate. The lactate/fructose and lactate/acetate ratios were 1.24 and 2.76, respectively. We then tested for lactate formation from methyl groups (derived from glycine betaine) and carbon monoxide. Indeed, also under these conditions lactate and acetate were formed in equimolar amounts with a lactate/acetate ratio of 1.13. When the electron-bifurcating lactate dehydrogenase/ETF complex was genetically deleted, lactate formation was completely abolished. These experiments demonstrate the capability of A. woodii to produce lactate from fructose but also from promising C1 substrates, methyl groups and carbon monoxide. This adds an important milestone towards generation of a value chain leading from CO2 to value-added compounds. KEY POINTS: • Resting cells of the ΔhydBA/hdcr mutant of Acetobacterium woodii produced lactate from fructose or methyl groups + CO • Lactate formation from methyl groups + CO was completely abolished after deletion of lctBCD • Metabolic engineering of a homoacetogen to lactate formation gives a potential for industrial applications.
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Affiliation(s)
- Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Lara M Waschinger
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, D-60438, Frankfurt, Germany.
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14
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Mudondo J, Lee HS, Jeong Y, Kim TH, Kim S, Sung BH, Park SH, Park K, Cha HG, Yeon YJ, Kim HT. Recent Advances in the Chemobiological Upcycling of Polyethylene Terephthalate (PET) into Value-Added Chemicals. J Microbiol Biotechnol 2023; 33:1-14. [PMID: 36451300 PMCID: PMC9895998 DOI: 10.4014/jmb.2208.08048] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 12/02/2022]
Abstract
Polyethylene terephthalate (PET) is a plastic material commonly applied to beverage packaging used in everyday life. Owing to PET's versatility and ease of use, its consumption has continuously increased, resulting in considerable waste generation. Several physical and chemical recycling processes have been developed to address this problem. Recently, biological upcycling is being actively studied and has come to be regarded as a powerful technology for overcoming the economic issues associated with conventional recycling methods. For upcycling, PET should be degraded into small molecules, such as terephthalic acid and ethylene glycol, which are utilized as substrates for bioconversion, through various degradation processes, including gasification, pyrolysis, and chemical/biological depolymerization. Furthermore, biological upcycling methods have been applied to biosynthesize value-added chemicals, such as adipic acid, muconic acid, catechol, vanillin, and glycolic acid. In this review, we introduce and discuss various degradation methods that yield substrates for bioconversion and biological upcycling processes to produce value-added biochemicals. These technologies encourage a circular economy, which reduces the amount of waste released into the environment.
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Affiliation(s)
- Joyce Mudondo
- Department of Food Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hoe-Suk Lee
- Department of Biochemical Engineering Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Yunhee Jeong
- Department of Food Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Tae Hee Kim
- Department of Food Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seungmi Kim
- Department of Food Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - See-Hyoung Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong 30016, Republic of Korea
| | - Kyungmoon Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong 30016, Republic of Korea
| | - Hyun Gil Cha
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea,Corresponding authors H.G. Cha Phone: +82-52-241-6317 Fax: +82-52-241-6349 E-mail:
| | - Young Joo Yeon
- Department of Biochemical Engineering Gangneung-Wonju National University, Gangneung 25457, Republic of Korea,Y.J. Yeon Phone: +82-33-640-2401 Fax: +82-33-640-2410 E-mail:
| | - Hee Taek Kim
- Department of Food Science and Technology, Chungnam National University, Daejeon 34134, Republic of Korea,H.T. Kim Phone: +82-42-821-6722 Fax:+82-42-821-8785 E-mail:
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15
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Utilization of nanoparticles for biogas production focusing on process stability and effluent quality. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-05222-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Abstract
One of the most important techniques for converting complex organic waste into renewable energy in the form of biogas and effluent is anaerobic digestion. Several issues have been raised related to the effectiveness of the anaerobic digestion process in recent years. Hence nanoparticles (NPs) have been used widely in anaerobic digestion process for converting organic wastes into useful biogas and effluent in an effective way. This review addresses the knowledge gaps and summarizes recent researchers’ findings concentrating on the stability and effluent quality of the cattle manure anaerobic digestion process using single and combinations nanoparticle. In summary, the utilization of NPs have beneficial effects on CH4 production, process optimization, and effluent quality. Their function, as key nutrient providers, aid in the synthesis of key enzymes and co-enzymes, and thus stimulate anaerobic microorganism activities when present at an optimum concentration (e.g., Fe NPs 100 mg/L; Ni NPs 2 mg/L; Co NPs 1 mg/L). Furthermore, utilizing Fe NPs at concentrations higher than 100 mg/L is more effective at reducing H2S production than increasing CH4, whereas Ni NPs and Co NPs at concentrations greater than 2 mg/L and 1 mg/L, respectively, reduce CH4 production. Effluent with Fe and Ni NPs showed stronger fertilizer values more than Co NPs. Fe/Ni/Co NP combinations are more efficient in enhancing CH4 production than single NPs. Therefore, it is possible to utilize NPs combinations as additives to improve the effectiveness of anaerobic digestion.
Article highlights
Single NPs (e.g., Fe, Ni, and Co NPs) in low concentrations are more effective in increasing CH4 production than reducing H2S production.
Optimal Fe, Ni, and Co NP concentrations enhance anaerobic digestion process performance.
Addition of Fe, Ni, and Co NPs above tolerated concentration causes irreversible inhibition in anaerobic digestion.
Effluent with Fe, Ni, and Co NPs showed stronger fertilizer values.
Nanoparticle combinations are more effective for increasing the CH4 production than signal NPs.
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16
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Lomwongsopon P, Varrone C. Critical Review on the Progress of Plastic Bioupcycling Technology as a Potential Solution for Sustainable Plastic Waste Management. Polymers (Basel) 2022; 14:polym14224996. [PMID: 36433123 PMCID: PMC9692586 DOI: 10.3390/polym14224996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Plastic production worldwide has doubled in the last two decades and is expected to reach a four-fold increase by 2050. The durability of plastic makes them a perfect material for many applications, but it is also a key limitation to their end-of-life management. The current plastic lifecycle is far from circular, with only 13% being collected for recycling and 9% being successfully recycled, indicating the failure of current recycling technology. The remaining plastic waste streams are thus incinerated, landfilled, or worse, mismanaged, leading to them leaking into the environment. To promote plastic circularity, keeping material in the loop is a priority and represents a more sustainable solution. This can be achieved through the reuse of plastic items, or by using plastic waste as a resource for new materials, instead of discarding them as waste. As the discovery of plastic-degrading/utilizing microorganisms and enzymes has been extensively reported recently, the possibility of developing biological plastic upcycling processes is opening up. An increasing amount of studies have investigated the use of plastic as a carbon source for biotechnological processes to produce high-value compounds such as bioplastics, biochemicals, and biosurfactants. In the current review, the advancements in fossil-based plastic bio- and thermochemical upcycling technologies are presented and critically discussed. In particular, we highlight the developed (bio)depolymerization coupled with bioconversion/fermentation processes to obtain industrially valuable products. This review is expected to contribute to the future development and scale-up of effective plastic bioupcycling processes that can act as a drive to increase waste removal from the environment and valorize post-consumer plastic streams, thus accelerating the implementation of a circular (plastic) economy.
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17
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Kalathil S, Miller M, Reisner E. Microbial Fermentation of Polyethylene Terephthalate (PET) Plastic Waste for the Production of Chemicals or Electricity. Angew Chem Int Ed Engl 2022; 61:e202211057. [PMID: 36103351 PMCID: PMC9828132 DOI: 10.1002/anie.202211057] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 01/12/2023]
Abstract
Ideonella sakaiensis (I. sakaiensis) can grow on polyethylene terephthalate (PET) as the major carbon and energy source. Previous work has shown that PET conversion in the presence of oxygen released carbon dioxide and water while yielding adenosine triphosphate (ATP) through oxidative phosphorylation. This study demonstrates that I. sakaiensis is a facultative anaerobe that ferments PET to the feedstock chemicals acetate and ethanol in the absence of oxygen. In addition to PET, the pure monomer ethylene glycol (EG), the intermediate product ethanol, and the carbohydrate fermentation test substance maltose can also serve as fermenting substrates. Co-culturing of I. sakaiensis with the electrogenic and acetate-consuming Geobacter sulfurreducens produced electricity from PET or EG. This newly identified plastic fermentation process by I. sakaiensis provides thus a novel biosynthetic route to produce high-value chemicals or electricity from plastic waste streams.
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Affiliation(s)
- Shafeer Kalathil
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Melanie Miller
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
| | - Erwin Reisner
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeCB2 1EWUK
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18
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Hachisuka SI, Chong JF, Fujiwara T, Takayama A, Kawakami Y, Yoshida S. Ethylene glycol metabolism in the poly(ethylene terephthalate)-degrading bacterium Ideonella sakaiensis. Appl Microbiol Biotechnol 2022; 106:7867-7878. [DOI: 10.1007/s00253-022-12244-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/02/2022]
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19
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Barcoto MO, Rodrigues A. Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. Front Microbiol 2022; 13:812143. [PMID: 35685924 PMCID: PMC9171207 DOI: 10.3389/fmicb.2022.812143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.
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Affiliation(s)
- Mariana O. Barcoto
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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20
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Gao R, Pan H, Kai L, Han K, Lian J. Microbial degradation and valorization of poly(ethylene terephthalate) (PET) monomers. World J Microbiol Biotechnol 2022; 38:89. [PMID: 35426614 DOI: 10.1007/s11274-022-03270-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/23/2022] [Indexed: 12/22/2022]
Abstract
The polyethylene terephthalate (PET) is one of the major plastics with a huge annual production. Alongside with its mass production and wide applications, PET pollution is threatening and damaging the environment and human health. Although mechanical or chemical methods can deal with PET, the process suffers from high cost and the hydrolyzed monomers will cause secondary pollution. Discovery of plastic-degrading microbes and the corresponding enzymes emerges new hope to cope with this issue. Combined with synthetic biology and metabolic engineering, microbial cell factories not only provide a promising approach to degrade PET, but also enable the conversion of its monomers, ethylene glycol (EG) and terephthalic acid (TPA), into value-added compounds. In this way, PET wastes can be handled in environment-friendly and more potentially cost-effective processes. While PET hydrolases have been extensively reviewed, this review focuses on the microbes and metabolic pathways for the degradation of PET monomers. In addition, recent advances in the biotransformation of TPA and EG into value-added compounds are discussed in detail.
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Affiliation(s)
- Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 310027, Hangzhou, China
| | - Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China
| | - Lei Kai
- Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Sciences, Jiangsu Normal University, 22116, Xuzhou, China.,Jiangsu Keybio Co. LTD, 22116, Xuzhou, China
| | - Kun Han
- Jiangsu Keybio Co. LTD, 22116, Xuzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China. .,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 310027, Hangzhou, China.
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21
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Soong YHV, Sobkowicz MJ, Xie D. Recent Advances in Biological Recycling of Polyethylene Terephthalate (PET) Plastic Wastes. Bioengineering (Basel) 2022; 9:98. [PMID: 35324787 PMCID: PMC8945055 DOI: 10.3390/bioengineering9030098] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
Polyethylene terephthalate (PET) is one of the most commonly used polyester plastics worldwide but is extremely difficult to be hydrolyzed in a natural environment. PET plastic is an inexpensive, lightweight, and durable material, which can readily be molded into an assortment of products that are used in a broad range of applications. Most PET is used for single-use packaging materials, such as disposable consumer items and packaging. Although PET plastics are a valuable resource in many aspects, the proliferation of plastic products in the last several decades have resulted in a negative environmental footprint. The long-term risk of released PET waste in the environment poses a serious threat to ecosystems, food safety, and even human health in modern society. Recycling is one of the most important actions currently available to reduce these impacts. Current clean-up strategies have attempted to alleviate the adverse impacts of PET pollution but are unable to compete with the increasing quantities of PET waste exposed to the environment. In this review paper, current PET recycling methods to improve life cycle and waste management are discussed, which can be further implemented to reduce plastics pollution and its impacts on health and environment. Compared with conventional mechanical and chemical recycling processes, the biotechnological recycling of PET involves enzymatic degradation of the waste PET and the followed bioconversion of degraded PET monomers into value-added chemicals. This approach creates a circular PET economy by recycling waste PET or upcycling it into more valuable products with minimal environmental footprint.
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Affiliation(s)
- Ya-Hue Valerie Soong
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA;
| | - Margaret J. Sobkowicz
- Department of Plastics Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA;
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA;
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22
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Qi X, Yan W, Cao Z, Ding M, Yuan Y. Current Advances in the Biodegradation and Bioconversion of Polyethylene Terephthalate. Microorganisms 2021; 10:39. [PMID: 35056486 PMCID: PMC8779501 DOI: 10.3390/microorganisms10010039] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 01/04/2023] Open
Abstract
Polyethylene terephthalate (PET) is a widely used plastic that is polymerized by terephthalic acid (TPA) and ethylene glycol (EG). In recent years, PET biodegradation and bioconversion have become important in solving environmental plastic pollution. More and more PET hydrolases have been discovered and modified, which mainly act on and degrade the ester bond of PET. The monomers, TPA and EG, can be further utilized by microorganisms, entering the tricarboxylic acid cycle (TCA cycle) or being converted into high value chemicals, and finally realizing the biodegradation and bioconversion of PET. Based on synthetic biology and metabolic engineering strategies, this review summarizes the current advances in the modified PET hydrolases, engineered microbial chassis in degrading PET, bioconversion pathways of PET monomers, and artificial microbial consortia in PET biodegradation and bioconversion. Artificial microbial consortium provides novel ideas for the biodegradation and bioconversion of PET or other complex polymers. It is helpful to realize the one-step bioconversion of PET into high value chemicals.
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Affiliation(s)
- Xinhua Qi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Wenlong Yan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Zhibei Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Mingzhu Ding
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (X.Q.); (W.Y.); (Z.C.); (Y.Y.)
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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23
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Qin ZH, Mou JH, Chao CYH, Chopra SS, Daoud W, Leu SY, Ning Z, Tso CY, Chan CK, Tang S, Hathi ZJ, Haque MA, Wang X, Lin CSK. Biotechnology of Plastic Waste Degradation, Recycling, and Valorization: Current Advances and Future Perspectives. CHEMSUSCHEM 2021; 14:4103-4114. [PMID: 34137191 DOI: 10.1002/cssc.202100752] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/12/2021] [Indexed: 06/12/2023]
Abstract
Although fossil-based plastic products have many attractive characteristics, their production has led to severe environmental burdens that require immediate solutions. Despite these plastics being non-natural chemical compounds, they can be degraded and metabolized by some microorganisms, which suggests the potential application of biotechnologies based on the mechanism of plastic biodegradation. In this context, microbe-based strategies for the degradation, recycling, and valorization of plastic waste offer a feasible approach for alleviating environmental challenges created by the accumulation of plastic waste. This Minireview highlights recent advances in the biotechnology-based biodegradation of both traditional polymers and bio-based plastics, focusing on the mechanisms of biodegradation. From an application perspective, this Minireview also summarizes recent progress in the recycling and valorization of plastic waste, which are feasible solutions for tackling the plastic waste dilemma.
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Affiliation(s)
- Zi-Hao Qin
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Jin-Hua Mou
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | | | | | - Walid Daoud
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong
| | - Zhi Ning
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong
| | - Chi Yan Tso
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Chak Keung Chan
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Shixing Tang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510632, P. R. China
| | | | - Md Ariful Haque
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Xiang Wang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, P. R. China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Hong Kong
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24
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Moon J, Müller V. Physiology and genetics of ethanologenesis in the acetogenic bacterium Acetobacterium woodii. Environ Microbiol 2021; 23:6953-6964. [PMID: 34448343 DOI: 10.1111/1462-2920.15739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/22/2021] [Indexed: 11/28/2022]
Abstract
The acetogenic model bacterium Acetobacterium woodii is well-known to produce acetate by homoacetogenesis from sugars, but under certain conditions minor amounts of ethanol are produced in addition. Here, we have aimed to identify physiological conditions that increase electron and carbon flow towards ethanol production. Ethanol was only produced from fructose but not from H2 + CO2 , formate, pyruvate, lactate or alanine. In the absence of Na+ , the Wood-Ljungdahl pathway (WLP) of acetate formation is not functional. Therefore, the ethanol yield increased to 0.42 mol/mol (ethanol/fructose) with an ethanol/acetate ratio of 0.28 mol/mol. The presence of bicarbonate/CO2 stimulated electron and carbon flow through the WLP and led to less ethanol produced. Of the 11 potential alcohol dehydrogenase genes, the most upregulated during ethanologenesis was adh4. A deletion of adh4 led to an increase in ethanol production by 100% to a yield of 0.79 mol/mol (ethanol/fructose); this correlated with an increase in transcript abundance of adh6. In sum, our studies revealed low Na+ and bicarbonate/CO2 as factors that trigger ethanol formation and that a deletion of adh4 drastically increased ethanol formation in A. woodii.
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Affiliation(s)
- Jimyung Moon
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, Frankfurt, D-60438, Germany
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Wright RJ, Bosch R, Langille MGI, Gibson MI, Christie-Oleza JA. A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere. MICROBIOME 2021; 9:141. [PMID: 34154652 PMCID: PMC8215760 DOI: 10.1186/s40168-021-01054-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/19/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere. RESULTS We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation. CONCLUSIONS Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris. Video abstract.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Rafael Bosch
- University of the Balearic Islands, Palma, Spain
- IMEDEA (CSIC-UIB), Esporles, Spain
| | - Morgan G. I. Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Coventry, UK
- Medical School, University of Warwick, Coventry, UK
| | - Joseph A. Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry, UK
- University of the Balearic Islands, Palma, Spain
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Trifunović D, Moon J, Poehlein A, Daniel R, Müller V. Growth of the acetogenic bacterium Acetobacterium woodii on glycerol and dihydroxyacetone. Environ Microbiol 2021; 23:2648-2658. [PMID: 33817956 DOI: 10.1111/1462-2920.15503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 04/03/2021] [Indexed: 11/28/2022]
Abstract
More than 2 million tons of glycerol are produced during industrial processes each year and, therefore, glycerol is an inexpensive feedstock to produce biocommodities by bacterial fermentation. Acetogenic bacteria are interesting production platforms and there have been few reports in the literature on glycerol utilization by this ecophysiologically important group of strictly anaerobic bacteria. Here, we show that the model acetogen Acetobacterium woodii DSM1030 is able to grow on glycerol, but contrary to expectations, only for 2-3 transfers. Transcriptome analysis revealed the expression of the pdu operon encoding a propanediol dehydratase along with genes encoding bacterial microcompartments. Deletion of pduAB led to a stable growth of A. woodii on glycerol, consistent with the hypothesis that the propanediol dehydratase also acts on glycerol leading to a toxic end-product. Glycerol is oxidized to acetate and the reducing equivalents are reoxidized by reducing CO2 in the Wood-Ljungdahl pathway, leading to an additional acetate. The possible oxidation product of glycerol, dihydroxyacetone (DHA), also served as carbon and energy source for A. woodii and growth was stably maintained on that compound. DHA oxidation was also coupled to CO2 reduction. Based on transcriptome data and enzymatic analysis we present the first metabolic and bioenergetic schemes for glycerol and DHA utilization in A. woodii.
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Affiliation(s)
- Dragan Trifunović
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, Frankfurt, 60438, Germany
| | - Jimyung Moon
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, Frankfurt, 60438, Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, Frankfurt, 60438, Germany
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Maity W, Maity S, Bera S, Roy A. Emerging Roles of PETase and MHETase in the Biodegradation of Plastic Wastes. Appl Biochem Biotechnol 2021; 193:2699-2716. [PMID: 33797026 DOI: 10.1007/s12010-021-03562-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Abstract
Polyethylene terephthalate (PET) is extensively used in plastic products, and its accumulation in the environment has become a global concern. Being a non-degradable pollutant, a tremendous quantity of PET-bearing plastic materials have already accumulated in the environment, posing severe challenges towards the existence of various endangered species and consequently threatening the ecosystem and biodiversity. While conventional recycling and remediation methodologies so far have been ineffective in formulating a "green" degradation protocol, the bioremediation strategies-though nascent-are exhibiting greater promises towards achieving the target. Very recently, a novel bacterial strain called Ideonella sakaiensis 201-F6 has been discovered that produces a couple of unique enzymes, polyethylene terephthalate hydrolase and mono(2-hydroxyethyl) terephthalic acid hydrolase, enabling the bacteria to utilize PET as their sole carbon source. With a detailed understanding of the protein structure of these enzymes, possibilities for their optimization as PET degrading agents have started to emerge. In both proteins, several amino acids have been identified that are not only instrumental for catalysis but also provide avenues for the applications of genetic engineering strategies to improve the catalytic efficiencies of the enzymes. In this review, we focused on such unique structural features of these two enzymes and discussed their potential as molecular tools that can essentially become instrumental towards the development of sustainable bioremediation strategies. Degradation PET by wild type and genetically engineered PETase and MHETase. Effect of the MHETase-PETase chimeric protein and PETase expressed on the surface of yeast cells on PET degradation is also shown.
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Affiliation(s)
- Writtik Maity
- Indian Academy Degree College-Autonomous, Bangalore, Karnataka, 560043, India
| | - Subhasish Maity
- Indian Academy Degree College-Autonomous, Bangalore, Karnataka, 560043, India
| | - Soumen Bera
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, Tamil Nadu, 600048, India
| | - Amrita Roy
- Indian Academy Degree College-Autonomous, Bangalore, Karnataka, 560043, India.
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Zhu X, Blanco E, Bhatti M, Borrion A. Impact of metallic nanoparticles on anaerobic digestion: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143747. [PMID: 33257063 DOI: 10.1016/j.scitotenv.2020.143747] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/30/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion (AD) is one of the most energy-efficient waste treatment technologies for biodegradable wastes. Owing to the increasing trend of metallic nanoparticle applications in industry, they are ubiquitous to the waste streams, which may lead to remarkable impacts on the performance of the AD process. This review addresses the knowledge gaps and summarises the findings from the academic articles published from 2010 to 2019 focusing on the influences on both AD processes of biochemical hydrogen-generation and methane-production from selected metallic nano-materials. Both qualitative and quantitative analyses were conducted with selected indicators to evaluate the metallic nanoparticles' influences on the AD process. The selected metallic nanoparticles were grouped in the view of their chemical formulations aiming to point out the possible mechanisms behind their effects on AD processes. In summary, most metallic nanoparticles with trace-element-base (e.g. iron, cobalt, nickel) have positive effects on both AD hydrogen-generation and methane-production processes in terms of gas production, effluent quality, as well as process optimisation. Within an optimum concentration, they serve as key nutrients providers, aid key enzymes and co-enzymes synthesis, and thus stimulate anaerobic microorganism activities. As for the nano-additives without trace-element base, their positive influences are relied on providing active sites for the microorganism, as well as absorbing inhibitory factors. Moreover, comparisons of these nano-additives' impacts on the two gas-production phases were conducted, while methane-production phases are found to be more sensitive to additions of these nanoparticles then hydrogen-production phase. Research perspectives and research gaps in this area are discussed.
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Affiliation(s)
- Xiaowen Zhu
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK
| | - Edgar Blanco
- Anaero Technology Limited, Cowley Road, Cambridge, UK
| | - Manni Bhatti
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK
| | - Aiduan Borrion
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK.
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Chowdhury NP, Moon J, Müller V. Adh4, an alcohol dehydrogenase controls alcohol formation within bacterial microcompartments in the acetogenic bacterium Acetobacterium woodii. Environ Microbiol 2020; 23:499-511. [PMID: 33283462 DOI: 10.1111/1462-2920.15340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 01/23/2023]
Abstract
Acetobacterium woodii utilizes the Wood-Ljungdahl pathway for reductive synthesis of acetate from carbon dioxide. However, A. woodii can also perform non-acetogenic growth on 1,2-propanediol (1,2-PD) where instead of acetate, equal amounts of propionate and propanol are produced as metabolic end products. Metabolism of 1,2-PD occurs via encapsulated metabolic enzymes within large proteinaceous bodies called bacterial microcompartments. While the genome of A. woodii harbours 11 genes encoding putative alcohol dehydrogenases, the BMC-encapsulated propanol-generating alcohol dehydrogenase remains unidentified. Here, we show that Adh4 of A. woodii is the alcohol dehydrogenase required for propanol/ethanol formation within these microcompartments. It catalyses the NADH-dependent reduction of propionaldehyde or acetaldehyde to propanol or ethanol and primarily functions to recycle NADH within the BMC. Removal of adh4 gene from the A. woodii genome resulted in slow growth on 1,2-PD and the mutant displayed reduced propanol and enhanced propionate formation as a metabolic end product. In sum, the data suggest that Adh4 is responsible for propanol formation within the BMC and is involved in redox balancing in the acetogen, A. woodii.
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Affiliation(s)
- Nilanjan Pal Chowdhury
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Jimyung Moon
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
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Samak NA, Jia Y, Sharshar MM, Mu T, Yang M, Peh S, Xing J. Recent advances in biocatalysts engineering for polyethylene terephthalate plastic waste green recycling. ENVIRONMENT INTERNATIONAL 2020; 145:106144. [PMID: 32987219 DOI: 10.1016/j.envint.2020.106144] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 05/21/2023]
Abstract
The massive waste of poly(ethylene terephthalate) (PET) that ends up in the landfills and oceans and needs hundreds of years for degradation has attracted global concern. The poor stability and productivity of the available PET biocatalysts hinder their industrial applications. Active PET biocatalysts can provide a promising avenue for PET bioconversion and recycling. Therefore, there is an urgent need to develop new strategies that could enhance the stability, catalytic activity, solubility, productivity, and re-usability of these PET biocatalysts under harsh conditions such as high temperatures, pH, and salinity. This has raised great attention in using bioengineering strategies to improve PET biocatalysts' robustness and catalytic behavior. Herein, historical and forecasting data of plastic production and disposal were critically reviewed. Challenges facing the PET degradation process and available strategies that could be used to solve them were critically highlighted and summarized. In this review, we also discussed the recent progress in enzyme bioengineering approaches used for discovering new PET biocatalysts, elucidating the degradation mechanism, and improving the catalytic performance, solubility, and productivity, critically assess their strength and weakness and highlighting the gaps of the available data. Discovery of more potential PET hydrolases and studying their molecular mechanism extensively via solving their crystal structure will widen this research area to move forward the industrial application. A deeper knowledge of PET molecular and degradation mechanisms will give great insight into the future identification of related enzymes. The reported bioengineering strategies during this review could be used to reduce PET crystallinity and to increase the operational temperature of PET hydrolyzing enzymes.
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Affiliation(s)
- Nadia A Samak
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China; Processes Design and Development Department, Egyptian Petroleum Research Institute, Nasr City, 11727 Cairo, Egypt
| | - Yunpu Jia
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Moustafa M Sharshar
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Tingzhen Mu
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Maohua Yang
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Sumit Peh
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China
| | - Jianmin Xing
- CAS Key Laboratory of Green Process and Engineering & State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; College of Chemical Engineering, University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing 100049, PR China.
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Carr CM, Clarke DJ, Dobson ADW. Microbial Polyethylene Terephthalate Hydrolases: Current and Future Perspectives. Front Microbiol 2020; 11:571265. [PMID: 33262744 PMCID: PMC7686037 DOI: 10.3389/fmicb.2020.571265] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022] Open
Abstract
Plastic has rapidly transformed our world, with many aspects of human life now relying on a variety of plastic materials. Biological plastic degradation, which employs microorganisms and their degradative enzymes, has emerged as one way to address the unforeseen consequences of the waste streams that have resulted from mass plastic production. The focus of this review is microbial hydrolase enzymes which have been found to act on polyethylene terephthalate (PET) plastic. The best characterized examples are discussed together with the use of genomic and protein engineering technologies to obtain PET hydrolase enzymes for different applications. In addition, the obstacles which are currently limiting the development of efficient PET bioprocessing are presented. By continuing to study the possible mechanisms and the structural elements of key enzymes involved in microbial PET hydrolysis, and by assessing the ability of PET hydrolase enzymes to work under practical conditions, this research will help inform large-scale waste management operations. Finally, the contribution of microbial PET hydrolases in creating a potential circular PET economy will be explored. This review combines the current knowledge on enzymatic PET processing with proposed strategies for optimization and use, to help clarify the next steps in addressing pollution by PET and other plastics.
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Affiliation(s)
- Clodagh M. Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - David J. Clarke
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- SSPC-SFI Research Centre for Pharmaceuticals, University College Cork, Cork, Ireland
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Chowdhury NP, Alberti L, Linder M, Müller V. Exploring Bacterial Microcompartments in the Acetogenic Bacterium Acetobacterium woodii. Front Microbiol 2020; 11:593467. [PMID: 33178174 PMCID: PMC7593272 DOI: 10.3389/fmicb.2020.593467] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
The strictly anaerobic acetogenic bacterium Acetobacterium woodii is metabolically diverse and grows on variety of substrates which includes H2 + CO2, sugars, alcohols and diols. It is unique in producing bacterial microcompartments (BMC) during growth on different substrates such as 1,2-propanediol, 2,3-butanediol, ethanol or fructose. In this study, we analyzed the genetic organization and expression of the BMC genes within the A. woodii genome, the previously described 18 gene pdu cluster as well as four other cluster potentially encoding one or two shell proteins. Expression analysis of respective gene clusters revealed that the pdu gene cluster is highly expressed during growth on 1,2-PD, 2,3-BD, ethanol and ethylene glycol. The promoter region upstream of the pduA gene was identified and used to establish a reporter gene assay based on chloramphenicol acetyl transferase as a reporter protein. The reporter gene assay confirmed the qPCR data and demonstrated that 1,2-PD is superior over ethanol and ethylene glycol as inducer. BMCs were enriched from cells grown on 2,3- BD and 1,2-PD and shown to have typical structure in electron micrographs. Biochemical analyses revealed several of the protein encoded by the pdu cluster to be part of the isolated BMCs. These data demonstrate a very unique situation in A. woodii in which apparently one BMC gene cluster in expressed during growth on different substrates.
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Affiliation(s)
- Nilanjan Pal Chowdhury
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Lydia Alberti
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Mark Linder
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
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Abstract
Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl-CoA and ultimately acetate using the Wood-Ljungdahl pathway (WLP). This autotrophic metabolism plays a major role in the global carbon cycle and, if harnessed, can help reduce greenhouse gas emissions. Overall, the data presented here provide a framework for examining the ecology and evolution of the Acetobacterium genus and highlight the potential of these species as a source for production of fuels and chemicals from CO2 feedstocks. Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl coenzyme A (acetyl-CoA) and ultimately acetate using the Wood-Ljungdahl pathway (WLP). Acetobacterium woodii is the type strain of the Acetobacterium genus and has been critical for understanding the biochemistry and energy conservation in acetogens. Members of the Acetobacterium genus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done on the unique and various metabolisms of the genus. To gain a better appreciation for the metabolic breadth of the genus, we sequenced the genomes of 4 isolates (A. fimetarium, A. malicum, A. paludosum, and A. tundrae) and conducted a comparative genome analysis (pan-genome) of 11 different Acetobacterium genomes. A unifying feature of the Acetobacterium genus is the carbon-fixing WLP. The methyl (cluster II) and carbonyl (cluster III) branches of the Wood-Ljungdahl pathway are highly conserved across all sequenced Acetobacterium genomes, but cluster I encoding the formate dehydrogenase is not. In contrast to A. woodii, all but four strains encode two distinct Rnf clusters, Rnf being the primary respiratory enzyme complex. Metabolism of fructose, lactate, and H2:CO2 was conserved across the genus, but metabolism of ethanol, methanol, caffeate, and 2,3-butanediol varied. Additionally, clade-specific metabolic potential was observed, such as amino acid transport and metabolism in the psychrophilic species, and biofilm formation in the A. wieringae clade, which may afford these groups an advantage in low-temperature growth or attachment to solid surfaces, respectively. IMPORTANCE Acetogens are anaerobic bacteria capable of fixing CO2 or CO to produce acetyl-CoA and ultimately acetate using the Wood-Ljungdahl pathway (WLP). This autotrophic metabolism plays a major role in the global carbon cycle and, if harnessed, can help reduce greenhouse gas emissions. Overall, the data presented here provide a framework for examining the ecology and evolution of the Acetobacterium genus and highlight the potential of these species as a source for production of fuels and chemicals from CO2 feedstocks.
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Ru J, Huo Y, Yang Y. Microbial Degradation and Valorization of Plastic Wastes. Front Microbiol 2020; 11:442. [PMID: 32373075 PMCID: PMC7186362 DOI: 10.3389/fmicb.2020.00442] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/02/2020] [Indexed: 12/23/2022] Open
Abstract
A growing accumulation of plastic wastes has become a severe environmental and social issue. It is urgent to develop innovative approaches for the disposal of plastic wastes. In recent years, reports on biodegradation of synthetic plastics by microorganisms or enzymes have sprung up, and these offer a possibility to develop biological treatment technology for plastic wastes. In this review, we have comprehensively summarized the microorganisms and enzymes that are able to degrade a variety of generally used synthetic plastics, such as polyethylene (PE), polystyrene (PS), polypropylene (PP), polyvinyl chloride (PVC), polyurethane (PUR), and polyethylene terephthalate (PET). In addition, we have highlighted the microbial metabolic pathways for plastic depolymerization products and the current attempts toward utilization of such products as feedstocks for microbial production of chemicals with high value. Taken together, these findings will contribute to building a conception of bio-upcycling plastic wastes by connecting the biodegradation of plastic wastes to the biosynthesis of valuable chemicals in microorganisms. Last, but not least, we have discussed the challenges toward microbial degradation and valorization of plastic wastes.
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Affiliation(s)
- Jiakang Ru
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yixin Huo
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
- Key Laboratory of Molecular Medicine and Biotherapy, Beijing Institute of Technology, Beijing, China
| | - Yu Yang
- Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, China
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Trifunović D, Berghaus N, Müller V. Growth of the acetogenic bacterium Acetobacterium woodii by dismutation of acetaldehyde to acetate and ethanol. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:58-62. [PMID: 31715654 DOI: 10.1111/1758-2229.12811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 06/10/2023]
Abstract
Acetogenic bacteria are a group of strictly anaerobic bacteria that may have been first life forms on Earth since they employ an ancient pathway for CO2 fixation into acetyl-CoA that is coupled to the synthesis of ATP, the Wood-Ljungdahl pathway. Electrons for CO2 reduction are derived from oxidation of H2 or CO and thus, these bacteria can grow lithotrophically on gases present on early Earth. Among the organic molecules present on early Earth is acetaldehyde, a highly volatile C2 compound. Here, we demonstrate that the acetogenic model bacterium Acetobacterium woodii grows on acetaldehyde. Acetaldehyde is dismutated to ethanol and acetyl-CoA, most likely by the bifunctional alcohol dehydrogenase AdhE. Acetyl-CoA is converted to acetate by two subsequent enzymes, phosphotransacetylase and acetate kinase, accompanied by the synthesis of ATP by substrate-level phosphorylation. Apparently, growth on acetaldehyde does not employ the Wood-Ljungdahl pathway. Our finding opens the possibility of a simple and ancient metabolic pathway with only three enzymes that allows for biomass (acetyl-CoA) and ATP formation on early Earth.
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Affiliation(s)
- Dragan Trifunović
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Natalie Berghaus
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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Ali M, Elreedy A, Ibrahim MG, Fujii M, Nakatani K, Tawfik A. Regulating acidogenesis and methanogenesis for the separated bio-generation of hydrogen and methane from saline-to-hypersaline industrial wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 250:109546. [PMID: 31545177 DOI: 10.1016/j.jenvman.2019.109546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/22/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Given the limitations of acidogens and methanogens activities under saline environments, this work aims to optimize the main operational parameters affecting hydrogen and methane production from saline-to-hypersaline wastewater containing mono-ethylene glycol (MEG). MEG is the main contaminant in several saline industrial effluents. Anaerobic baffled reactor (ABR), as a multi-stage system, was used at different temperatures (i.e., 19-31 °C [ambient] and 35 °C), organic loading rates (OLRs) of 0.6-2.2 gCOD/L/d, and salinity of 5-35 gNaCl/L. Mesophilic conditions of 35 °C substantially promoted MEG biodegradability (92-98%) and hydrogen/methane productivity, even at elevated salinity. Hydrogen yield (HY) and methane yield (MY) peaked to 258 and 140 mL/gCODadd, respectively, at OLR 0.64 gCOD/L/d and salinity up to 20-25 gNaCl/L. An immobilized sludge ABR (ISABR), packed with polyurethane media, was further compared with classical ABR, resulting in 1.8-fold higher MY, at 35 gNaCl/L. Microbial analysis showed that introducing attached growth system (ISABR) substantially promoted methanogens abundance, which was dominated by genus Methanosarcina. Among bacterial genera, Acetobacterium was dominant, particularly in 1st compartment, representing MEG-degrading/salt-tolerant genus. At high salinity up to 35 gNaCl/L, the multi-phase and attached growth configuration can efficiently reduce the induced salt stress, particularly on methanogens, towards balanced and separated acidogenesis/methanogenesis. Overall, producing hydrogen and methane from anaerobic treatment of MEG-based saline wastewater is feasible at optimized parameters and configuration.
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Affiliation(s)
- Manal Ali
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan; Environmental Engineering Department, Egypt-Japan University of Science and Technology, Alexandria, 21934, Egypt; Civil Engineering Department, Aswan University, Aswan, 81511, Egypt
| | - Ahmed Elreedy
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan; Sanitary Engineering Department, Alexandria University, Alexandria, 21544, Egypt.
| | - Mona G Ibrahim
- Environmental Engineering Department, Egypt-Japan University of Science and Technology, Alexandria, 21934, Egypt; Environmental Health Department, High Institute of Public Health, Alexandria University, Alexandria, 21544, Egypt
| | - Manabu Fujii
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan
| | - Kota Nakatani
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan
| | - Ahmed Tawfik
- Water Pollution Research Department, National Research Centre, Giza, 12622, Egypt
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Evans MV, Getzinger G, Luek JL, Hanson AJ, McLaughlin MC, Blotevogel J, Welch SA, Nicora CD, Purvine SO, Xu C, Cole DR, Darrah TH, Hoyt DW, Metz TO, Lee Ferguson P, Lipton MS, Wilkins MJ, Mouser PJ. In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing. THE ISME JOURNAL 2019; 13:2690-2700. [PMID: 31243331 PMCID: PMC6794257 DOI: 10.1038/s41396-019-0466-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/09/2019] [Accepted: 05/24/2019] [Indexed: 11/08/2022]
Abstract
In the last decade, extensive application of hydraulic fracturing technologies to unconventional low-permeability hydrocarbon-rich formations has significantly increased natural-gas production in the United States and abroad. The injection of surface-sourced fluids to generate fractures in the deep subsurface introduces microbial cells and substrates to low-permeability rock. A subset of injected organic additives has been investigated for their ability to support biological growth in shale microbial community members; however, to date, little is known on how complex xenobiotic organic compounds undergo biotransformations in this deep rock ecosystem. Here, high-resolution chemical, metagenomic, and proteomic analyses reveal that widely-used surfactants are degraded by the shale-associated taxa Halanaerobium, both in situ and under laboratory conditions. These halotolerant bacteria exhibit surfactant substrate specificities, preferring polymeric propoxylated glycols (PPGs) and longer alkyl polyethoxylates (AEOs) over polyethylene glycols (PEGs) and shorter AEOs. Enzymatic transformation occurs through repeated terminal-end polyglycol chain shortening during co-metabolic growth through the methylglyoxal bypass. This work provides the first evidence that shale microorganisms can transform xenobiotic surfactants in fracture fluid formulations, potentially affecting the efficiency of hydrocarbon recovery, and demonstrating an important association between injected substrates and microbial growth in an engineered subsurface ecosystem.
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Affiliation(s)
- Morgan V Evans
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Gordon Getzinger
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708, USA
| | - Jenna L Luek
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, 03824, USA
| | - Andrea J Hanson
- Department of Civil & Environmental Engineering, Colorado State University, Ft. Collins, CO, 80523, USA
| | - Molly C McLaughlin
- Department of Civil & Environmental Engineering, Colorado State University, Ft. Collins, CO, 80523, USA
| | - Jens Blotevogel
- Department of Civil & Environmental Engineering, Colorado State University, Ft. Collins, CO, 80523, USA
| | - Susan A Welch
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Carrie D Nicora
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Samuel O Purvine
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Chengdong Xu
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - David R Cole
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Thomas H Darrah
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - David W Hoyt
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Thomas O Metz
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - P Lee Ferguson
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, 27708, USA
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Mary S Lipton
- Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Ft. Collins, CO, 80523, USA
| | - Paula J Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, NH, 03824, USA.
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38
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McAdams BC, Carter KE, Blotevogel J, Borch T, Hakala JA. In situ transformation of hydraulic fracturing surfactants from well injection to produced water. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2019; 21:1777-1786. [PMID: 31588952 DOI: 10.1039/c9em00153k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chemical changes to hydraulic fracturing fluids (HFFs) within fractured unconventional reservoirs may affect hydrocarbon recovery and, in turn, the environmental impact of unconventional oil and gas development. Ethoxylated alcohol surfactants, which include alkyl ethoxylates (AEOs) and polyethylene glycols (PEGs), are often present in HFF as solvents, non-emulsifiers, and corrosion inhibitors. We present detailed analysis of polyethoxylates in HFF at the time of injection into three hydraulically fractured Marcellus Shale wells and in the produced water returning to the surface. Despite the addition of AEOs to the injection fluid during almost all stages, they were rarely detected in the produced water. Conversely, while PEGs were nearly absent in the injection fluid, they were the dominant constituents in the produced water. Similar numbers of ethoxylate units support downhole transformation of AEOs to PEGs through central cleavage of the ethoxylate chain from the alkyl group. We also observed a decrease in the average ethoxylate (EO) number of the PEG-EOs in the produced water over time, consistent with biodegradation during production. Our results elucidate an overlooked surfactant transformation pathway that may affect the efficacy of HFF to maximize oil and gas recovery from unconventional shale reservoirs.
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Affiliation(s)
- Brandon C McAdams
- National Energy Technology Laboratory, United States Department of Energy, 626 Cochrans Mill Road, Pittsburgh, Pennsylvania 15236, USA.
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39
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Wade Y, Daniel RA, Leak DJ. Heterologous Microcompartment Assembly in Bacillaceae: Establishing the Components Necessary for Scaffold Formation. ACS Synth Biol 2019; 8:1642-1654. [PMID: 31242391 DOI: 10.1021/acssynbio.9b00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial microcompartments (BMCs) are organelles that host specific biochemical reactions for both anabolic and catabolic functions. Engineered morphologically diverse BMCs bearing heterologous enzymatic pathways have shown enhanced productivity for commodity chemicals, which makes BMCs an important focus for metabolic engineering. Gaining control of BMC assembly and incorporation of a heterologous enzymatic cargo has yet to be achieved in thermophiles. Herein, we address this by first conducting a detailed bioinformatic analysis of the propanediol utilization (pdu) operon in the thermophile Parageobacillus thermoglucosidasius. We then demonstrated, in vivo, the ability to assemble the native BMCs at an elevated temperature of 60 °C. Heterologous expression of Pdu shell proteins from P. thermoglucosidasius in Bacillus subtilis resulted in the assembly of a single tubular BMC with an average length of 1.4 μm; BMCs assembled after a 20 min induction of expression of the shell operons. Moreover, we show that it is possible to target the monomeric superfolder GFP (msfGFP) to the interior of the compartment by fusion of an N-terminal sequence of the propanediol utilization protein (PduP) of at least 24 amino acids. This study establishes the feasibility of constructing cell factories for small molecules in industrially important Bacillus and Geobacillus spp. by heterologous cargo-carrying BMC production and assembly. Additionally, the study provides experimental confirmation that BMCs are produced in thermophilic bacteria, which opens a path for future research on repurposing the native organelles to provide new functionality at elevated temperatures.
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Affiliation(s)
- Yana Wade
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne, NE2 4AX, U.K
| | - Richard A. Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne, NE2 4AX, U.K
| | - David J. Leak
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K
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40
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Booker AE, Hoyt DW, Meulia T, Eder E, Nicora CD, Purvine SO, Daly RA, Moore JD, Wunch K, Pfiffner SM, Lipton MS, Mouser PJ, Wrighton KC, Wilkins MJ. Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp. Appl Environ Microbiol 2019; 85:e00018-19. [PMID: 30979840 PMCID: PMC6544827 DOI: 10.1128/aem.00018-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/10/2019] [Indexed: 01/12/2023] Open
Abstract
Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause "clumping" of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.
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Affiliation(s)
- Anne E Booker
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tea Meulia
- College of Food, Agricultural, and Environmental Sciences, Ohio State University, Columbus, Ohio, USA
| | - Elizabeth Eder
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Rebecca A Daly
- Department of Microbiology, Ohio State University, Columbus, Ohio, USA
| | - Joseph D Moore
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Kenneth Wunch
- DowDuPont Industrial Biosciences, Wilmington, Delaware, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mary S Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Paula J Mouser
- Department of Civil and Environmental Engineering, University of New Hampshire, Durham, New Hampshire, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
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41
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Salvador M, Abdulmutalib U, Gonzalez J, Kim J, Smith AA, Faulon JL, Wei R, Zimmermann W, Jimenez JI. Microbial Genes for a Circular and Sustainable Bio-PET Economy. Genes (Basel) 2019; 10:E373. [PMID: 31100963 PMCID: PMC6562992 DOI: 10.3390/genes10050373] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 02/03/2023] Open
Abstract
Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for the synthesis of novel PET as well as become a potential carbon source for microorganisms. In addition, microorganisms and biomass can be used for the synthesis of the constituent monomers of PET from renewable sources. The combination of both biodegradation and biosynthesis would enable a completely circular bio-PET economy beyond the conventional recycling processes. Circular strategies like this could contribute to significantly decreasing the environmental impact of our dependence on this polymer. Here we review the efforts made towards turning PET into a viable feedstock for microbial transformations. We highlight current bottlenecks in degradation of the polymer and metabolism of the monomers, and we showcase fully biological or semisynthetic processes leading to the synthesis of PET from sustainable substrates.
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Affiliation(s)
- Manuel Salvador
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Umar Abdulmutalib
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Jaime Gonzalez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Juhyun Kim
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Alex A Smith
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
- SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
- CNRS-UMR8030/Laboratoire iSSB, Université Paris-Saclay, 91000 Évry, France.
| | - Ren Wei
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany.
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany.
| | - Jose I Jimenez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK.
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42
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Keller A, Schink B, Müller N. Alternative Pathways of Acetogenic Ethanol and Methanol Degradation in the Thermophilic Anaerobe Thermacetogenium phaeum. Front Microbiol 2019; 10:423. [PMID: 30949135 PMCID: PMC6436200 DOI: 10.3389/fmicb.2019.00423] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/18/2019] [Indexed: 11/26/2022] Open
Abstract
Growth of the anaerobic thermophile Thermacetogenium phaeum with methanol, ethanol, ethanolamine, and acetate was investigated in axenic cultures and in syntrophic cultures with Methanothermobacter thermautotrophicus. Microcompartment genes were identified in the T. phaeum genome, and presence of microcompartments was confirmed by transmission electron microscopy and proteome analysis. These genes were expressed only during growth with ethanolamine. Proteome data were compared after growth with all four substrates, and activities of key enzymes of the Wood–Ljungdahl pathway and of enzyme systems leading to production or degradation of acetaldehyde such as alcohol dehydrogenase, aldehyde:ferredoxin oxidoreductase, acetate kinase, and phosphate acetyltransferase were measured in cytoplasmic fractions. Accounting of fermentation stoichiometries and growth yields with all four substrates showed that ethanol and methanol oxidation follow the same stoichiometries as in Acetobacterium woodii. On the other hand, the pathways of ethanol and methanol degradations vary between both organisms. Growth yields of T. phaeum were substantially lower than reported for A. woodii. Since T. phaeum has no Rnf complex encoded in its genome, the mechanisms of ATP synthesis have to be different from those of A. woodii. In addition to the central degradation pathways also found in A. woodii, T. phaeum maintains enzyme systems that compensate for the absence of an Rnf-complex but which on the other hand cause a loss of energy. On the basis of our data, pathways of methanol and ethanol degradation in T. phaeum are discussed.
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Affiliation(s)
- Anja Keller
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Bernhard Schink
- Department of Biology, Universität Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, Konstanz, Germany
| | - Nicolai Müller
- Department of Biology, Universität Konstanz, Konstanz, Germany
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43
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Elreedy A, Fujii M, Koyama M, Nakasaki K, Tawfik A. Enhanced fermentative hydrogen production from industrial wastewater using mixed culture bacteria incorporated with iron, nickel, and zinc-based nanoparticles. WATER RESEARCH 2019; 151:349-361. [PMID: 30616047 DOI: 10.1016/j.watres.2018.12.043] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 11/26/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
The present study assessed the efficiency of utilizing mixed culture bacteria (MCB) incorporated with individual nanoparticles (NPs), i.e., hematite (α-Fe2O3), nickel oxide (NiO), and zinc oxide (ZnO), dual NPs (α-Fe2O3 + NiO, α-Fe2O3 + ZnO, and NiO + ZnO), and multi-NPs (α-Fe2O3 + NiO + ZnO) for hydrogen production (HP) from industrial wastewater containing mono-ethylene glycol (MEG). When MCB was individually supplemented with α-Fe2O3 (200 mg/L), NiO (20 mg/L), and ZnO NPs (10 mg/L), HP improved significantly by 41, 30, and 29%, respectively. Further, key enzymes associated with MEG metabolism, such as alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), and hydrogenase (hyd), were rapidly and substantially enhanced in the medium. NiO and ZnO NPs notably promoted ADH and ALDH activities, respectively, while α-Fe2O3 exhibited superior impact on hyd activity. Maximum hydrogen production rate was concomitant with higher acetic acid production and lower residual acetaldehyde and ethanol. HP using MCB supplemented with individual NiO (20 mg/L) and ZnO NPs (10 mg/L) further improved by 8.0%-14% when dual and multi-NPs were used; the highest HP was recorded when multi-NPs were used. In addition, NPs incorporation resulted in substantial increase in the relative abundance of Clostridiales (belonging to family Clostridiaceae; > 83%). Overall, this study provides significant insights into the impact of NPs on hydrogen production from MEG-contaminated wastewater.
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Affiliation(s)
- Ahmed Elreedy
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan; Sanitary Engineering Department, Faculty of Engineering, Alexandria University, Alexandria, 21544, Egypt.
| | - Manabu Fujii
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan.
| | - Mitsuhiko Koyama
- School of Environment and Society, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Kiyohiko Nakasaki
- School of Environment and Society, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ahmed Tawfik
- Water Pollution Research Department, National Research Centre, Giza, 12622, Egypt
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44
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Dönig J, Müller V. Alanine, a Novel Growth Substrate for the Acetogenic Bacterium Acetobacterium woodii. Appl Environ Microbiol 2018; 84:e02023-18. [PMID: 30242008 PMCID: PMC6238063 DOI: 10.1128/aem.02023-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/16/2018] [Indexed: 11/20/2022] Open
Abstract
Acetogenic bacteria are an ecophysiologically important group of strictly anaerobic bacteria that grow lithotrophically on H2 plus CO2 or on CO or heterotrophically on different substrates such as sugars, alcohols, aldehydes, or acids. Amino acids are rarely used. Here, we describe that the model acetogen Acetobacterium woodii can use alanine as the sole carbon and energy source, which is in contrast to the description of the type strain. The alanine degradation genes have been identified and characterized. A key to alanine degradation is an alanine dehydrogenase which has been characterized biochemically. The resulting pyruvate is further degraded to acetate by the known pathways involving the Wood-Ljungdahl pathway. Our studies culminate in a metabolic and bioenergetic scheme for alanine-dependent acetogenesis in A. woodiiIMPORTANCE Peptides and amino acids are widespread in nature, but there are only a few reports that demonstrated use of amino acids as carbon and energy sources by acetogenic bacteria, a central and important group in the anaerobic food web. Our finding that A. woodii can perform alanine oxidation coupled to reduction of carbon dioxide not only increases the number of substrates that can be used by this model acetogen but also raises the possibility that other acetogens may also be able to use alanine. Indeed, the alanine genes are also present in at least two more acetogens, for which growth on alanine has not been reported so far. Alanine may be a promising substrate for industrial fermentations, since acid formation goes along with the production of a base (NH3) and pH regulation is a minor issue.
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Affiliation(s)
- Judith Dönig
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt, Germany
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45
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Kremp F, Poehlein A, Daniel R, Müller V. Methanol metabolism in the acetogenic bacterium Acetobacterium woodii. Environ Microbiol 2018; 20:4369-4384. [PMID: 30003650 DOI: 10.1111/1462-2920.14356] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/07/2018] [Indexed: 11/29/2022]
Abstract
Methanol derived from plant tissue is ubiquitous in anaerobic sediments and a good substrate for anaerobes growing on C1 compounds such as methanogens and acetogens. In contrast to methanogens little is known about the physiology, biochemistry and bioenergetics of methanol utilization in acetogenic bacteria. To fill this gap, we have used the model acetogen Acetobacterium woodii to study methanol metabolism using physiological and biochemical experiments paired with molecular studies and transcriptome analysis. These studies identified the genes and enzymes involved in acetogenesis from methanol and the redox carriers involved. We will present the first comprehensive model for carbon and electron flow from methanol in an acetogen and the bioenergetics of acetogenesis from methanol.
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Affiliation(s)
- Florian Kremp
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg August University, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438, Frankfurt, Germany
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46
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Lechtenfeld M, Heine J, Sameith J, Kremp F, Müller V. Glycine betaine metabolism in the acetogenic bacteriumAcetobacterium woodii. Environ Microbiol 2018; 20:4512-4525. [DOI: 10.1111/1462-2920.14389] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/10/2018] [Accepted: 08/17/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Mats Lechtenfeld
- Department of Molecular Microbiology & BioenergeticsInstitute of Molecular Biosciences, Johann Wolfgang Goethe University Max‐von‐Laue Str. 9, D‐60438 Frankfurt Germany
| | - Julia Heine
- Department of Molecular Microbiology & BioenergeticsInstitute of Molecular Biosciences, Johann Wolfgang Goethe University Max‐von‐Laue Str. 9, D‐60438 Frankfurt Germany
| | - Janin Sameith
- Department of Molecular Microbiology & BioenergeticsInstitute of Molecular Biosciences, Johann Wolfgang Goethe University Max‐von‐Laue Str. 9, D‐60438 Frankfurt Germany
| | - Florian Kremp
- Department of Molecular Microbiology & BioenergeticsInstitute of Molecular Biosciences, Johann Wolfgang Goethe University Max‐von‐Laue Str. 9, D‐60438 Frankfurt Germany
| | - Volker Müller
- Department of Molecular Microbiology & BioenergeticsInstitute of Molecular Biosciences, Johann Wolfgang Goethe University Max‐von‐Laue Str. 9, D‐60438 Frankfurt Germany
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Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters. Biochem Soc Trans 2017; 45:635-652. [PMID: 28620026 DOI: 10.1042/bst20160281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 11/17/2022]
Abstract
We present a systems biology view on pseudoenzymes that acknowledges that genes are not selfish: the genome is. With network function as the selectable unit, there has been an evolutionary bonus for recombination of functions of and within proteins. Many proteins house a functionality by which they 'read' the cell's state, and one by which they 'write' and thereby change that state. Should the writer domain lose its cognate function, a 'pseudoenzyme' or 'pseudosignaler' arises. GlnK involved in Escherichia coli ammonia assimilation may well be a pseudosignaler, associating 'reading' the nitrogen state of the cell to 'writing' the ammonium uptake activity. We identify functional pseudosignalers in the cyclin-dependent kinase complexes regulating cell-cycle progression. For the mitogen-activated protein kinase pathway, we illustrate how a 'dead' pseudosignaler could produce potentially selectable functionalities. Four billion years ago, bioenergetics may have shuffled 'electron-writers', producing various networks that all served the same function of anaerobic ATP synthesis and carbon assimilation from hydrogen and carbon dioxide, but at different ATP/acetate ratios. This would have enabled organisms to deal with variable challenges of energy need and substrate supply. The same principle might enable 'gear-shifting' in real time, by dynamically generating different pseudo-redox enzymes, reshuffling their coenzymes, and rerouting network fluxes. Non-stationary pH gradients in thermal vents together with similar such shuffling mechanisms may have produced a first selectable proton-motivated pyrophosphate synthase and subsequent ATP synthase. A combination of functionalities into enzymes, signalers, and the pseudo-versions thereof may offer fitness in terms of plasticity, both in real time and in evolution.
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