101
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Poblete-Castro I, Wittmann C, Nikel PI. Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species. Microb Biotechnol 2019; 13:32-53. [PMID: 30883020 PMCID: PMC6922529 DOI: 10.1111/1751-7915.13400] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/17/2019] [Accepted: 02/23/2019] [Indexed: 11/30/2022] Open
Abstract
The use of renewable waste feedstocks is an environment‐friendly choice contributing to the reduction of waste treatment costs and increasing the economic value of industrial by‐products. Glycerol (1,2,3‐propanetriol), a simple polyol compound widely distributed in biological systems, constitutes a prime example of a relatively cheap and readily available substrate to be used in bioprocesses. Extensively exploited as an ingredient in the food and pharmaceutical industries, glycerol is also the main by‐product of biodiesel production, which has resulted in a progressive drop in substrate price over the years. Consequently, glycerol has become an attractive substrate in biotechnology, and several chemical commodities currently produced from petroleum have been shown to be obtained from this polyol using whole‐cell biocatalysts with both wild‐type and engineered bacterial strains. Pseudomonas species, endowed with a versatile and rich metabolism, have been adopted for the conversion of glycerol into value‐added products (ranging from simple molecules to structurally complex biopolymers, e.g. polyhydroxyalkanoates), and a number of metabolic engineering strategies have been deployed to increase the number of applications of glycerol as a cost‐effective substrate. The unique genetic and metabolic features of glycerol‐grown Pseudomonas are presented in this review, along with relevant examples of bioprocesses based on this substrate – and the synthetic biology and metabolic engineering strategies implemented in bacteria of this genus aimed at glycerol valorization.
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Affiliation(s)
- Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Natural Sciences, Universidad Andrés Bello, Santiago de Chile, Chile
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Universität des Saarlandes, Saarbrücken, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
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102
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Combination of ssDNA recombineering and CRISPR-Cas9 for Pseudomonas putida KT2440 genome editing. Appl Microbiol Biotechnol 2019; 103:2783-2795. [DOI: 10.1007/s00253-019-09654-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 12/17/2022]
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103
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Enhanced synthesis of medium-chain-length poly(3-hydroxyalkanoates) by inactivating the tricarboxylate transport system of Pseudomonas putida KT2440 and process development using waste vegetable oil. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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104
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High-Quality Draft Genome Sequence of Pseudomonas reidholzensis Strain CCOS 865 T. Microbiol Resour Announc 2019; 8:MRA01502-18. [PMID: 30687835 PMCID: PMC6346167 DOI: 10.1128/mra.01502-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 11/20/2022] Open
Abstract
We have sequenced and assembled the genome of Pseudomonas reidholzensis CCOS 865T, which was isolated in 2014 from forest soil. Members of the genus Pseudomonas play important roles in environmental systems and are utilized in many biotechnological processes. We have sequenced and assembled the genome of Pseudomonas reidholzensis CCOS 865T, which was isolated in 2014 from forest soil. Members of the genus Pseudomonas play important roles in environmental systems and are utilized in many biotechnological processes. The genome of this species may provide an important resource for the discovery of novel enzyme activities.
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105
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Calero P, Nikel PI. Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms. Microb Biotechnol 2019; 12:98-124. [PMID: 29926529 PMCID: PMC6302729 DOI: 10.1111/1751-7915.13292] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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106
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Wilkes RA, Mendonca CM, Aristilde L. A Cyclic Metabolic Network in Pseudomonas protegens Pf-5 Prioritizes the Entner-Doudoroff Pathway and Exhibits Substrate Hierarchy during Carbohydrate Co-Utilization. Appl Environ Microbiol 2019; 85:e02084-18. [PMID: 30366991 PMCID: PMC6293094 DOI: 10.1128/aem.02084-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/17/2018] [Indexed: 11/20/2022] Open
Abstract
The genetic characterization of Pseudomonas protegens Pf-5 was recently completed. However, the inferred metabolic network structure has not yet been evaluated experimentally. Here, we employed 13C-tracers and quantitative flux analysis to investigate the intracellular network for carbohydrate metabolism. In lieu of the direct phosphorylation of glucose by glucose kinase, glucose catabolism was characterized primarily by the oxidation of glucose to gluconate and 2-ketogluconate before the phosphorylation of these metabolites to feed the Entner-Doudoroff (ED) pathway. In the absence of phosphofructokinase activity, a cyclic flux from the ED pathway to the upper Embden-Meyerhof-Parnas (EMP) pathway was responsible for routing glucose-derived carbons to the non-oxidative pentose phosphate (PP) pathway. Consistent with the lack of annotated genes in P. protegens Pf-5 for the transport or initial catabolism of pentoses and galactose, only glucose was assimilated into intracellular metabolites in the presence of xylose, arabinose, or galactose. However, when glucose was fed simultaneously with fructose or mannose, co-uptake of these hexoses was evident, but glucose was preferred over fructose (3 to 1) and over mannose (4 to 1). Despite gene annotation of mannose catabolism to fructose-6-phosphate, metabolite labeling patterns revealed that mannose was assimilated into fructose-1,6-bisphosphate, similarly to fructose catabolism. Remarkably, carbons from mannose and fructose were also found to cycle backward through the upper EMP pathway toward the ED pathway. Therefore, the operational metabolic network for processing carbohydrates in P. protegens Pf-5 prioritizes flux through the ED pathway to channel carbons to EMP, PP, and downstream pathways.IMPORTANCE Species of the Pseudomonas genus thrive in various nutritional environments and have strong biocatalytic potential due to their diverse metabolic capabilities. Carbohydrate substrates are ubiquitous both in environmental matrices and in feedstocks for engineered bioconversion. Here, we investigated the metabolic network for carbohydrate metabolism in Pseudomonas protegens Pf-5. Metabolic flux quantitation revealed the relative involvement of different catabolic routes in channeling carbohydrate carbons through a cyclic metabolic network. We also uncovered that mannose catabolism was similar to fructose catabolism, despite the annotation of a different pathway in the genome. Elucidation of the constitutive metabolic network in P. protegens is important for understanding its innate carbohydrate processing, thus laying the foundation for targeting metabolic engineering of this untapped Pseudomonas species.
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Affiliation(s)
- Rebecca A Wilkes
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Caroll M Mendonca
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
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107
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High-Quality Draft Genome Sequence of Pseudomonas wadenswilerensis CCOS 864 T. Microbiol Resour Announc 2018; 7:MRA01059-18. [PMID: 30533735 PMCID: PMC6256571 DOI: 10.1128/mra.01059-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/01/2018] [Indexed: 12/31/2022] Open
Abstract
Pseudomonas wadenswilerensis CCOS 864T was isolated in 2014 from forest soil. The organism belongs taxonomically to the Pseudomonas putida group, members of which have been well studied for their potential in biotechnological applications. We present here the draft genome sequence of P. wadenswilerensis CCOS 864T.
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108
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Balasubramani G, Induja K, Aiswarya D, Deepak P, Arul D, Kavitha M, Amutha V, Perumal P. Isolation and Characterization of Human Foot Crack–Associated Bacterium,Pseudomonas Otitidis, and Its Biological Propensity. SMART SCIENCE 2018. [DOI: 10.1080/23080477.2018.1551305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Kathiravan Induja
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
| | - Dilipkumar Aiswarya
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
| | - Paramasivam Deepak
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
| | - Dhayalan Arul
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
| | - Mathialagan Kavitha
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
| | - Vadivelu Amutha
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
| | - Pachiappan Perumal
- Department of Biotechnology, School of Biosciences, Periyar University, Salem, India
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109
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Nikel PI, de Lorenzo V. Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans-metabolism. Metab Eng 2018; 50:142-155. [DOI: 10.1016/j.ymben.2018.05.005] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/07/2018] [Accepted: 05/10/2018] [Indexed: 12/12/2022]
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110
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Dynamics of Pseudomonas putida biofilms in an upscale experimental framework. ACTA ACUST UNITED AC 2018; 45:899-911. [DOI: 10.1007/s10295-018-2070-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
Abstract
Exploitation of biofilms for industrial processes requires them to adopt suitable physical structures for rendering them efficient and predictable. While hydrodynamics could be used to control material features of biofilms of the platform strain Pseudomonas putida KT2440 there is a dearth of experimental data on surface-associated growth behavior in such settings. Millimeter scale biofilm patterns formed by its parental strain P. putida mt-2 under different Reynolds numbers (Re) within laminar regime were analyzed using an upscale experimental continuous cultivation assembly. A tile-scan image acquisition process combined with a customized image analysis revealed patterns of dense heterogeneous structures at Re = 1000, but mostly flattened coverings sparsely patched for Re < 400. These results not only fix the somewhat narrow hydrodynamic regime under which P. putida cells form stable coatings on surfaces destined for large-scale processes, but also provide useful sets of parameters for engineering catalytic biofilms based on this important bacterium as a cell factory.
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111
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Tamayo-Ramos JA, Rumbo C, Caso F, Rinaldi A, Garroni S, Notargiacomo A, Romero-Santacreu L, Cuesta-López S. Analysis of Polycaprolactone Microfibers as Biofilm Carriers for Biotechnologically Relevant Bacteria. ACS APPLIED MATERIALS & INTERFACES 2018; 10:32773-32781. [PMID: 30168313 DOI: 10.1021/acsami.8b07245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Polymeric electrospun fibers are becoming popular in microbial biotechnology because of their exceptional physicochemical characteristics, biodegradability, surface-to-volume ratio, and compatibility with biological systems, which give them a great potential as microbial supports to be used in production processes or environmental applications. In this work, we analyzed and compared the ability of Escherichia coli, Pseudomonas putida, Brevundimonas diminuta, and Sphingobium fuliginis to develop biofilms on different types of polycaprolactone (PCL) microfibers. These bacterial species are relevant in the production of biobased chemicals, enzymes, and proteins for therapeutic use and bioremediation. The obtained results demonstrated that all selected species were able to attach efficiently to the PCL microfibers. Also, the ability of pure cultures of S. fuliginis (former Flavobacterium sp. ATCC 27551, a very relevant strain in the bioremediation of organophosphorus compounds) to form dense biofilms was observed for the first time, opening the possibility of new applications for this microorganism. This material showed to have a high microbial loading capacity, regardless of the mesh density and fiber diameter. A comparative analysis between PCL and polylactic acid (PLA) electrospun microfibers indicated that both surfaces have a similar bacterial loading capacity, but the former material showed higher resistance to microbial degradation than PLA.
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Affiliation(s)
- Juan Antonio Tamayo-Ramos
- International Research Centre in Critical Raw Materials-ICCRAM , University of Burgos , Plaza Misael Banuelos s/n , 09001 Burgos , Spain
| | - Carlos Rumbo
- International Research Centre in Critical Raw Materials-ICCRAM , University of Burgos , Plaza Misael Banuelos s/n , 09001 Burgos , Spain
- Departamento de Química, Facultad de Ciencias , University of Burgos , Plaza Misael Bañuelos s/n , 09001 Burgos , Spain
| | - Federica Caso
- Nanofaber srl. , Via Anguillarese 301 , 00123 Rome , Italy
| | - Antonio Rinaldi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) , Casaccia Research Centre , Via Anguillarese 301 , 00123 Rome , Italy
| | - Sebastiano Garroni
- International Research Centre in Critical Raw Materials-ICCRAM , University of Burgos , Plaza Misael Banuelos s/n , 09001 Burgos , Spain
| | - Andrea Notargiacomo
- Institute for Photonics and Nanotechnology , CNR , Via Cineto Romano 42 , 00156 Rome , Italy
| | - Lorena Romero-Santacreu
- International Research Centre in Critical Raw Materials-ICCRAM , University of Burgos , Plaza Misael Banuelos s/n , 09001 Burgos , Spain
- Advanced Materials, Nuclear Technology and Applied Bio/Nanotechnology, Consolidated Research Unit UIC-154 , University of Burgos , Hospital del Rey s/n , Burgos , 09001 , Castilla y León, Spain
| | - Santiago Cuesta-López
- International Research Centre in Critical Raw Materials-ICCRAM , University of Burgos , Plaza Misael Banuelos s/n , 09001 Burgos , Spain
- Advanced Materials, Nuclear Technology and Applied Bio/Nanotechnology, Consolidated Research Unit UIC-154 , University of Burgos , Hospital del Rey s/n , Burgos , 09001 , Castilla y León, Spain
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112
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Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP. Jungle Express is a versatile repressor system for tight transcriptional control. Nat Commun 2018; 9:3617. [PMID: 30190458 PMCID: PMC6127294 DOI: 10.1038/s41467-018-05857-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 07/30/2018] [Indexed: 11/09/2022] Open
Abstract
Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of 'Jungle Express', an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 µM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale.
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Affiliation(s)
- Thomas L Ruegg
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Institute of Botany, University of Basel, 4001, Basel, Switzerland
| | - Jose H Pereira
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joseph C Chen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - Andy DeGiovanni
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Pavel Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Giovani P Tomaleri
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Michael P Thelen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA.
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113
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Barzen-Hanson KA, Wilkes RA, Aristilde L. Quantitation of carbohydrate monomers and dimers by liquid chromatography coupled with high-resolution mass spectrometry. Carbohydr Res 2018; 468:30-35. [PMID: 30121416 DOI: 10.1016/j.carres.2018.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/08/2018] [Accepted: 08/11/2018] [Indexed: 01/16/2023]
Abstract
As remnants of plant wastes or plant secretions, carbohydrates are widely found in various environmental matrices. Carbohydrate-containing feedstocks represent important carbon sources for engineered bioproduction of commodity compounds. Routine monitoring and quantitation of heterogenous carbohydrate mixtures requires fast, accurate, and precise analytical methods. Here we present two methods to quantify carbohydrates mixtures by coupling hydrophilic interaction liquid chromatography with electrospray ionization high-resolution mass spectrometry. Method 1 was optimized for eleven different carbohydrates: three pentoses (ribose, arabinose, xylose), three hexoses (glucose, fructose, mannose), and five dimers (sucrose, cellobiose, maltose, trehalose, lactose). Method 1 can monitor these carbohydrates simultaneously, except in the case of co-elution of xylose/arabinose and lactose/maltose/cellobiose peaks. Using the same stationary and mobile phases as in Method 1, Method 2 was developed to separate glucose and galactose, which were indistinguishable in Method 1. Both methods have low limits of detection (0.019-0.40 μM) and quantification (0.090-1.3 μM), good precision (2.4-13%) except sucrose (18%), and low mass error (0.0-2.4 ppm). Method 1 was robust at analyzing high ionic strength solutions, but a moderate matrix effect was observed. Finally, we apply Method 1 to track concurrently the extracellular depletion of five carbohydrates (xylose, glucose, fructose, mannose, and maltose) by Pseudomonas protegens Pf-5, a biotechnologically-important soil bacterial species.
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Affiliation(s)
- Krista A Barzen-Hanson
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Rebecca A Wilkes
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853, USA.
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114
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Sánchez-Hevia DL, Yuste L, Moreno R, Rojo F. Influence of the Hfq and Crc global regulators on the control of iron homeostasis inPseudomonas putida. Environ Microbiol 2018; 20:3484-3503. [DOI: 10.1111/1462-2920.14263] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Dione L. Sánchez-Hevia
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Renata Moreno
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
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115
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Volke DC, Nikel PI. Getting Bacteria in Shape: Synthetic Morphology Approaches for the Design of Efficient Microbial Cell Factories. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800111] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel C. Volke
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
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116
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Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose. Metab Eng 2018; 48:94-108. [DOI: 10.1016/j.ymben.2018.05.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/15/2018] [Accepted: 05/31/2018] [Indexed: 01/02/2023]
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117
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Svenningsen NB, Martínez-García E, Nicolaisen MH, de Lorenzo V, Nybroe O. The biofilm matrix polysaccharides cellulose and alginate both protect Pseudomonas putida mt-2 against reactive oxygen species generated under matric stress and copper exposure. Microbiology (Reading) 2018; 164:883-888. [DOI: 10.1099/mic.0.000667] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Nanna B. Svenningsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Mette H. Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Victor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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118
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Löwe H, Sinner P, Kremling A, Pflüger-Grau K. Engineering sucrose metabolism in Pseudomonas putida highlights the importance of porins. Microb Biotechnol 2018; 13:97-106. [PMID: 29808622 PMCID: PMC6922520 DOI: 10.1111/1751-7915.13283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 12/19/2022] Open
Abstract
Using agricultural wastes as a substrate for biotechnological processes is of great interest in industrial biotechnology. A prerequisite for using these wastes is the ability of the industrially relevant microorganisms to metabolize the sugars present therein. Therefore, many metabolic engineering approaches are directed towards widening the substrate spectrum of the workhorses of industrial biotechnology like Escherichia coli, yeast or Pseudomonas putida. For instance, neither xylose or arabinose from cellulosic residues, nor sucrose, the main sugar in waste molasses, can be metabolized by most E. coli and P. putida wild types. We evaluated a new, so far uncharacterized gene cluster for sucrose metabolism from Pseudomonas protegens Pf‐5 and showed that it enables P. putida to grow on sucrose as the sole carbon and energy source. Even when integrated into the genome of P. putida, the resulting strain grew on sucrose at rates similar to the rate of the wild type on glucose – making it the fastest growing, plasmid‐free P. putida strain known so far using sucrose as substrate. Next, we elucidated the role of the porin, an orthologue of the sucrose porin ScrY, in the gene cluster and found that in P. putida, a porin is needed for sucrose transport across the outer membrane. Consequently, native porins were not sufficient to allow unlimited growth on sucrose. Therefore, we concluded that the outer membrane can be a considerable barrier for substrate transport, depending on strain, genotype and culture conditions, all of which should be taken into account in metabolic engineering approaches. We additionally showed the potential of the engineered P. putida strains by growing them on molasses with efficiencies twice as high as obtained with the wild‐type P. putida. This can be seen as a further step towards the production of low‐value chemicals and biofuels with P. putida from alternative and more affordable substrates in the future.
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Affiliation(s)
- Hannes Löwe
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
| | - Peter Sinner
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
| | - Andreas Kremling
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
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119
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Markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida. Metab Eng 2018; 47:463-474. [PMID: 29751103 DOI: 10.1016/j.ymben.2018.05.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/05/2018] [Accepted: 05/06/2018] [Indexed: 11/22/2022]
Abstract
Pseudomonas putida has gained much interest among metabolic engineers as a workhorse for producing valuable natural products. While a few gene knockout tools for P. putida have been reported, integration of heterologous genes into the chromosome of P. putida, an essential strategy to develop stable industrial strains producing heterologous bioproducts, requires development of a more efficient method. Current methods rely on time-consuming homologous recombination techniques and transposon-mediated random insertions. Here we report a RecET recombineering system for markerless integration of heterologous genes into the P. putida chromosome. The efficiency and capacity of the recombineering system were first demonstrated by knocking out various genetic loci on the P. putida chromosome with knockout lengths widely spanning 0.6-101.7 kb. The RecET recombineering system developed here allowed successful integration of biosynthetic gene clusters for four proof-of-concept bioproducts, including protein, polyketide, isoprenoid, and amino acid derivative, into the target genetic locus of P. putida chromosome. The markerless recombineering system was completed by combining Cre/lox system and developing efficient plasmid curing systems, generating final strains free of antibiotic markers and plasmids. This markerless recombineering system for efficient gene knockout and integration will expedite metabolic engineering of P. putida, a bacterial host strain of increasing academic and industrial interest.
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Kohlstedt M, Starck S, Barton N, Stolzenberger J, Selzer M, Mehlmann K, Schneider R, Pleissner D, Rinkel J, Dickschat JS, Venus J, B.J.H. van Duuren J, Wittmann C. From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida. Metab Eng 2018; 47:279-293. [DOI: 10.1016/j.ymben.2018.03.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 12/31/2022]
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121
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Engineering Complexity in Bacterial Regulatory Circuits for Biotechnological Applications. mSystems 2018; 3:mSystems00151-17. [PMID: 29657966 PMCID: PMC5895878 DOI: 10.1128/msystems.00151-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/14/2018] [Indexed: 01/29/2023] Open
Abstract
Engineering microbial systems allows the generation of new technologies having significant impact in the biotechnological industry and on human health. In the past few years, several synthetic biology approaches have been implemented in bacteria to allow precise engineering of novel regulatory circuits for several applications. Engineering microbial systems allows the generation of new technologies having significant impact in the biotechnological industry and on human health. In the past few years, several synthetic biology approaches have been implemented in bacteria to allow precise engineering of novel regulatory circuits for several applications. The advent of high-throughput technologies and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based DNA editing techniques have been pivotal in this process. Yet, despite the tremendous advances experienced recently, there are still a number of bottlenecks that need to be overcome in order to generate high-performance redesigned living machines, and the use of novel computer-aided approaches would be essential for this task. In this perspective, we discuss some of the main advances in the field of microbial engineering and the new technologies and approaches that should allow the construction of on demand synthetic microbial factories through the redesign of regulatory complexity.
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122
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Wang S, Bilal M, Zong Y, Hu H, Wang W, Zhang X. Development of a Plasmid-Free Biosynthetic Pathway for Enhanced Muconic Acid Production in Pseudomonas chlororaphis HT66. ACS Synth Biol 2018; 7:1131-1142. [PMID: 29608278 DOI: 10.1021/acssynbio.8b00047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Muconic acid is a platform chemical and an important intermediate in the degradation process of a series of aromatic compounds. Herein, a plasmid-free synthetic pathway in Pseudomonas chlororaphis HT66 is constructed for the enhanced biosynthesis of muconic acid by connecting endogenous ubiquinone biosynthesis pathway with protocatechuate degradation pathway using chromosomal integration. Instead of being plasmid and inducer dependent, the engineered strains could steadily produce the high muconic acid using glycerol as a carbon source. The engineered strain HT66-MA6 achieved a 3376 mg/L muconic acid production with a yield of 187.56 mg/g glycerol via the following strategies: (1) block muconic acid conversion and enhance muconic acid efflux pumping with phenazine biosynthesis cluster; (2) increase the muconic acid precursors supply through overexpressing the rate-limiting step, and (3) coexpress the "3-dehydroshikimate-derived" route in parallel with the "4-hydroxybenzoic acid-derived" route to create a synthetic "metabolic funnel". Finally, on the basis of the glycerol feeding strategies, the muconic acid yield reached 0.122 mol/mol glycerol. The results suggest that the construction of synthetic pathway with a plasmid-free strategy in P. chlororaphis displays a high biotechnological perspective.
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123
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Sun J, Wang Q, Jiang Y, Wen Z, Yang L, Wu J, Yang S. Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system. Microb Cell Fact 2018. [PMID: 29534717 PMCID: PMC5851096 DOI: 10.1186/s12934-018-0887-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background The soil bacterium Pseudomonas putida KT2440 is a “generally recognized as safe”-certified strain with robust property and versatile metabolism. Thus, it is an ideal candidate for synthetic biology, biodegradation, and other biotechnology applications. The known genome editing approaches of Pseudomonas are suboptimal; thus, it is necessary to develop a high efficiency genome editing tool. Results In this study, we established a fast and convenient CRISPR–Cas9 method in P. putida KT2440. Gene deletion, gene insertion and gene replacement could be achieved within 5 days, and the mutation efficiency reached > 70%. Single nucleotide replacement could be realized, overcoming the limitations of protospacer adjacent motif sequences. We also applied nuclease-deficient Cas9 binding at three locations upstream of enhanced green fluorescent protein (eGFP) for transcriptional inhibition, and the expression intensity of eGFP reduced to 28.5, 29.4, and 72.1% of the control level, respectively. Furthermore, based on this CRISPR–Cas9 system, we also constructed a CRISPR–Cpf1 system, which we validated for genome editing in P. putida KT2440. Conclusions In this research, we established CRISPR based genome editing and regulation control systems in P. putida KT2440. These fast and efficient approaches will greatly facilitate the application of P. putida KT2440.![]() Electronic supplementary material The online version of this article (10.1186/s12934-018-0887-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Sun
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Qingzhuo Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yu Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.,Shanghai Research and Development Center of Industrial Biotechnology, Shanghai, 201206, China
| | - Zhiqiang Wen
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. .,Shanghai Research and Development Center of Industrial Biotechnology, Shanghai, 201206, China. .,Jiangsu National Synergetic Innovation Center for Advanced Materials, SICAM, Nanjing, 210009, China.
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Wehrmann M, Klebensberger J. Engineering thermal stability and solvent tolerance of the soluble quinoprotein PedE from Pseudomonas putida KT2440 with a heterologous whole-cell screening approach. Microb Biotechnol 2018; 11:399-408. [PMID: 29239114 PMCID: PMC5812247 DOI: 10.1111/1751-7915.13036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/18/2017] [Accepted: 11/12/2017] [Indexed: 12/16/2022] Open
Abstract
Due to their ability for direct electron transfer to electrodes, the utilization of rare earth metals as cofactor, and their periplasmic localization, pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) represent an interesting class of biocatalysts for various biotechnological applications. For most biocatalysts protein stability is crucial, either to increase the performance of the protein under a given process condition or to maximize robustness of the protein towards mutational manipulations, which are often needed to enhance or introduce a functionality of interest. In this study, we describe a whole-cell screening assay, suitable for probing PQQ-ADH activities in Escherichia coli BL21(DE3) cells, and use this assay to screen smart mutant libraries for increased thermal stability of the PQQ-ADH PedE (PP_2674) from Pseudomonas putida KT2440. Upon three consecutive rounds of screening, we identified three different amino acid positions, which significantly improve enzyme stability. The subsequent combination of the beneficial mutations finally results in the triple mutant R91D/E408P/N410K, which not only exhibits a 7°C increase in thermal stability but also a twofold increase in residual activity upon incubation with up to 50% dimethyl sulfoxide (DMSO), while showing no significant difference in enzymatic efficiency (kcat /KM ).
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Affiliation(s)
- Matthias Wehrmann
- Institute of Technical BiochemistryUniversity of StuttgartStuttgartGermany
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125
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de Lorenzo V, Schmidt M. Biological standards for the Knowledge-Based BioEconomy: What is at stake. N Biotechnol 2018; 40:170-180. [DOI: 10.1016/j.nbt.2017.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/03/2017] [Indexed: 02/07/2023]
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126
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Aparicio T, de Lorenzo V, Martínez-García E. CRISPR/Cas9-Based Counterselection Boosts Recombineering Efficiency in Pseudomonas putida. Biotechnol J 2017; 13:e1700161. [PMID: 29058367 DOI: 10.1002/biot.201700161] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/15/2017] [Indexed: 12/13/2022]
Abstract
While adoption of single-stranded DNA recombineering techniques has greatly eased genetic design of the platform strain Pseudomonas putida KT2440, available methods still produce the desired modifications/deletions at low frequencies. This makes isolation of mutants that do not display selectable or conspicuous phenotypes considerably difficult. To overcome this limitation, the authors have merged ssDNA recombineering with CRISPR/Cas9 technology in this bacterium for efficient killing of unmodified cells and thus non-phenotypic selection of bacteria bearing the mutations of interest. After incorporating the system into standardized pSEVA plasmids the authors tested its functional efficiency by targeting different types of changes that ranged from single nucleotide substitutions to one-gene deletions-to even the removal of the large flagellar cluster (≈69 kb). Simultaneous introduction of two independent gene deletions was tested as well. In all cases, directing the crRNA/Cas9 complexes toward non-modified, wild-type genomic sequences boosted dramatically the appearance of the mutants at stake in the absence of any phenotypic selection. The results presented here upgrade the engineering possibilities of the genome of this environmental bacterium (and possibly other Gram-negatives) to obtain modifications that are otherwise cumbersome to generate.
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Affiliation(s)
- Tomás Aparicio
- T. Aparicio, V. de Lorenzo, E. Martínez-García, Systems Biology Program, National Center of Biotechnology CSIC, Madrid, 28049 Spain
| | - Víctor de Lorenzo
- T. Aparicio, V. de Lorenzo, E. Martínez-García, Systems Biology Program, National Center of Biotechnology CSIC, Madrid, 28049 Spain
| | - Esteban Martínez-García
- T. Aparicio, V. de Lorenzo, E. Martínez-García, Systems Biology Program, National Center of Biotechnology CSIC, Madrid, 28049 Spain
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127
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Calero P, Jensen SI, Bojanovič K, Lennen RM, Koza A, Nielsen AT. Genome-wide identification of tolerance mechanisms toward p-coumaric acid in Pseudomonas putida. Biotechnol Bioeng 2017; 115:762-774. [PMID: 29131301 PMCID: PMC5814926 DOI: 10.1002/bit.26495] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 10/16/2017] [Accepted: 11/08/2017] [Indexed: 01/12/2023]
Abstract
The soil bacterium Pseudomonas putida KT2440 has gained increasing biotechnological interest due to its ability to tolerate different types of stress. Here, the tolerance of P. putida KT2440 toward eleven toxic chemical compounds was investigated. P. putida was found to be significantly more tolerant toward three of the eleven compounds when compared to Escherichia coli. Increased tolerance was for example found toward p‐coumaric acid, an interesting precursor for polymerization with a significant industrial relevance. The tolerance mechanism was therefore investigated using the genome‐wide approach, Tn‐seq. Libraries containing a large number of miniTn5‐Km transposon insertion mutants were grown in the presence and absence of p‐coumaric acid, and the enrichment or depletion of mutants was quantified by high‐throughput sequencing. Several genes, including the ABC transporter Ttg2ABC and the cytochrome c maturation system (ccm), were identified to play an important role in the tolerance toward p‐coumaric acid of this bacterium. Most of the identified genes were involved in membrane stability, suggesting that tolerance toward p‐coumaric acid is related to transport and membrane integrity.
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Affiliation(s)
- Patricia Calero
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Sheila I Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Klara Bojanovič
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Rebecca M Lennen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Anna Koza
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Alex T Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
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128
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Mougiakos I, Mohanraju P, Bosma EF, Vrouwe V, Finger Bou M, Naduthodi MIS, Gussak A, Brinkman RBL, van Kranenburg R, van der Oost J. Characterizing a thermostable Cas9 for bacterial genome editing and silencing. Nat Commun 2017; 8:1647. [PMID: 29162801 PMCID: PMC5698299 DOI: 10.1038/s41467-017-01591-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/03/2017] [Indexed: 01/05/2023] Open
Abstract
CRISPR-Cas9-based genome engineering tools have revolutionized fundamental research and biotechnological exploitation of both eukaryotes and prokaryotes. However, the mesophilic nature of the established Cas9 systems does not allow for applications that require enhanced stability, including engineering at elevated temperatures. Here we identify and characterize ThermoCas9 from the thermophilic bacterium Geobacillus thermodenitrificans T12. We show that in vitro ThermoCas9 is active between 20 and 70 °C, has stringent PAM-preference at lower temperatures, tolerates fewer spacer-protospacer mismatches than SpCas9 and its activity at elevated temperatures depends on the sgRNA-structure. We develop ThermoCas9-based engineering tools for gene deletion and transcriptional silencing at 55 °C in Bacillus smithii and for gene deletion at 37 °C in Pseudomonas putida. Altogether, our findings provide fundamental insights into a thermophilic CRISPR-Cas family member and establish a Cas9-based bacterial genome editing and silencing tool with a broad temperature range.
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Affiliation(s)
- Ioannis Mougiakos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Elleke F Bosma
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet B220, 2800 Kgs, Lyngby, Denmark
| | - Valentijn Vrouwe
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Max Finger Bou
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Mihris I S Naduthodi
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Alex Gussak
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | | | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Corbion, Arkelsedijk 46, 4206 AC, Gorinchem, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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129
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Ricaurte DE, Martínez-García E, Nyerges Á, Pál C, de Lorenzo V, Aparicio T. A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities. Microb Biotechnol 2017; 11:176-188. [PMID: 29094478 PMCID: PMC5743808 DOI: 10.1111/1751-7915.12846] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/27/2017] [Accepted: 08/03/2017] [Indexed: 11/29/2022] Open
Abstract
Bacterial recombineering typically relies on genomic incorporation of synthetic oligonucleotides as mediated by Escherichia coli λ phage recombinase β - an occurrence largely limited to enterobacterial strains. While a handful of similar recombinases have been documented, recombineering efficiencies usually fall short of expectations for practical use. In this work, we aimed to find an efficient Recβ homologue demonstrating activity in model soil bacterium Pseudomonas putida EM42. To this end, a genus-wide protein survey was conducted to identify putative recombinase candidates for study. Selected novel proteins were assayed in a standardized test to reveal their ability to introduce the K43T substitution into the rpsL gene of P. putida. An ERF superfamily protein, here termed Rec2, exhibited activity eightfold greater than that of the previous leading recombinase. To bolster these results, we demonstrated Rec2 ability to enter a range of mutations into the pyrF gene of P. putida at similar frequencies. Our results not only confirm the utility of Rec2 as a Recβ functional analogue within the P. putida model system, but also set a complete workflow for deploying recombineering in other bacterial strains/species. Implications range from genome editing of P. putida for metabolic engineering to extended applications within other Pseudomonads - and beyond.
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Affiliation(s)
- Deirdre E Ricaurte
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain
| | - Esteban Martínez-García
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain
| | - Tomás Aparicio
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, 28049, Spain
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130
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Oliva-Arancibia B, Órdenes-Aenishanslins N, Bruna N, Ibarra PS, Zacconi FC, Pérez-Donoso JM, Poblete-Castro I. Co-synthesis of medium-chain-length polyhydroxyalkanoates and CdS quantum dots nanoparticles in Pseudomonas putida KT2440. J Biotechnol 2017; 264:29-37. [PMID: 29056529 DOI: 10.1016/j.jbiotec.2017.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 10/17/2017] [Accepted: 10/18/2017] [Indexed: 12/15/2022]
Abstract
Microbial polymers and nanomaterials production is a promising alternative for sustainable bioeconomics. To this end, we used Pseudomonas putida KT2440 as a cell factory in batch cultures to coproduce two important nanotechnology materials- medium-chain-length (MCL)-polyhydroxyalkanoates (PHAs) and CdS fluorescent nanoparticles (i.e. quantum dots [QDots]). Due to high cadmium resistance, biomass and PHA yields were almost unaffected by coproduction conditions. Fluorescent nanocrystal biosynthesis was possible only in presence of cysteine. Furthermore, this process took place exclusively in the cell, displaying the classical emission spectra of CdS QDots under UV-light exposure. Cell fluorescence, zeta potential values, and particles size of QDots depended on cadmium concentration and exposure time. Using standard PHA-extraction procedures, the biosynthesized QDots remained associated with the biomass, and the resulting PHAs presented no traces of CdS QDots. Transmission electron microscopy located the synthesized PHAs in the cell cytoplasm, whereas CdS nanocrystals were most likely located within the periplasmic space, exhibiting no apparent interaction. This is the first report presenting the microbial coproduction of MCL-PHAs and CdS QDots in P. putida KT2440, thus constituting a foundation for further bioprocess developments and strain engineering towards the efficient synthesis of these highly relevant bioproducts for nanotechnology.
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Affiliation(s)
- Barbara Oliva-Arancibia
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Nicolás Órdenes-Aenishanslins
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Nicolas Bruna
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Paula S Ibarra
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Flavia C Zacconi
- Departamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, 78204336 Santiago, Chile
| | - José M Pérez-Donoso
- BioNanotechnology and Microbiology Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, República 239, 8370146 Santiago, Chile.
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131
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Autotransporter-Based Surface Display of Hemicellulases onPseudomonas putida: Whole-Cell Biocatalysts for the Degradation of Biomass. ChemCatChem 2017. [DOI: 10.1002/cctc.201700577] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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132
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Wang Y, Li Y, Wang J, Wang X. FleQ regulates both the type VI secretion system and flagella inPseudomonas putida. Biotechnol Appl Biochem 2017; 65:419-427. [DOI: 10.1002/bab.1611] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/29/2017] [Accepted: 09/12/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Yuzhou Wang
- School of BiotechnologyJiangnan University Wuxi People's Republic of China
| | - Ye Li
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi People's Republic of China
| | - Jianli Wang
- School of BiotechnologyJiangnan University Wuxi People's Republic of China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi People's Republic of China
- School of BiotechnologyJiangnan University Wuxi People's Republic of China
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133
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Martínez-García E, de Lorenzo V. Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas. Curr Opin Biotechnol 2017; 47:120-132. [DOI: 10.1016/j.copbio.2017.06.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/19/2017] [Indexed: 11/26/2022]
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134
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Biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass. J Biotechnol 2017; 257:211-221. [DOI: 10.1016/j.jbiotec.2016.11.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 01/17/2023]
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135
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Mol M, Kabra R, Singh S. Genome modularity and synthetic biology: Engineering systems. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 132:43-51. [PMID: 28801037 DOI: 10.1016/j.pbiomolbio.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/05/2017] [Indexed: 12/15/2022]
Abstract
Whole genome sequencing projects running in various laboratories around the world has generated immense data. A systematic phylogenetic analysis of this data shows that genome complexity goes on decreasing as it evolves, due to its modular nature. This modularity can be harnessed to minimize the genome further to reduce it with the bare minimum essential genes. A reduced modular genome, can fuel progress in the area of synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health.
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Affiliation(s)
- Milsee Mol
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India
| | - Ritika Kabra
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India.
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136
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Sigida EN, Fedonenko YP, Shashkov AS, Zdorovenko EL, Ignatov VV, Knirel YA. Structural studies of the O-specific polysaccharide from detergent degrading bacteria Pseudomonas putida TSh-18. Carbohydr Res 2017; 448:1-5. [DOI: 10.1016/j.carres.2017.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 10/19/2022]
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137
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Borrero-de Acuña JM, Hidalgo-Dumont C, Pacheco N, Cabrera A, Poblete-Castro I. A novel programmable lysozyme-based lysis system in Pseudomonas putida for biopolymer production. Sci Rep 2017; 7:4373. [PMID: 28663596 PMCID: PMC5491512 DOI: 10.1038/s41598-017-04741-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/25/2017] [Indexed: 11/09/2022] Open
Abstract
Cell lysis is crucial for the microbial production of industrial fatty acids, proteins, biofuels, and biopolymers. In this work, we developed a novel programmable lysis system based on the heterologous expression of lysozyme. The inducible lytic system was tested in two Gram-negative bacterial strains, namely Escherichia coli and Pseudomonas putida KT2440. Before induction, the lytic system did not significantly arrest essential physiological parameters in the recombinant E. coli (ECPi) and P. putida (JBOi) strain such as specific growth rate and biomass yield under standard growth conditions. A different scenario was observed in the recombinant JBOi strain when subjected to PHA-producing conditions, where biomass production was reduced by 25% but the mcl-PHA content was maintained at about 30% of the cell dry weight. Importantly, the genetic construct worked well under PHA-producing conditions (nitrogen-limiting phase), where more than 95% of the cell population presented membrane disruption 16 h post induction, with 75% of the total synthesized biopolymer recovered at the end of the fermentation period. In conclusion, this new lysis system circumvents traditional, costly mechanical and enzymatic cell-disrupting procedures.
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Affiliation(s)
- José Manuel Borrero-de Acuña
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, Santiago, Chile.
| | - Cristian Hidalgo-Dumont
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicolás Pacheco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, Santiago, Chile
| | - Alex Cabrera
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, Santiago, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology (CBIB), Faculty of Biological Sciences, Universidad Andres Bello, Santiago, Chile.
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138
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Functional Role of Lanthanides in Enzymatic Activity and Transcriptional Regulation of Pyrroloquinoline Quinone-Dependent Alcohol Dehydrogenases in Pseudomonas putida KT2440. mBio 2017; 8:mBio.00570-17. [PMID: 28655819 PMCID: PMC5487730 DOI: 10.1128/mbio.00570-17] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The oxidation of alcohols and aldehydes is crucial for detoxification and efficient catabolism of various volatile organic compounds (VOCs). Thus, many Gram-negative bacteria have evolved periplasmic oxidation systems based on pyrroloquinoline quinone-dependent alcohol dehydrogenases (PQQ-ADHs) that are often functionally redundant. Here we report the first description and characterization of a lanthanide-dependent PQQ-ADH (PedH) in a nonmethylotrophic bacterium based on the use of purified enzymes from the soil-dwelling model organism Pseudomonas putida KT2440. PedH (PP_2679) exhibits enzyme activity on a range of substrates similar to that of its Ca2+-dependent counterpart PedE (PP_2674), including linear and aromatic primary and secondary alcohols, as well as aldehydes, but only in the presence of lanthanide ions, including La3+, Ce3+, Pr3+, Sm3+, or Nd3+ Reporter assays revealed that PedH not only has a catalytic function but is also involved in the transcriptional regulation of pedE and pedH, most likely acting as a sensory module. Notably, the underlying regulatory network is responsive to as little as 1 to 10 nM lanthanum, a concentration assumed to be of ecological relevance. The present study further demonstrates that the PQQ-dependent oxidation system is crucial for efficient growth with a variety of volatile alcohols. From these results, we conclude that functional redundancy and inverse regulation of PedE and PedH represent an adaptive strategy of P. putida KT2440 to optimize growth with volatile alcohols in response to the availability of different lanthanides.IMPORTANCE Because of their low bioavailability, lanthanides have long been considered biologically inert. In recent years, however, the identification of lanthanides as a cofactor in methylotrophic bacteria has attracted tremendous interest among various biological fields. The present study reveals that one of the two PQQ-ADHs produced by the model organism P. putida KT2440 also utilizes lanthanides as a cofactor, thus expanding the scope of lanthanide-employing bacteria beyond the methylotrophs. Similar to the system described in methylotrophic bacteria, a complex regulatory network is involved in lanthanide-responsive switching between the two PQQ-ADHs encoded by P. putida KT2440. We further show that the functional production of at least one of the enzymes is crucial for efficient growth with several volatile alcohols. Overall, our study provides a novel understanding of the redundancy of PQQ-ADHs observed in many organisms and further highlights the importance of lanthanides for bacterial metabolism, particularly in soil environments.
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139
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Wilkes RA, Aristilde L. Degradation and metabolism of synthetic plastics and associated products by Pseudomonas sp.: capabilities and challenges. J Appl Microbiol 2017; 123:582-593. [PMID: 28419654 DOI: 10.1111/jam.13472] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/17/2017] [Accepted: 04/10/2017] [Indexed: 11/27/2022]
Abstract
Synthetic plastics, which are widely present in materials of everyday use, are ubiquitous and slowly-degrading polymers in environmental wastes. Of special interest are the capabilities of microorganisms to accelerate their degradation. Members of the metabolically diverse genus Pseudomonas are of particular interest due to their capabilities to degrade and metabolize synthetic plastics. Pseudomonas species isolated from environmental matrices have been identified to degrade polyethylene, polypropylene, polyvinyl chloride, polystyrene, polyurethane, polyethylene terephthalate, polyethylene succinate, polyethylene glycol and polyvinyl alcohol at varying degrees of efficiency. Here, we present a review of the current knowledge on the factors that control the ability of Pseudomonas sp. to process these different plastic polymers and their by-products. These factors include cell surface attachment within biofilms, catalytic enzymes involved in oxidation or hydrolysis of the plastic polymer, metabolic pathways responsible for uptake and assimilation of plastic fragments and chemical factors that are advantageous or inhibitory to the biodegradation process. We also highlight future research directions required in order to harness fully the capabilities of Pseudomonas sp. in bioremediation strategies towards eliminating plastic wastes.
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Affiliation(s)
- R A Wilkes
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - L Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
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140
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Hintermayer SB, Weuster-Botz D. Experimental validation of in silico estimated biomass yields of Pseudomonas putida KT2440. Biotechnol J 2017; 12. [PMID: 28294579 DOI: 10.1002/biot.201600720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/12/2017] [Accepted: 03/13/2017] [Indexed: 11/09/2022]
Abstract
Pseudomonas putida is rapidly becoming a microbial cell platform for biotechnological applications. In order to understand genotype-phenotype relationships genome scale models represent helpful tools. However, the validation of in silico predictions of genome scale models is a task that is rarely performed. In this study the theoretical biomass yields of Pseudomonas putida KT2440 were estimated for 57 different carbon sources based on a genome scale stoichiometric model applying flux balance analysis. The batch growth of P. putida KT2440 with six individual carbon sources covering the range of maximal to minimal in silico biomass yields (acetate, glycerol, citrate, succinate, malate and methanol, respectively) was studied in a defined mineral medium in a fully controlled stirred-tank bioreactor on a 3 L scale. The highest growth rate of P. putida KT2440 was measured with succinate as carbon source (0.51 h-1 ). Among the 57 carbon sources tested, glycerol resulted in the highest estimated biomass yield (0.61 molCBiomass molC-1Glycerol ) which was experimentally confirmed. The comparison of experimental determined biomass yields with a modified version of the model iJP815 showed deviations of only up to 10%. The experimental data generated in this study can also be used in future studies to further improve the genome scale models of P. putida KT2440. Improved models will then help to gain deeper insights in genotype-phenotype relationships.
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Affiliation(s)
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technische Universität München, Garching, Germany
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141
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Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida. Appl Environ Microbiol 2017; 83:AEM.03236-16. [PMID: 28130298 DOI: 10.1128/aem.03236-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/19/2017] [Indexed: 12/24/2022] Open
Abstract
Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study, the transcriptional response of Pseudomonas putida KT2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mRNAs and small RNAs (sRNAs). A total of 440 sRNA transcripts were detected, of which 10% correspond to previously annotated sRNAs, 40% to novel intergenic transcripts, and 50% to novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed under at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a larger fraction of differentially expressed sRNAs than of mRNAs with >5-fold expression changes. The work provides detailed insights into the mechanisms through which P. putida responds to different stress conditions and increases understanding of bacterial adaptation in natural and industrial settings.IMPORTANCE This study maps the complete transcriptional response of P. putida KT2440 to osmotic, oxidative, and imipenem stress conditions at short and long exposure times. Over 400 sRNA transcripts, consisting of both intergenic and antisense transcripts, were detected, increasing the number of identified sRNA transcripts in the strain by a factor of 10. Unique responses to each type of stress are documented, including both the extent and dynamics of the gene expression changes. The work adds rich detail to previous knowledge of stress response mechanisms due to the depth of the RNA sequencing data. Almost half of the sRNAs exhibit significant expression changes under at least one condition, suggesting their involvement in adaptation to stress conditions and identifying interesting candidates for further functional characterization.
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142
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Ravi K, García-Hidalgo J, Gorwa-Grauslund MF, Lidén G. Conversion of lignin model compounds by Pseudomonas putida KT2440 and isolates from compost. Appl Microbiol Biotechnol 2017; 101:5059-5070. [PMID: 28299400 PMCID: PMC5486835 DOI: 10.1007/s00253-017-8211-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/21/2017] [Accepted: 02/26/2017] [Indexed: 11/29/2022]
Abstract
Starting from mature vegetable compost, four bacterial strains were selected using a lignin-rich medium. 16S ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. for three out of four isolates. Further characterization of growth on mixtures of six selected lignin model compounds (vanillin, vanillate, 4-hydroxybenzoate, p-coumarate, benzoate, and ferulate) was carried out with three of the Pseudomonas isolates and in addition with the strain Pseudomonas putida KT2440 from a culture collection. The specific growth rates on benzoate, p-coumarate, and 4-hydroxybenzoate were considerably higher (0.26–0.27 h−1) than those on ferulate and vanillate (0.21 and 0.22 h−1), as were the uptake rates. There was no direct growth of P. putida KT2440 on vanillin, but instead, vanillin was rapidly converted into vanillate at a rate of 4.87 mmol (gCDW h)−1 after which the accumulated vanillate was taken up. The growth curve reflected a diauxic growth when mixtures of the model compounds were used as carbon source. Vanillin, 4-hydroxybenzoate, and benzoate were preferentially consumed first, whereas ferulate was always the last substrate to be taken in. These results contribute to a better understanding of the aromatic metabolism of P. putida in terms of growth and uptake rates, which will be helpful for the utilization of these bacteria as cell factories for upgrading lignin-derived mixtures of aromatic molecules.
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Affiliation(s)
- Krithika Ravi
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
| | - Javier García-Hidalgo
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
| | - Marie F Gorwa-Grauslund
- Department of Chemistry, Applied Microbiology, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden
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143
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Fontaine P, Mosrati R, Corroler D. Medium chain length polyhydroxyalkanoates biosynthesis in Pseudomonas putida mt-2 is enhanced by co-metabolism of glycerol/octanoate or fatty acids mixtures. Int J Biol Macromol 2017; 98:430-435. [PMID: 28174083 DOI: 10.1016/j.ijbiomac.2017.01.115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
Abstract
The synthesis of medium chain length polyhydroxyalkanoates (mcl-PHAs) by Pseudomonas putida mt-2 was investigated under nitrogen-rich then deficient conditions with glycerol/octanoate or long-chain fatty acids (LCFAs) as carbon sources. When mixed, glycerol and octanoate were co-assimilated regardless of nitrogen availability but provided that glycerol uptake has been already triggered under non-limiting nutrient conditions. This concomitant consumption allowed to enhance mcl-PHAs accumulation (up to 57% of cell dry weight (CDW)) under both non-limiting and nitrogen deficient conditions. Octanoate then mostly drove anabolism of the polyester with 3-hydroxyoctanoate (3HO) synthesized as the main monomer (83%). If the preferred PHA precursor octanoate was supplied, glycerol was mainly involved in cell growth and/or maintenance but very little in PHA production even under nitrogen starvation. P. putida cells accumulated higher amounts of mcl-PHAs when grown on mixtures of LCFAs compared to LCFAs supplied as single substrate (25% and 9% of CDW, respectively). However, only a weak enrichment of the polyester was observed after transfer of cells in a fresh nitrogen-free medium containing the same combination of LCFAs. Some typical units within the polyester were related to the LCFAs ratio supplied in the medium indicating that tailor-made monomers could be synthesized.
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Affiliation(s)
- Paul Fontaine
- Normandie Univ., UNICAEN, UR ABTE, 14000 Caen, France
| | - Ridha Mosrati
- Normandie Univ., UNICAEN, UR ABTE, 14000 Caen, France
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144
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Affiliation(s)
- Fernando Rojo
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Campus UAM; Cantoblanco Madrid 28049 Spain
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145
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Oesterle S, Wuethrich I, Panke S. Toward Genome-Based Metabolic Engineering in Bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2017; 101:49-82. [PMID: 29050667 DOI: 10.1016/bs.aambs.2017.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Prokaryotes modified stably on the genome are of great importance for production of fine and commodity chemicals. Traditional methods for genome engineering have long suffered from imprecision and low efficiencies, making construction of suitable high-producer strains laborious. Here, we review the recent advances in discovery and refinement of molecular precision engineering tools for genome-based metabolic engineering in bacteria for chemical production, with focus on the λ-Red recombineering and the clustered regularly interspaced short palindromic repeats/Cas9 nuclease systems. In conjunction, they enable the integration of in vitro-synthesized DNA segments into specified locations on the chromosome and allow for enrichment of rare mutants by elimination of unmodified wild-type cells. Combination with concurrently developing improvements in important accessory technologies such as DNA synthesis, high-throughput screening methods, regulatory element design, and metabolic pathway optimization tools has resulted in novel efficient microbial producer strains and given access to new metabolic products. These new tools have made and will likely continue to make a big impact on the bioengineering strategies that transform the chemical industry.
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146
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Construction of pDUO: A bicistronic shuttle vector series for dual expression of recombinant proteins. Plasmid 2017; 89:16-21. [DOI: 10.1016/j.plasmid.2016.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/08/2016] [Accepted: 12/12/2016] [Indexed: 02/06/2023]
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147
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Biological valorization of low molecular weight lignin. Biotechnol Adv 2016; 34:1318-1346. [DOI: 10.1016/j.biotechadv.2016.10.001] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/06/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022]
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148
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Hernández-Arranz S, Sánchez-Hevia D, Rojo F, Moreno R. Effect of Crc and Hfq proteins on the transcription, processing, and stability of the Pseudomonas putida CrcZ sRNA. RNA (NEW YORK, N.Y.) 2016; 22:1902-1917. [PMID: 27777366 PMCID: PMC5113210 DOI: 10.1261/rna.058313.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/02/2016] [Indexed: 05/23/2023]
Abstract
In Pseudomonas putida, the Hfq and Crc proteins regulate the expression of many genes in response to nutritional and environmental cues, by binding to mRNAs that bear specific target motifs and inhibiting their translation. The effect of these two proteins is antagonized by the CrcZ and CrcY small RNAs (sRNAs), the levels of which vary greatly according to growth conditions. The crcZ and crcY genes are transcribed from promoters PcrcZ and PcrcY, respectively, a process that relies on the CbrB transcriptional activator and the RpoN σ factor. Here we show that crcZ can also be transcribed from the promoter of the immediate upstream gene, cbrB, a weak constitutive promoter. The cbrB-crcZ transcript was processed to render a sRNA very similar in size to the CrcZ produced from promoter PcrcZ The processed sRNA, termed CrcZ*, was able to antagonize Hfq/Crc because, when provided in trans, it relieved the deregulated Hfq/Crc-dependent hyperrepressing phenotype of a ΔcrcZΔcrcY strain. CrcZ* may help in attaining basal levels of CrcZ/CrcZ* that are sufficient to protect the cell from an excessive Hfq/Crc-dependent repression. Since a functional sRNA can be produced from PcrcZ, an inducible strong promoter, or by cleavage of the cbrB-crcZ mRNA, crcZ can be considered a 3'-untranslated region of the cbrB-crcZ mRNA. In the absence of Hfq, the processed form of CrcZ was not observed. In addition, we show that Crc and Hfq increase CrcZ stability, which supports the idea that these proteins can form a complex with CrcZ and protect it from degradation by RNases.
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Affiliation(s)
- Sofía Hernández-Arranz
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Dione Sánchez-Hevia
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, 28049 Madrid, Spain
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149
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Martínez-García E, de Lorenzo V. The quest for the minimal bacterial genome. Curr Opin Biotechnol 2016; 42:216-224. [DOI: 10.1016/j.copbio.2016.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 01/09/2023]
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150
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Yu S, Plan MR, Winter G, Krömer JO. Metabolic Engineering of Pseudomonas putida KT2440 for the Production of para-Hydroxy Benzoic Acid. Front Bioeng Biotechnol 2016; 4:90. [PMID: 27965953 PMCID: PMC5124731 DOI: 10.3389/fbioe.2016.00090] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/10/2016] [Indexed: 11/13/2022] Open
Abstract
para-Hydroxy benzoic acid (PHBA) is the key component for preparing parabens, a common preservatives in food, drugs, and personal care products, as well as high-performance bioplastics such as liquid crystal polymers. Pseudomonas putida KT2440 was engineered to produce PHBA from glucose via the shikimate pathway intermediate chorismate. To obtain the PHBA production strain, chorismate lyase UbiC from Escherichia coli and a feedback resistant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase encoded by gene aroGD146N were overexpressed individually and simultaneously. In addition, genes related to product degradation (pobA) or competing for the precursor chorismate (pheA and trpE) were deleted from the genome. To further improve PHBA production, the glucose metabolism repressor hexR was knocked out in order to increase erythrose 4-phosphate and NADPH supply. The best strain achieved a maximum titer of 1.73 g L−1 and a carbon yield of 18.1% (C-mol C-mol−1) in a non-optimized fed-batch fermentation. This is to date the highest PHBA concentration produced by P. putida using a chorismate lyase.
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Affiliation(s)
- Shiqin Yu
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia
| | - Manuel R Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia; Metabolomics Australia (Queensland Node), The University of Queensland, Brisbane, QLD, Australia
| | - Gal Winter
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia; School of Science and Technology, The University of New England, Armidale, NSW, Australia
| | - Jens O Krömer
- Centre for Microbial Electrochemical Systems (CEMES), The University of Queensland, Brisbane, QLD, Australia; Advanced Water Management Centre (AWMC), The University of Queensland, Brisbane, QLD, Australia
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