1
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Sanchez-Londono M, Rust S, Hernández-Tamayo R, Gomes-Filho JV, Thanbichler M, Randau L. Visualization of Type IV-A1 CRISPR-mediated repression of gene expression and plasmid replication. Nucleic Acids Res 2024:gkae879. [PMID: 39380487 DOI: 10.1093/nar/gkae879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/20/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024] Open
Abstract
Type IV CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) effector complexes are often encoded on plasmids and are proposed to prevent the replication of competing plasmids. The Type IV-A1 CRISPR-Cas system of Pseudomonas oleovorans additionally harbors a CRISPR RNA (crRNA) that tightly regulates the transcript levels of a chromosomal target and represents a natural CRISPR interference (CRISPRi) tool. This study investigates CRISPRi effects of this system using synthetic crRNAs against genome and plasmid sequences. Targeting of reporter genes revealed extended interference in P. oleovorans and Escherichia coli cells producing recombinant CRISPR ribonucleoprotein (crRNP) complexes. RNA sequencing (RNA-seq) analyses of Type IV-A1 CRISPRi-induced transcriptome alterations demonstrated highly effective long-range downregulation of histidine operon expression, whereas CRISPRi effects of dCas9 remained limited to the vicinity of its binding site. Single-molecule microscopy uncovered the localization dynamics of crRNP complexes. The tracks of fluorescently labeled crRNPs co-localized with regions of increased plasmid replication, supporting efficient plasmid targeting. These results identify mechanistic principles that facilitate the application of Type IV-A1 CRISPRi for the regulation of gene expression and plasmid replication.
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Affiliation(s)
- Mariana Sanchez-Londono
- Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Selina Rust
- Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Rogelio Hernández-Tamayo
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Straße 14, 35043 Marburg, Germany
| | - José Vicente Gomes-Filho
- Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Martin Thanbichler
- Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Straße 14, 35043 Marburg, Germany
| | - Lennart Randau
- Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Straße 14, 35043 Marburg, Germany
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2
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Hernández-Sancho JM, Boudigou A, Alván-Vargas MVG, Freund D, Arnling Bååth J, Westh P, Jensen K, Noda-García L, Volke DC, Nikel PI. A versatile microbial platform as a tunable whole-cell chemical sensor. Nat Commun 2024; 15:8316. [PMID: 39333077 PMCID: PMC11436707 DOI: 10.1038/s41467-024-52755-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Biosensors are used to detect and quantify chemicals produced in industrial microbiology with high specificity, sensitivity, and portability. Most biosensors, however, are limited by the need for transcription factors engineered to recognize specific molecules. In this study, we overcome the limitations typically associated with traditional biosensors by engineering Pseudomonas putida for whole-cell sensing of a variety of chemicals. Our approach integrates fluorescent reporters with synthetic auxotrophies within central metabolism that can be complemented by target analytes in growth-coupled setups. This platform enables the detection of a wide array of structurally diverse chemicals under various conditions, including co-cultures of producer cell factories and sensor strains. We also demonstrate the applicability of this versatile biosensor platform for monitoring complex biochemical processes, including plastic degradation by either purified hydrolytic enzymes or engineered bacteria. This microbial system provides a rapid, sensitive, and readily adaptable tool for monitoring cell factory performance and for environmental analyzes.
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Affiliation(s)
- Javier M Hernández-Sancho
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Arnaud Boudigou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maria V G Alván-Vargas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dekel Freund
- Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Jenny Arnling Bååth
- Department of Biotechnology and Biomedicine Interfacial Enzymology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine Interfacial Enzymology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Lianet Noda-García
- Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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3
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Asin-Garcia E, Martin-Pascual M, de Buck C, Allewijn M, Müller A, Martins dos Santos VAP. GenoMine: a CRISPR-Cas9-based kill switch for biocontainment of Pseudomonas putida. Front Bioeng Biotechnol 2024; 12:1426107. [PMID: 39351062 PMCID: PMC11439788 DOI: 10.3389/fbioe.2024.1426107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/15/2024] [Indexed: 10/04/2024] Open
Abstract
Synthetic genetic circuits have revolutionised our capacity to control cell viability by conferring microorganisms with programmable functionalities to limit survival to specific environmental conditions. Here, we present the GenoMine safeguard, a CRISPR-Cas9-based kill switch for the biotechnological workhorse Pseudomonas putida that employs repetitive genomic elements as cleavage targets to unleash a highly genotoxic response. To regulate the system's activation, we tested various circuit-based mechanisms including the digitalised version of an inducible expression system that operates at the transcriptional level and different options of post-transcriptional riboregulators. All of them were applied not only to directly control Cas9 and its lethal effects, but also to modulate the expression of two of its inhibitors: the AcrIIA4 anti-CRISPR protein and the transcriptional repressor TetR. Either upon direct induction of the endonuclease or under non-induced conditions of its inhibitors, the presence of Cas9 suppressed cell survival which could be exploited beyond biocontainment in situations where further CRISPR genome editing is undesirable.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
- Bioprocess Engineering Group, Wageningen University & Research, Wageningen, Netherlands
| | - Maria Martin-Pascual
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Claudia de Buck
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Max Allewijn
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Alexandra Müller
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
- Bioprocess Engineering Group, Wageningen University & Research, Wageningen, Netherlands
- LifeGlimmer GmbH, Berlin, Germany
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4
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Weimer A, Pause L, Ries F, Kohlstedt M, Adrian L, Krömer J, Lai B, Wittmann C. Systems biology of electrogenic Pseudomonas putida - multi-omics insights and metabolic engineering for enhanced 2-ketogluconate production. Microb Cell Fact 2024; 23:246. [PMID: 39261865 PMCID: PMC11389600 DOI: 10.1186/s12934-024-02509-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/10/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Pseudomonas putida KT2440 has emerged as a promising host for industrial bioproduction. However, its strictly aerobic nature limits the scope of applications. Remarkably, this microbe exhibits high bioconversion efficiency when cultured in an anoxic bio-electrochemical system (BES), where the anode serves as the terminal electron acceptor instead of oxygen. This environment facilitates the synthesis of commercially attractive chemicals, including 2-ketogluconate (2KG). To better understand this interesting electrogenic phenotype, we studied the BES-cultured strain on a systems level through multi-omics analysis. Inspired by our findings, we constructed novel mutants aimed at improving 2KG production. RESULTS When incubated on glucose, P. putida KT2440 did not grow but produced significant amounts of 2KG, along with minor amounts of gluconate, acetate, pyruvate, succinate, and lactate. 13C tracer studies demonstrated that these products are partially derived from biomass carbon, involving proteins and lipids. Over time, the cells exhibited global changes on both the transcriptomic and proteomic levels, including the shutdown of translation and cell motility, likely to conserve energy. These adaptations enabled the cells to maintain significant metabolic activity for several weeks. Acetate formation was shown to contribute to energy supply. Mutants deficient in acetate production demonstrated superior 2KG production in terms of titer, yield, and productivity. The ∆aldBI ∆aldBII double deletion mutant performed best, accumulating 2KG at twice the rate of the wild type and with an increased yield (0.96 mol/mol). CONCLUSIONS By integrating transcriptomic, proteomic, and metabolomic analyses, this work provides the first systems biology insight into the electrogenic phenotype of P. putida KT2440. Adaptation to anoxic-electrogenic conditions involved coordinated changes in energy metabolism, enabling cells to sustain metabolic activity for extended periods. The metabolically engineered mutants are promising for enhanced 2KG production under these conditions. The attenuation of acetate synthesis represents the first systems biology-informed metabolic engineering strategy for enhanced 2KG production in P. putida. This non-growth anoxic-electrogenic mode expands our understanding of the interplay between growth, glucose phosphorylation, and glucose oxidation into gluconate and 2KG in P. putida.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Laura Pause
- Systems Biotechnology Group, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Fabian Ries
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lorenz Adrian
- Department of Molecular Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jens Krömer
- Systems Biotechnology Group, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Bin Lai
- BMBF Junior Research Group Biophotovoltaics, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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5
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Chi SI, Akuma M, Xu R, Plante V, Hadinezhad M, Tambong JT. Phenazines are involved in the antagonism of a novel subspecies of Pseudomonas chlororaphis strain S1Bt23 against Pythium ultimum. Sci Rep 2024; 14:20517. [PMID: 39227476 PMCID: PMC11372166 DOI: 10.1038/s41598-024-71418-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 08/27/2024] [Indexed: 09/05/2024] Open
Abstract
Long-term use of chemical fungicides to control plant diseases caused by fungi and oomycetes has led to pathogen resistance and negative impacts on public health and environment. There is a global search for eco-friendly methods and antagonistic bacteria are emerging as alternatives. We isolated a potent antagonistic bacterial strain (S1Bt23) from woodland soil in Québec, Canada. Taxonomic characterization by 16S rRNA, multi-locus sequence analysis, pairwise whole-genome comparisons, phylogenomics and phenotypic data identified strain S1Bt23 as a novel subspecies within Pseudomonas chlororaphis. In dual culture studies, strain S1Bt23 exhibited potent mycelial growth inhibition (60.2-66.7%) against Pythium ultimum. Furthermore, strain S1Bt23 was able to significantly bioprotect potato tuber slices from the development of necrosis inducible by P. ultimum. Annotations of the whole genome sequence of S1Bt23 revealed the presence of an arsenal of secondary metabolites including the complete phenazine biosynthetic cluster (phzABCDEFG). Thin-layer (TLC) and high-performance liquid (HPLC) chromatographic analyses of S1Bt23 extracts confirmed the production of phenazines, potent antifungal compounds. CRISPR/Cas9-mediated deletion of phzB (S1Bt23ΔphzB) or phzF (S1Bt23ΔphzF) gene abrogated phenazine production based on TLC and HPLC analyses. Also, S1Bt23ΔphzB and S1Bt23ΔphzF mutants lost antagonistic activity and bioprotection ability of potato tubers against P. ultimum. This demonstrated that phenazines are involved in the antagonistic activity of S1Bt23 against P. ultimum. Finally, based on genotypic and phenotypic data, we taxonomically conclude that S1Bt23 represents a novel subspecies for which the name Pseudomonas chlororaphis subsp. phenazini is proposed.
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Affiliation(s)
- Sylvia I Chi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
- Canadian Blood Service, Ottawa, ON, K1G 4J5, Canada
| | - Mercy Akuma
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
- University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Véronique Plante
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Mehri Hadinezhad
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada.
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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6
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Meng H, Köbbing S, Blank LM. Establishing a straightforward I-SceI-mediated recombination one-plasmid system for efficient genome editing in P. putida KT2440. Microb Biotechnol 2024; 17:e14531. [PMID: 39031514 PMCID: PMC11258999 DOI: 10.1111/1751-7915.14531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/04/2024] [Indexed: 07/22/2024] Open
Abstract
Pseudomonas putida has become an increasingly important chassis for producing valuable bioproducts. This development is not least due to the ever-improving genetic toolbox, including gene and genome editing techniques. Here, we present a novel, one-plasmid design of a critical genetic tool, the pEMG/pSW system, guaranteeing one engineering cycle to be finalized in 3 days. The pEMG/pSW system proved in the last decade to be valuable for targeted genome engineering in Pseudomonas, as it enables the deletion of large regions of the genome, the integration of heterologous gene clusters or the targeted generation of point mutations. Here, to expedite genetic engineering, two alternative plasmids were constructed: (1) The sacB gene from Bacillus subtilis was integrated into the I-SceI expressing plasmid pSW-2 as a counterselection marker to accelerated plasmid curing; (2) double-strand break introducing gene I-sceI and sacB counterselection marker were integrated into the backbone of the original pEMG vector, named pEMG-RIS. The single plasmid of pEMG-RIS allows rapid genome editing despite the low transcriptional activity of a single copy of the I-SceI encoding gene. Here, the usability of the pEMG-RIS is shown in P. putida KT2440 by integrating an expression cassette including an msfGFP gene in 3 days. In addition, a large fragment of 12.1 kb was also integrated. In summary, we present an updated pEMG/pSW genome editing system that allows efficient and rapid genome editing in P. putida. All plasmids designed in this study will be available via the Addgene platform.
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Affiliation(s)
- Hao Meng
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Sebastian Köbbing
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Lars M. Blank
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
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7
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Körner D, Schäfer NM, Lagares Jr. A, Birmes L, Oehlmann NN, Addison H, Pöhl S, Thanbichler M, Rebelein JG, Petersen J, Becker A. Modular Low-Copy-Number Plasmid Vectors for Rhodobacterales with Extended Host Range in Alphaproteobacteria. ACS Synth Biol 2024; 13:1537-1548. [PMID: 38718218 PMCID: PMC11107812 DOI: 10.1021/acssynbio.4c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
Members of the alphaproteobacterial order Rhodobacterales are metabolically diverse and highly abundant in the ocean. They are becoming increasingly interesting for marine biotechnology, due to their ecological adaptability, wealth of versatile low-copy-number plasmids, and their ability to produce secondary metabolites. However, molecular tools for engineering strains of this bacterial lineage are limited. Here, we expand the genetic toolbox by establishing standardized, modular repABC-based plasmid vectors of four well-characterized compatibility groups from the Roseobacter group applicable in the Rhodobacterales, and likely in further alphaproteobacterial orders (Hyphomicrobiales, Rhodospirillales, Caulobacterales). We confirmed replication of these newly constructed pABC vectors in two members of Rhodobacterales, namely, Dinoroseobacter shibae DFL 12 and Rhodobacter capsulatus B10S, as well as in two members of the alphaproteobacterial order Hyphomicrobiales (synonym: Rhizobiales; Ensifer meliloti 2011 and "Agrobacterium fabrum" C58). Maintenance of the pABC vectors in the biotechnologically valuable orders Rhodobacterales and Hyphomicrobiales facilitates the shuttling of genetic constructs between alphaproteobacterial genera and orders. Additionally, plasmid replication was verified in one member of Rhodospirillales (Rhodospirillum rubrum S1) as well as in one member of Caulobacterales (Caulobacter vibrioides CB15N). The modular construction of pABC vectors and the usage of four compatible replication systems, which allows their coexistence in a host cell, are advantageous features for future implementations of newly designed synthetic pathways. The vector applicability was demonstrated by functional complementation of a nitrogenase mutant phenotype by two complementary pABC-based plasmids in R. capsulatus.
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Affiliation(s)
- Désirée Körner
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Niklas M. Schäfer
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Antonio Lagares Jr.
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Lukas Birmes
- Leibniz-Institut
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig 38124, Germany
| | - Niels N. Oehlmann
- Max
Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Holly Addison
- Max
Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Sebastian Pöhl
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Martin Thanbichler
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
- Max
Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Johannes G. Rebelein
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
- Max
Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Jörn Petersen
- Leibniz-Institut
DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig 38124, Germany
| | - Anke Becker
- Center
for Synthetic Microbiology (SYNMIKRO) and Department of Biology, Philipps-Universität Marburg, Marburg 35043, Germany
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8
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García-Romero I, de Dios R, Reyes-Ramírez F. An improved genome editing system for Sphingomonadaceae. Access Microbiol 2024; 6:000755.v3. [PMID: 38868378 PMCID: PMC11165598 DOI: 10.1099/acmi.0.000755.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/05/2024] [Indexed: 06/14/2024] Open
Abstract
The sphingomonads encompass a diverse group of bacteria within the family Sphingomonadaceae, with the presence of sphingolipids on their cell surface instead of lipopolysaccharide as their main common feature. They are particularly interesting for bioremediation purposes due to their ability to degrade or metabolise a variety of recalcitrant organic pollutants. However, research and development on their full bioremediation potential has been hampered because of the limited number of tools available to investigate and modify their genome. Here, we present a markerless genome editing method for Sphingopyxis granuli TFA, which can be further optimised for other sphingomonads. This procedure is based on a double recombination triggered by a DNA double-strand break in the chromosome. The strength of this protocol lies in forcing the second recombination rather than favouring it by pressing a counterselection marker, thus avoiding laborious restreaking or passaging screenings. Additionally, we introduce a modification with respect to the original protocol to increase the efficiency of the screening after the first recombination event. We show this procedure step by step and compare our modified method with respect to the original one by deleting ecfG2, the master regulator of the general stress response in S. granuli TFA. This adds to the genetic tool repertoire that can be applied to sphingomonads and stands as an efficient option for fast genome editing of this bacterial group.
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Affiliation(s)
- Inmaculada García-Romero
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, 41013 Sevilla, Spain
| | - Rubén de Dios
- Division of Biosciences, Department of Life Sciences, Centre of Inflammation Research and Translational Medicine, College of Health, Medicine and Life Sciences,, Brunel University London, Uxbridge, UK
| | - Francisca Reyes-Ramírez
- Departamento de Biología Molecular e Ingeniería Bioquímica, Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, 41013 Sevilla, Spain
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9
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Nieto-Domínguez M, Sako A, Enemark-Rasmussen K, Gotfredsen CH, Rago D, Nikel PI. Enzymatic synthesis of mono- and trifluorinated alanine enantiomers expands the scope of fluorine biocatalysis. Commun Chem 2024; 7:104. [PMID: 38724655 PMCID: PMC11082193 DOI: 10.1038/s42004-024-01188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
Fluorinated amino acids serve as an entry point for establishing new-to-Nature chemistries in biological systems, and novel methods are needed for the selective synthesis of these building blocks. In this study, we focused on the enzymatic synthesis of fluorinated alanine enantiomers to expand fluorine biocatalysis. The alanine dehydrogenase from Vibrio proteolyticus and the diaminopimelate dehydrogenase from Symbiobacterium thermophilum were selected for in vitro production of (R)-3-fluoroalanine and (S)-3-fluoroalanine, respectively, using 3-fluoropyruvate as the substrate. Additionally, we discovered that an alanine racemase from Streptomyces lavendulae, originally selected for setting an alternative enzymatic cascade leading to the production of these non-canonical amino acids, had an unprecedented catalytic efficiency in β-elimination of fluorine from the monosubstituted fluoroalanine. The in vitro enzymatic cascade based on the dehydrogenases of V. proteolyticus and S. thermophilum included a cofactor recycling system, whereby a formate dehydrogenase from Pseudomonas sp. 101 (either native or engineered) coupled formate oxidation to NAD(P)H formation. Under these conditions, the reaction yields for (R)-3-fluoroalanine and (S)-3-fluoroalanine reached >85% on the fluorinated substrate and proceeded with complete enantiomeric excess. The selected dehydrogenases also catalyzed the conversion of trifluoropyruvate into trifluorinated alanine as a first-case example of fluorine biocatalysis with amino acids carrying a trifluoromethyl group.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aboubakar Sako
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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10
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Lu C, Wijffels RH, Martins dos Santos VAP, Weusthuis RA. Pseudomonas putida as a platform for medium-chain length α,ω-diol production: Opportunities and challenges. Microb Biotechnol 2024; 17:e14423. [PMID: 38528784 PMCID: PMC10963910 DOI: 10.1111/1751-7915.14423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 03/27/2024] Open
Abstract
Medium-chain-length α,ω-diols (mcl-diols) play an important role in polymer production, traditionally depending on energy-intensive chemical processes. Microbial cell factories offer an alternative, but conventional strains like Escherichia coli and Saccharomyces cerevisiae face challenges in mcl-diol production due to the toxicity of intermediates such as alcohols and acids. Metabolic engineering and synthetic biology enable the engineering of non-model strains for such purposes with P. putida emerging as a promising microbial platform. This study reviews the advancement in diol production using P. putida and proposes a four-module approach for the sustainable production of diols. Despite progress, challenges persist, and this study discusses current obstacles and future opportunities for leveraging P. putida as a microbial cell factory for mcl-diol production. Furthermore, this study highlights the potential of using P. putida as an efficient chassis for diol synthesis.
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Affiliation(s)
- Chunzhe Lu
- Bioprocess EngineeringWageningen University & ResearchWageningenThe Netherlands
- Groningen Biomolecular Sciences & Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Rene H. Wijffels
- Bioprocess EngineeringWageningen University & ResearchWageningenThe Netherlands
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | | | - Ruud A. Weusthuis
- Bioprocess EngineeringWageningen University & ResearchWageningenThe Netherlands
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11
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Chhun A, Moriano-Gutierrez S, Zoppi F, Cabirol A, Engel P, Schaerli Y. An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment. PLoS Biol 2024; 22:e3002523. [PMID: 38442124 PMCID: PMC10914260 DOI: 10.1371/journal.pbio.3002523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/26/2024] [Indexed: 03/07/2024] Open
Abstract
The honey bee is a powerful model system to probe host-gut microbiota interactions, and an important pollinator species for natural ecosystems and for agriculture. While bacterial biosensors can provide critical insight into the complex interplay occurring between a host and its associated microbiota, the lack of methods to noninvasively sample the gut content, and the limited genetic tools to engineer symbionts, have so far hindered their development in honey bees. Here, we built a versatile molecular tool kit to genetically modify symbionts and reported for the first time in the honey bee a technique to sample their feces. We reprogrammed the native bee gut bacterium Snodgrassella alvi as a biosensor for IPTG, with engineered cells that stably colonize the gut of honey bees and report exposure to the molecules in a dose-dependent manner through the expression of a fluorescent protein. We showed that fluorescence readout can be measured in the gut tissues or noninvasively in the feces. These tools and techniques will enable rapid building of engineered bacteria to answer fundamental questions in host-gut microbiota research.
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Affiliation(s)
- Audam Chhun
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Florian Zoppi
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Amélie Cabirol
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Yolanda Schaerli
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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12
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Kozaeva E, Nielsen ZS, Nieto-Domínguez M, Nikel P. The pAblo·pCasso self-curing vector toolset for unconstrained cytidine and adenine base-editing in Gram-negative bacteria. Nucleic Acids Res 2024; 52:e19. [PMID: 38180826 PMCID: PMC10899774 DOI: 10.1093/nar/gkad1236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 12/11/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024] Open
Abstract
A synthetic biology toolkit, exploiting clustered regularly interspaced short palindromic repeats (CRISPR) and modified CRISPR-associated protein (Cas) base-editors, was developed for genome engineering in Gram-negative bacteria. Both a cytidine base-editor (CBE) and an adenine base-editor (ABE) have been optimized for precise single-nucleotide modification of plasmid and genome targets. CBE comprises a cytidine deaminase conjugated to a Cas9 nickase from Streptococcus pyogenes (SpnCas9), resulting in C→T (or G→A) substitutions. Conversely, ABE consists of an adenine deaminase fused to SpnCas9 for A→G (or T→C) editing. Several nucleotide substitutions were achieved using these plasmid-borne base-editing systems and a novel protospacer adjacent motif (PAM)-relaxed SpnCas9 (SpRY) variant. Base-editing was validated in Pseudomonas putida and other Gram-negative bacteria by inserting premature STOP codons into target genes, thereby inactivating both fluorescent proteins and metabolic (antibiotic-resistance) functions. The functional knockouts obtained by engineering STOP codons via CBE were reverted to the wild-type genotype using ABE. Additionally, a series of induction-responsive vectors was developed to facilitate the curing of the base-editing platform in a single cultivation step, simplifying complex strain engineering programs without relying on homologous recombination and yielding plasmid-free, modified bacterial cells.
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Affiliation(s)
- Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Zacharias S Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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13
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Zhou L, Höfte M, Hennessy RC. Does regulation hold the key to optimizing lipopeptide production in Pseudomonas for biotechnology? Front Bioeng Biotechnol 2024; 12:1363183. [PMID: 38476965 PMCID: PMC10928948 DOI: 10.3389/fbioe.2024.1363183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Lipopeptides (LPs) produced by Pseudomonas spp. are specialized metabolites with diverse structures and functions, including powerful biosurfactant and antimicrobial properties. Despite their enormous potential in environmental and industrial biotechnology, low yield and high production cost limit their practical use. While genome mining and functional genomics have identified a multitude of LP biosynthetic gene clusters, the regulatory mechanisms underlying their biosynthesis remain poorly understood. We propose that regulation holds the key to unlocking LP production in Pseudomonas for biotechnology. In this review, we summarize the structure and function of Pseudomonas-derived LPs and describe the molecular basis for their biosynthesis and regulation. We examine the global and specific regulator-driven mechanisms controlling LP synthesis including the influence of environmental signals. Understanding LP regulation is key to modulating production of these valuable compounds, both quantitatively and qualitatively, for industrial and environmental biotechnology.
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Affiliation(s)
- Lu Zhou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Rosanna C. Hennessy
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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14
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Ferreira MR, Queiroga V, Moreira LM. Genomic editing in Burkholderia multivorans by CRISPR/Cas9. Appl Environ Microbiol 2024; 90:e0225023. [PMID: 38299816 PMCID: PMC10880607 DOI: 10.1128/aem.02250-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
Burkholderia cepacia complex bacteria have emerged as opportunistic pathogens in patients with cystic fibrosis and immunocompromised individuals, causing life-threatening infections. Because of the relevance of these microorganisms, genetic manipulation is crucial for explaining the genetic mechanisms leading to pathogenesis. Despite the availability of allelic exchange tools to obtain unmarked gene deletions in Burkholderia, these require a step of merodiploid formation and another of merodiploid resolution through two independent homologous recombination events, making the procedure long-lasting. The CRISPR/Cas9-based system could ease this constraint, as only one step is needed for allelic exchange. Here, we report the modification of a two-plasmid system (pCasPA and pACRISPR) for genome editing in Burkholderia multivorans. Several modifications were implemented, including selection marker replacement, the optimization of araB promoter induction for the expression of Cas9 and λ-Red system encoding genes, and the establishment of plasmid curing procedures based on the sacB gene or growth at a sub-optimal temperature of 18°C-20°C with serial passages. We have shown the efficiency of this CRISPR/Cas9 method in the precise and unmarked deletion of different genes (rpfR, bceF, cepR, and bcsB) from two strains of B. multivorans, as well as its usefulness in the targeted insertion of the gfp gene encoding the green fluorescence protein into a precise genome location. As pCasPA was successfully introduced in other Burkholderia cepacia complex species, this study opens up the possibility of using CRISPR/Cas9-based systems as efficient tools for genome editing in these species, allowing faster and more cost-effective genetic manipulation.IMPORTANCEBurkholderia encompasses different species of bacteria, some of them pathogenic to animals and plants, but others are beneficial by promoting plant growth through symbiosis or as biocontrol agents. Among these species, Burkholderia multivorans, a member of the Burkholderia cepacia complex, is one of the predominant species infecting the lungs of cystic fibrosis patients, often causing respiratory chronic infections that are very difficult to eradicate. Since the B. multivorans species is understudied, we have developed a genetic tool based on the CRISPR/Cas9 system to delete genes efficiently from the genomes of these strains. We could also insert foreign genes that can be precisely placed in a chosen genomic region. This method, faster than other conventional strategies based on allelic exchange, will have a major contribution to understanding the virulence mechanisms in B. multivorans, but it can likely be extended to other Burkholderia species.
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Affiliation(s)
- Mirela R. Ferreira
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Vasco Queiroga
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Leonilde M. Moreira
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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15
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Lammens EM, Volke DC, Schroven K, Voet M, Kerremans A, Lavigne R, Hendrix H. A SEVA-based, CRISPR-Cas3-assisted genome engineering approach for Pseudomonas with efficient vector curing. Microbiol Spectr 2023; 11:e0270723. [PMID: 37975669 PMCID: PMC10715078 DOI: 10.1128/spectrum.02707-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The CRISPR-Cas3 editing system as presented here facilitates the creation of genomic alterations in Pseudomonas putida and Pseudomonas aeruginosa in a straightforward manner. By providing the Cas3 system as a vector set with Golden Gate compatibility and different antibiotic markers, as well as by employing the established Standard European Vector Architecture (SEVA) vector set to provide the homology repair template, this system is flexible and can readily be ported to a multitude of Gram-negative hosts. Besides genome editing, the Cas3 system can also be used as an effective and universal tool for vector curing. This is achieved by introducing a spacer that targets the origin-of-transfer, present on the majority of established (SEVA) vectors. Based on this, the Cas3 system efficiently removes up to three vectors in only a few days. As such, this curing approach may also benefit other genomic engineering methods or remove naturally occurring plasmids from bacteria.
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Affiliation(s)
| | - Daniel Christophe Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Kaat Schroven
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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16
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Pankratz D, Gomez NO, Nielsen A, Mustafayeva A, Gür M, Arce-Rodriguez F, Nikel PI, Häussler S, Arce-Rodriguez A. An expanded CRISPR-Cas9-assisted recombineering toolkit for engineering genetically intractable Pseudomonas aeruginosa isolates. Nat Protoc 2023; 18:3253-3288. [PMID: 37798358 DOI: 10.1038/s41596-023-00882-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/28/2023] [Indexed: 10/07/2023]
Abstract
Much of our current understanding of microbiology is based on the application of genetic engineering procedures. Since their inception (more than 30 years ago), methods based largely on allelic exchange and two-step selection processes have become a cornerstone of contemporary bacterial genetics. While these tools are established for adapted laboratory strains, they have limited applicability in clinical or environmental isolates displaying a large and unknown genetic repertoire that are recalcitrant to genetic modifications. Hence, new tools allowing genetic engineering of intractable bacteria must be developed to gain a comprehensive understanding of them in the context of their biological niche. Herein, we present a method for precise, efficient and rapid engineering of the opportunistic pathogen Pseudomonas aeruginosa. This procedure relies on recombination of short single-stranded DNA facilitated by targeted double-strand DNA breaks mediated by a synthetic Cas9 coupled with the efficient Ssr recombinase. Possible applications include introducing single-nucleotide polymorphisms, short or long deletions, and short DNA insertions using synthetic single-stranded DNA templates, drastically reducing the need of PCR and cloning steps. Our toolkit is encoded on two plasmids, harboring an array of different antibiotic resistance cassettes; hence, this approach can be successfully applied to isolates displaying natural antibiotic resistances. Overall, this toolkit substantially reduces the time required to introduce a range of genetic manipulations to a minimum of five experimental days, and enables a variety of research and biotechnological applications in both laboratory strains and difficult-to-manipulate P. aeruginosa isolates.
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Affiliation(s)
- Debbie Pankratz
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Nicolas Oswaldo Gomez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agnes Nielsen
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ayten Mustafayeva
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melisa Gür
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Fabián Arce-Rodriguez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| | - Alejandro Arce-Rodriguez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.
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17
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Wirth NT, Rohr K, Danchin A, Nikel PI. Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440. mBio 2023; 14:e0108123. [PMID: 37732760 PMCID: PMC10653934 DOI: 10.1128/mbio.01081-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Investigating fundamental aspects of metabolism is vital for advancing our understanding of the diverse biochemical capabilities and biotechnological applications of bacteria. The origin of the essential thymidylate kinase function in the model bacterium Pseudomonas putida KT2440, seemingly interrupted due to the presence of a large genomic island that disrupts the cognate gene, eluded a satisfactory explanation thus far. This is a first-case example of an essential metabolic function, likely acquired by horizontal gene transfer, which "landed" in a locus encoding the same activity. As such, foreign DNA encoding an essential dNMPK could immediately adjust to the recipient host-instead of long-term accommodation and adaptation. Understanding how these functions evolve is a major biological question, and the work presented here is a decisive step toward this direction. Furthermore, identifying essential and accessory genes facilitates removing those deemed irrelevant in industrial settings-yielding genome-reduced cell factories with enhanced properties and genetic stability.
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Affiliation(s)
- Nicolas T. Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - Katja Rohr
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - Antoine Danchin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
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18
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van Schaik J, Li Z, Cheadle J, Crook N. Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant-Microbe Interactions. ACS Synth Biol 2023; 12:3030-3040. [PMID: 37712562 DOI: 10.1021/acssynbio.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Sustainably enhancing crop production is a global necessity to meet the escalating demand for staple crops while sustainably managing their associated carbon/nitrogen inputs. Leveraging plant-associated microbiomes is a promising avenue for addressing this demand. However, studying these communities and engineering them for sustainable enhancement of crop production have remained a challenge due to limited genetic tools and methods. In this work, we detail the development of the Maize Root Microbiome ToolKit (MRMTK), a rapid Modular Cloning (MoClo) toolkit that only takes 2.5 h to generate desired constructs (5400 potential plasmids) that replicate and express heterologous genes in Enterobacter ludwigii strain AA4 (Elu), Pseudomonas putida strain AA7 (Ppu), Herbaspirillum robiniae strain AA6 (Hro), Stenotrophomonas maltophilia strain AA1 (Sma), and Brucella pituitosa strain AA2 (Bpi), which comprise a model maize root synthetic community (SynCom). In addition to these genetic tools, we describe a highly efficient transformation protocol (107-109 transformants/μg of DNA) 1 for each of these strains. Utilizing this highly efficient transformation protocol, we identified endogenous Expression Sequences (ES; promoter and ribosomal binding sites) for each strain via genomic promoter trapping. Overall, MRMTK is a scalable and adaptable platform that expands the genetic engineering toolbox while providing a standardized, high-efficiency transformation method across a diverse group of root commensals. These results unlock the ability to elucidate and engineer plant-microbe interactions promoting plant growth for each of the 5 bacterial strains in this study.
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Affiliation(s)
- John van Schaik
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - John Cheadle
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
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19
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Volke DC, Orsi E, Nikel PI. Emergent CRISPR-Cas-based technologies for engineering non-model bacteria. Curr Opin Microbiol 2023; 75:102353. [PMID: 37413959 DOI: 10.1016/j.mib.2023.102353] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) technologies brought a transformative change in the way bacterial genomes are edited, and a plethora of studies contributed to developing multiple tools based on these approaches. Prokaryotic biotechnology benefited from the implementation of such genome engineering strategies, with an increasing number of non-model bacterial species becoming genetically tractable. In this review, we summarize the recent trends in engineering non-model microbes using CRISPR-Cas technologies, discussing their potential in supporting cell factory design towards biotechnological applications. These efforts include, among other examples, genome modifications as well as tunable transcriptional regulation (both positive and negative). Moreover, we examine how CRISPR-Cas toolkits for engineering non-model organisms enabled the exploitation of emergent biotechnological processes (e.g. native and synthetic assimilation of one-carbon substrates). Finally, we discuss our slant on the future of bacterial genome engineering for domesticating non-model organisms in light of the most recent advances in the ever-expanding CRISPR-Cas field.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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20
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Volke DC, Gurdo N, Milanesi R, Nikel PI. Time-resolved, deuterium-based fluxomics uncovers the hierarchy and dynamics of sugar processing by Pseudomonas putida. Metab Eng 2023; 79:159-172. [PMID: 37454792 DOI: 10.1016/j.ymben.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Pseudomonas putida, a microbial host widely adopted for metabolic engineering, processes glucose through convergent peripheral pathways that ultimately yield 6-phosphogluconate. The periplasmic gluconate shunt (PGS), composed by glucose and gluconate dehydrogenases, sequentially transforms glucose into gluconate and 2-ketogluconate. Although the secretion of these organic acids by P. putida has been extensively recognized, the mechanism and spatiotemporal regulation of the PGS remained elusive thus far. To address this challenge, we adopted a dynamic 13C- and 2H-metabolic flux analysis strategy, termed D-fluxomics. D-fluxomics demonstrated that the PGS underscores a highly dynamic metabolic architecture in glucose-dependent batch cultures of P. putida, characterized by hierarchical carbon uptake by the PGS throughout the cultivation. Additionally, we show that gluconate and 2-ketogluconate accumulation and consumption can be solely explained as a result of the interplay between growth rate-coupled and decoupled metabolic fluxes. As a consequence, the formation of these acids in the PGS is inversely correlated to the bacterial growth rate-unlike the widely studied overflow metabolism of Escherichia coli and yeast. Our findings, which underline survival strategies of soil bacteria thriving in their natural environments, open new avenues for engineering P. putida towards efficient, sugar-based bioprocesses.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - Nicolas Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Riccardo Milanesi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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21
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Zheng W, Xia Y, Wang X, Gao S, Zhou D, Ravichandran V, Jiang C, Tu Q, Yin Y, Zhang Y, Fu J, Li R, Yin J. Precise genome engineering in Pseudomonas using phage-encoded homologous recombination and the Cascade-Cas3 system. Nat Protoc 2023; 18:2642-2670. [PMID: 37626246 DOI: 10.1038/s41596-023-00856-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 05/11/2023] [Indexed: 08/27/2023]
Abstract
A lack of generic and effective genetic manipulation methods for Pseudomonas has restricted fundamental research and utilization of this genus for biotechnology applications. Phage-encoded homologous recombination (PEHR) is an efficient tool for bacterial genome engineering. This PEHR system is based on a lambda Red-like operon (BAS) from Pseudomonas aeruginosa phage Ab31 and a Rac bacteriophage RecET-like operon (Rec-TEPsy) from P. syringae pv. syringae B728a and also contains exogenous elements, including the RecBCD inhibitor (Redγ or Pluγ) or single-stranded DNA-binding protein (SSB), that were added to enhance the PEHR recombineering efficiency. To solve the problem of false positives in Pseudomonas editing with the PEHR system, the processive enzyme Cas3 with a minimal Type I-C Cascade-based system was combined with PEHR. This protocol describes the utilization of a Pseudomonas-specific PEHR-Cas3 system that was designed to universally and proficiently modify the genomes of Pseudomonas species. The pipeline uses standardized cassettes combined with the concerted use of SacB counterselection and Cre site-specific recombinase for markerless or seamless genome modification, in association with vectors that possess the selectively replicating template R6K to minimize recombineering background. Compared with the traditional allelic exchange editing method, the PEHR-Cas3 system does not need to construct suicide plasmids carrying long homologous arms, thus simplifying the experimental procedure and shortening the traceless editing period. Compared with general editing systems based on phage recombinases, the PEHR-Cas3 system can effectively improve the screening efficiency of mutants using the cutting ability of Cas3 protein. The entire procedure requires ~12 days.
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Affiliation(s)
- Wentao Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yandong Xia
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
- College of Life Science and Technology, Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-wood Forest Cultivation and Conservation of Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Xue Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shiqing Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Diao Zhou
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | | | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qiang Tu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yulong Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Ruijuan Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China.
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22
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Gurdo N, Volke DC, McCloskey D, Nikel PI. Automating the design-build-test-learn cycle towards next-generation bacterial cell factories. N Biotechnol 2023; 74:1-15. [PMID: 36736693 DOI: 10.1016/j.nbt.2023.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023]
Abstract
Automation is playing an increasingly significant role in synthetic biology. Groundbreaking technologies, developed over the past 20 years, have enormously accelerated the construction of efficient microbial cell factories. Integrating state-of-the-art tools (e.g. for genome engineering and analytical techniques) into the design-build-test-learn cycle (DBTLc) will shift the metabolic engineering paradigm from an almost artisanal labor towards a fully automated workflow. Here, we provide a perspective on how a fully automated DBTLc could be harnessed to construct the next-generation bacterial cell factories in a fast, high-throughput fashion. Innovative toolsets and approaches that pushed the boundaries in each segment of the cycle are reviewed to this end. We also present the most recent efforts on automation of the DBTLc, which heralds a fully autonomous pipeline for synthetic biology in the near future.
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Affiliation(s)
- Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Douglas McCloskey
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark.
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23
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Schwanemann T, Otto M, Wynands B, Marienhagen J, Wierckx N. A Pseudomonas taiwanensis malonyl-CoA platform strain for polyketide synthesis. Metab Eng 2023; 77:219-230. [PMID: 37031949 DOI: 10.1016/j.ymben.2023.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 04/11/2023]
Abstract
Malonyl-CoA is a central precursor for biosynthesis of a wide range of complex secondary metabolites. The development of platform strains with increased malonyl-CoA supply can contribute to the efficient production of secondary metabolites, especially if such strains exhibit high tolerance towards these chemicals. In this study, Pseudomonas taiwanensis VLB120 was engineered for increased malonyl-CoA availability to produce bacterial and plant-derived polyketides. A multi-target metabolic engineering strategy focusing on decreasing the malonyl-CoA drain and increasing malonyl-CoA precursor availability, led to an increased production of various malonyl-CoA-derived products, including pinosylvin, resveratrol and flaviolin. The production of flaviolin, a molecule deriving from five malonyl-CoA molecules, was doubled compared to the parental strain by this malonyl-CoA increasing strategy. Additionally, the engineered platform strain enabled production of up to 84 mg L-1 resveratrol from supplemented p-coumarate. One key finding of this study was that acetyl-CoA carboxylase overexpression majorly contributed to an increased malonyl-CoA availability for polyketide production in dependence on the used strain-background and whether downstream fatty acid synthesis was impaired, reflecting its complexity in metabolism. Hence, malonyl-CoA availability is primarily determined by competition of the production pathway with downstream fatty acid synthesis, while supply reactions are of secondary importance for compounds that derive directly from malonyl-CoA in Pseudomonas.
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Affiliation(s)
- Tobias Schwanemann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Maike Otto
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany; Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, D-52074, Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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24
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Schada von Borzyskowski L, Schulz-Mirbach H, Troncoso Castellanos M, Severi F, Gómez-Coronado PA, Paczia N, Glatter T, Bar-Even A, Lindner SN, Erb TJ. Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol. Metab Eng 2023; 76:97-109. [PMID: 36731627 DOI: 10.1016/j.ymben.2023.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023]
Abstract
Ethylene glycol (EG) is a promising next generation feedstock for bioprocesses. It is a key component of the ubiquitous plastic polyethylene terephthalate (PET) and other polyester fibers and plastics, used in antifreeze formulations, and can also be generated by electrochemical conversion of syngas, which makes EG a key compound in a circular bioeconomy. The majority of biotechnologically relevant bacteria assimilate EG via the glycerate pathway, a wasteful metabolic route that releases CO2 and requires reducing equivalents as well as ATP. In contrast, the recently characterized β-hydroxyaspartate cycle (BHAC) provides a more efficient, carbon-conserving route for C2 assimilation. Here we aimed at overcoming the natural limitations of EG metabolism in the industrially relevant strain Pseudomonas putida KT2440 by replacing the native glycerate pathway with the BHAC. We first prototyped the core reaction sequence of the BHAC in Escherichia coli before establishing the complete four-enzyme BHAC in Pseudomonas putida. Directed evolution on EG resulted in an improved strain that exhibits 35% faster growth and 20% increased biomass yield compared to a recently reported P. putida strain that was evolved to grow on EG via the glycerate pathway. Genome sequencing and proteomics highlight plastic adaptations of the genetic and metabolic networks in response to the introduction of the BHAC into P. putida and identify key mutations for its further integration during evolution. Taken together, our study shows that the BHAC can be utilized as 'plug-and-play' module for the metabolic engineering of two important microbial platform organisms, paving the way for multiple applications for a more efficient and carbon-conserving upcycling of EG in the future.
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Affiliation(s)
- Lennart Schada von Borzyskowski
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
| | - Helena Schulz-Mirbach
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Mauricio Troncoso Castellanos
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Francesca Severi
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Paul A Gómez-Coronado
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Nicole Paczia
- Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Biochemistry, Charité Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Tobias J Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany.
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25
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Bruinsma L, Wenk S, Claassens NJ, Martins Dos Santos VAP. Paving the way for synthetic C1 - Metabolism in Pseudomonas putida through the reductive glycine pathway. Metab Eng 2023; 76:215-224. [PMID: 36804222 DOI: 10.1016/j.ymben.2023.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
One-carbon (C1) compounds such as methanol, formate, and CO2 are alternative, sustainable microbial feedstocks for the biobased production of chemicals and fuels. In this study, we engineered the carbon metabolism of the industrially important bacterium Pseudomonas putida to modularly assimilate these three substrates through the reductive glycine pathway. First, we demonstrated the functionality of the C1-assimilation module by coupling the growth of auxotrophic strains to formate assimilation. Next, we extended the module in the auxotrophic strains from formate to methanol-dependent growth using both NAD and PQQ-dependent methanol dehydrogenases. Finally, we demonstrated, for the first time, engineered CO2-dependent formation of part of the biomass through CO2 reduction to formate by the native formate dehydrogenase, which required short-term evolution to rebalance the cellular NADH/NAD + ratio. This research paves the way to further engineer P. putida towards full growth on formate, methanol, and CO2 as sole feedstocks, thereby substantially expanding its potential as a sustainable and versatile cell factory.
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Affiliation(s)
- Lyon Bruinsma
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708, WE, the Netherlands
| | - Sebastian Wenk
- Systems and Synthetic Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, 6708, WE, the Netherlands.
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708, WE, the Netherlands; LifeGlimmer GmbH, Berlin, 12163, Germany; Bioprocess Engineering, Wageningen University & Research, Wageningen, 6708, WE, the Netherlands.
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26
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Lee HJ, Kim HJ, Lee SJ. Miniature CRISPR-Cas12f1-Mediated Single-Nucleotide Microbial Genome Editing Using 3'-Truncated sgRNA. CRISPR J 2023; 6:52-61. [PMID: 36576897 PMCID: PMC9942177 DOI: 10.1089/crispr.2022.0071] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The CRISPR-Cas system has been used as a convenient tool for genome editing because the nuclease that cuts the target DNA and the guide RNA that recognizes the target are separated into modules. Cas12f1, which has a smaller size than that of other Cas nucleases, is easily loaded into vectors and is emerging as a new genome editing tool. In this study, AsCas12f1 was used to negatively select only Escherichia coli cells obtained by oligonucleotide-directed genome editing. Although double-, triple-, and quadruple-base substitutions were accurately and efficiently performed in the genome, the performance of single-base editing was poor. To resolve this limitation, we serially truncated the 3'-end of sgRNAs and determined the maximal truncation required to maintain the target DNA cleavage activity of Cas12f1. Negative selection of single-nucleotide-edited cells was efficiently performed with the maximally 3'-truncated sgRNA-Cas12f1 complex in vivo. Moreover, Sanger sequencing showed that the accuracy of single-nucleotide substitution, insertion, and deletion in the microbial genome was improved. These results demonstrated that a truncated sgRNA approach could be widely used for accurate CRISPR-mediated genome editing.
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Affiliation(s)
- Ho Joung Lee
- Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong, Republic of Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong, Republic of Korea.,Address correspondence to: Sang Jun Lee, Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea.
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27
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Bruinsma L, Martin-Pascual M, Kurnia K, Tack M, Hendriks S, van Kranenburg R, dos Santos VAPM. Increasing cellular fitness and product yields in Pseudomonas putida through an engineered phosphoketolase shunt. Microb Cell Fact 2023; 22:14. [PMID: 36658566 PMCID: PMC9850600 DOI: 10.1186/s12934-022-02015-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/31/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Pseudomonas putida has received increasing interest as a cell factory due to its remarkable features such as fast growth, a versatile and robust metabolism, an extensive genetic toolbox and its high tolerance to oxidative stress and toxic compounds. This interest is driven by the need to improve microbial performance to a level that enables biologically possible processes to become economically feasible, thereby fostering the transition from an oil-based economy to a more sustainable bio-based one. To this end, one of the current strategies is to maximize the product-substrate yield of an aerobic biocatalyst such as P. putida during growth on glycolytic carbon sources, such as glycerol and xylose. We demonstrate that this can be achieved by implementing the phosphoketolase shunt, through which pyruvate decarboxylation is prevented, and thus carbon loss is minimized. RESULTS In this study, we introduced the phosphoketolase shunt in the metabolism of P. putida KT2440. To maximize the effect of this pathway, we first tested and selected a phosphoketolase (Xfpk) enzyme with high activity in P. putida. Results of the enzymatic assays revealed that the most efficient Xfpk was the one isolated from Bifidobacterium breve. Using this enzyme, we improved the P. putida growth rate on glycerol and xylose by 44 and 167%, respectively, as well as the biomass yield quantified by OD600 by 50 and 30%, respectively. Finally, we demonstrated the impact on product formation and achieved a 38.5% increase in mevalonate and a 25.9% increase in flaviolin yield from glycerol. A similar effect was observed on the mevalonate-xylose and flaviolin-xylose yields, which increased by 48.7 and 49.4%, respectively. CONCLUSIONS Pseudomonas putida with the implemented Xfpk shunt grew faster, reached a higher final OD600nm and provided better product-substrate yields than the wild type. By reducing the pyruvate decarboxylation flux, we significantly improved the performance of this important workhorse for industrial applications. This work encompasses the first steps towards full implementation of the non-oxidative glycolysis (NOG) or the glycolysis alternative high carbon yield cycle (GATCHYC), in which a substrate is converted into products without CO2 loss These enhanced properties of P. putida will be crucial for its subsequent use in a range of industrial processes.
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Affiliation(s)
- Lyon Bruinsma
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Maria Martin-Pascual
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Kesi Kurnia
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands ,grid.502801.e0000 0001 2314 6254Present Address: Faculty of Engineering and Natural Sciences, Tampere University, 33100 Tampere, Finland
| | - Marieken Tack
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Simon Hendriks
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Richard van Kranenburg
- grid.425710.50000 0004 4907 2152Corbion, 4206 AC Gorinchem, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - Vitor A. P. Martins dos Santos
- grid.4818.50000 0001 0791 5666Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Laboratory Bioprocess Engineering, Wageningen University & Research, 6708 WE Wageningen, The Netherlands ,grid.435730.6LifeGlimmer GmbH, 12163 Berlin, Germany
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28
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Martínez-García E, Fraile S, Algar E, Aparicio T, Velázquez E, Calles B, Tas H, Blázquez B, Martín B, Prieto C, Sánchez-Sampedro L, Nørholm MH, Volke D, Wirth N, Dvořák P, Alejaldre L, Grozinger L, Crowther M, Goñi-Moreno A, Nikel P, Nogales J, de Lorenzo V. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Res 2023; 51:D1558-D1567. [PMID: 36420904 PMCID: PMC9825617 DOI: 10.1093/nar/gkac1059] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/27/2022] Open
Abstract
The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.
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Affiliation(s)
- Esteban Martínez-García
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Sofía Fraile
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Elena Algar
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Tomás Aparicio
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Elena Velázquez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Huseyin Tas
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Blas Blázquez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | | | | | | | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pavel Dvořák
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500 Czech Republic
| | - Lorea Alejaldre
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
| | - Lewis Grozinger
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
- School of Computing, Newcastle University, NE4 5TG, UK
| | - Matthew Crowther
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
- School of Computing, Newcastle University, NE4 5TG, UK
| | - Angel Goñi-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Juan Nogales
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
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29
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Borgert SR, Henke S, Witzgall F, Schmelz S, Zur Lage S, Hotop SK, Stephen S, Lübken D, Krüger J, Gomez NO, van Ham M, Jänsch L, Kalesse M, Pich A, Brönstrup M, Häussler S, Blankenfeldt W. Moonlighting chaperone activity of the enzyme PqsE contributes to RhlR-controlled virulence of Pseudomonas aeruginosa. Nat Commun 2022; 13:7402. [PMID: 36456567 PMCID: PMC9715718 DOI: 10.1038/s41467-022-35030-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Pseudomonas aeruginosa is a major cause of nosocomial infections and also leads to severe exacerbations in cystic fibrosis or chronic obstructive pulmonary disease. Three intertwined quorum sensing systems control virulence of P. aeruginosa, with the rhl circuit playing the leading role in late and chronic infections. The majority of traits controlled by rhl transcription factor RhlR depend on PqsE, a dispensable thioesterase in Pseudomonas Quinolone Signal (PQS) biosynthesis that interferes with RhlR through an enigmatic mechanism likely involving direct interaction of both proteins. Here we show that PqsE and RhlR form a 2:2 protein complex that, together with RhlR agonist N-butanoyl-L-homoserine lactone (C4-HSL), solubilizes RhlR and thereby renders the otherwise insoluble transcription factor active. We determine crystal structures of the complex and identify residues essential for the interaction. To corroborate the chaperone-like activity of PqsE, we design stability-optimized variants of RhlR that bypass the need for C4-HSL and PqsE in activating PqsE/RhlR-controlled processes of P. aeruginosa. Together, our data provide insight into the unique regulatory role of PqsE and lay groundwork for developing new P. aeruginosa-specific pharmaceuticals.
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Affiliation(s)
- Sebastian Roman Borgert
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Steffi Henke
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Florian Witzgall
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Stefan Schmelz
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Susanne Zur Lage
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Sven-Kevin Hotop
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Steffi Stephen
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Dennis Lübken
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Jonas Krüger
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Nicolas Oswaldo Gomez
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Marco van Ham
- Cellular Proteomics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Markus Kalesse
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Andreas Pich
- Institute for Toxicology, Core Facility Proteomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Mark Brönstrup
- Department Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Susanne Häussler
- Department Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany.
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany.
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30
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Calero P, Gurdo N, Nikel PI. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ Microbiol 2022; 24:5082-5104. [PMID: 35726888 PMCID: PMC9796867 DOI: 10.1111/1462-2920.16110] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
Abstract
The presence of mineral fluoride (F- ) in the environment has both a geogenic and anthropogenic origin, and the halide has been described to be toxic in virtually all living organisms. While the evidence gathered in different microbial species supports this notion, a systematic exploration of the effects of F- salts on the metabolism and physiology of environmental bacteria remained underexplored thus far. In this work, we studied and characterized tolerance mechanisms deployed by the model soil bacterium Pseudomonas putida KT2440 against NaF. By adopting systems-level omic approaches, including functional genomics and metabolomics, we gauged the impact of this anion at different regulatory levels under conditions that impair bacterial growth. Several genes involved in halide tolerance were isolated in a genome-wide Tn-Seq screening-among which crcB, encoding an F- -specific exporter, was shown to play the predominant role in detoxification. High-resolution metabolomics, combined with the assessment of intracellular and extracellular pH values and quantitative physiology experiments, underscored the key nodes in central carbon metabolism affected by the presence of F- . Taken together, our results indicate that P. putida undergoes a general, multi-level stress response when challenged with NaF that significantly differs from that caused by other saline stressors. While microbial stress responses to saline and oxidative challenges have been extensively studied and described in the literature, very little is known about the impact of fluoride (F- ) on bacterial physiology and metabolism. This state of affairs contrasts with the fact that F- is more abundant than other halides in the Earth crust (e.g. in some soils, the F- concentration can reach up to 1 mg gsoil -1 ). Understanding the global effects of NaF treatment on bacterial physiology is not only relevant to unveil distinct mechanisms of detoxification but it could also guide microbial engineering approaches for the target incorporation of fluorine into value-added organofluorine molecules. In this regard, the soil bacterium P. putida constitutes an ideal model to explore such scenarios, since this species is particularly known for its high level of stress resistance against a variety of physicochemical perturbations.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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Integrated rational and evolutionary engineering of genome-reduced Pseudomonas putida strains promotes synthetic formate assimilation. Metab Eng 2022; 74:191-205. [DOI: 10.1016/j.ymben.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/05/2022] [Accepted: 10/23/2022] [Indexed: 11/07/2022]
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de Dios R, Gadar K, McCarthy RR. A high-efficiency scar-free genome-editing toolkit for Acinetobacter baumannii. J Antimicrob Chemother 2022; 77:3390-3398. [PMID: 36216579 PMCID: PMC9704439 DOI: 10.1093/jac/dkac328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 09/05/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The current mutagenesis tools for Acinetobacter baumannii leave selection markers or residual sequences behind, or involve tedious counterselection and screening steps. Furthermore, they are usually adapted for model strains, rather than for MDR clinical isolates. OBJECTIVES To develop a scar-free genome-editing tool suitable for chromosomal and plasmid modifications in MDR A. baumannii AB5075. METHODS We prove the efficiency of our adapted genome-editing system by deleting the multidrug efflux pumps craA, cmlA5 and resistance island 2 (RI2), as well as curing plasmid p1AB5075, and combining these mutations. We then characterized the susceptibility of the mutants compared with the WT to different antibiotics (i.e. chloramphenicol, amikacin and tobramycin) by disc diffusion assays and determined the MIC for each strain. RESULTS We successfully adapted the genome-editing protocol to A. baumannii AB5075, achieving a double recombination frequency close to 100% and routinely securing the construction of a mutant within 10 working days. Furthermore, we show that both CraA and p1AB5075 are involved in chloramphenicol resistance, and that RI2 and p1AB5075 play a role in resistance to amikacin and tobramycin. CONCLUSIONS We have developed a versatile and highly efficient genome-editing tool for A. baumannii. We have demonstrated it can be used to modify both the chromosome and native plasmids. By challenging the method, we show the role of CraA and p1AB5075 in antibiotic resistance.
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Affiliation(s)
- Rubén de Dios
- Division of Biosciences, Department of Life Sciences, Centre of Inflammation Research and Translational Medicine, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Kavita Gadar
- Division of Biosciences, Department of Life Sciences, Centre of Inflammation Research and Translational Medicine, College of Health and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
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Characterization of the self-targeting Type IV CRISPR interference system in Pseudomonas oleovorans. Nat Microbiol 2022; 7:1870-1878. [PMID: 36175516 DOI: 10.1038/s41564-022-01229-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/04/2022] [Indexed: 11/08/2022]
Abstract
Bacterial Type IV CRISPR-Cas systems are thought to rely on multi-subunit ribonucleoprotein complexes to interfere with mobile genetic elements, but the substrate requirements and potential DNA nuclease activities for many systems within this type are uncharacterized. Here we show that the native Pseudomonas oleovorans Type IV-A CRISPR-Cas system targets DNA in a PAM-dependent manner and elicits interference without showing DNA nuclease activity. We found that the first crRNA of P. oleovorans contains a perfect match in the host gene coding for the Type IV pilus biogenesis protein PilN. Deletion of the native Type IV CRISPR array resulted in upregulation of pilN operon transcription in the absence of genome cleavage, indicating that Type IV-A CRISPR-Cas systems can function in host gene regulation. These systems resemble CRISPR interference (CRISPRi) methodology but represent a natural CRISPRi-like system that is found in many Pseudomonas and Klebsiella species and allows for gene silencing using engineered crRNAs.
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Wirth NT, Gurdo N, Krink N, Vidal-Verdú À, Donati S, Férnandez-Cabezón L, Wulff T, Nikel PI. A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes. Metab Eng 2022; 74:83-97. [PMID: 36155822 DOI: 10.1016/j.ymben.2022.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/17/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022]
Abstract
Acetyl-coenzyme A (AcCoA) is a metabolic hub in virtually all living cells, serving as both a key precursor of essential biomass components and a metabolic sink for catabolic pathways for a large variety of substrates. Owing to this dual role, tight growth-production coupling schemes can be implemented around the AcCoA node. Building on this concept, a synthetic C2 auxotrophy was implemented in the platform bacterium Pseudomonas putida through an in silico-informed engineering approach. A growth-coupling strategy, driven by AcCoA demand, allowed for direct selection of an alternative sugar assimilation route-the phosphoketolase (PKT) shunt from bifidobacteria. Adaptive laboratory evolution forced the synthetic P. putida auxotroph to rewire its metabolic network to restore C2 prototrophy via the PKT shunt. Large-scale structural chromosome rearrangements were identified as possible mechanisms for adjusting the network-wide proteome profile, resulting in improved PKT-dependent growth phenotypes. 13C-based metabolic flux analysis revealed an even split between the native Entner-Doudoroff pathway and the synthetic PKT bypass for glucose processing, leading to enhanced carbon conservation. These results demonstrate that the P. putida metabolism can be radically rewired to incorporate a synthetic C2 metabolism, creating novel network connectivities and highlighting the importance of unconventional engineering strategies to support efficient microbial production.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Nicolas Krink
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Àngela Vidal-Verdú
- Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980, Paterna, Spain
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Lorena Férnandez-Cabezón
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220 2800, Kongens Lyngby, Denmark.
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35
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LeBlanc N, Charles TC. Bacterial genome reductions: Tools, applications, and challenges. Front Genome Ed 2022; 4:957289. [PMID: 36120530 PMCID: PMC9473318 DOI: 10.3389/fgeed.2022.957289] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.
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Affiliation(s)
- Nicole LeBlanc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Nicole LeBlanc,
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
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36
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De Wannemaeker L, Bervoets I, De Mey M. Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv 2022; 60:108028. [PMID: 36031082 DOI: 10.1016/j.biotechadv.2022.108028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/02/2022]
Abstract
Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.
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Affiliation(s)
- Lien De Wannemaeker
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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37
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Asin-Garcia E, Batianis C, Li Y, Fawcett JD, de Jong I, Dos Santos VAPM. Phosphite synthetic auxotrophy as an effective biocontainment strategy for the industrial chassis Pseudomonas putida. Microb Cell Fact 2022; 21:156. [PMID: 35934698 PMCID: PMC9358898 DOI: 10.1186/s12934-022-01883-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/26/2022] [Indexed: 11/12/2022] Open
Abstract
The inclusion of biosafety strategies into strain engineering pipelines is crucial for safe-by-design biobased processes. This in turn might enable a more rapid regulatory acceptance of bioengineered organisms in both industrial and environmental applications. For this reason, we equipped the industrially relevant microbial chassis Pseudomonas putida KT2440 with an effective biocontainment strategy based on a synthetic dependency on phosphite, which is generally not readily available in the environment. The produced PSAG-9 strain was first engineered to assimilate phosphite through the genome-integration of a phosphite dehydrogenase and a phosphite-specific transport complex. Subsequently, to deter the strain from growing on naturally assimilated phosphate, all native genes related to its transport were identified and deleted generating a strain unable to grow on media containing any phosphorous source other than phosphite. PSAG-9 exhibited fitness levels with phosphite similar to those of the wild type with phosphate, and low levels of escape frequency. Beyond biosafety, this strategy endowed P. putida with the capacity to be cultured under non-sterile conditions using phosphite as the sole phosphorous source with a reduced risk of contamination by other microbes, while displaying enhanced NADH regenerative capacity. These industrially beneficial features complement the metabolic advantages for which this species is known for, thereby strengthening it as a synthetic biology chassis with potential uses in industry, with suitability towards environmental release.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - Yunsong Li
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - James D Fawcett
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, SW72BX, UK
| | - Ivar de Jong
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands.
- LifeGlimmer GmbH, 12163, Berlin, Germany.
- Bioprocess Engineering Group, Wageningen University & Research, Wageningen, 6700 AA, The Netherlands.
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38
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Fernández-Cabezón L, Rosich I Bosch B, Kozaeva E, Gurdo N, Nikel PI. Dynamic flux regulation for high-titer anthranilate production by plasmid-free, conditionally-auxotrophic strains of Pseudomonas putida. Metab Eng 2022; 73:11-25. [PMID: 35659519 DOI: 10.1016/j.ymben.2022.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/05/2022] [Accepted: 05/29/2022] [Indexed: 10/18/2022]
Abstract
Anthranilate, an intermediate of the shikimate pathway, is a high-value aromatic compound widely used as a precursor in the production of dyes, fragrances, plastics and pharmaceuticals. Traditional strategies adopted for microbial anthranilate production rely on the implementation of auxotrophic strains-which requires aromatic amino acids or complex additives to be supplemented in the culture medium, negatively impacting production costs. In this work, we engineered the soil bacterium Pseudomonas putida for high-titer, glucose-dependent anthranilate production by repurposing elements of the Esa quorum sensing (QS) system of Pantoea stewartii. The PesaS promoter mediated a self-regulated transcriptional response that effectively knocked-down the expression of the trpDC genes. Next, we harnessed the synthetic QS elements to engineer a growth-to-anthranilate production switch. The resulting plasmid-free P. putida strain produced the target compound at 3.8 ± 0.3 mM in shaken-flask cultures after 72 h-a titer >2-fold higher than anthranilate levels reported thus far. Our results highlight the value of dynamic flux regulation for the production of intermediate metabolites within highly-regulated routes (such as the shikimate pathway), thereby circumventing the need of expensive additives.
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Affiliation(s)
- Lorena Fernández-Cabezón
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Berta Rosich I Bosch
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo Iván Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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39
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Volke DC, Martino RA, Kozaeva E, Smania AM, Nikel PI. Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing. Nat Commun 2022; 13:3026. [PMID: 35641501 PMCID: PMC9156665 DOI: 10.1038/s41467-022-30780-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
CRISPR/Cas technologies constitute a powerful tool for genome engineering, yet their use in non-traditional bacteria depends on host factors or exogenous recombinases, which limits both efficiency and throughput. Here we mitigate these practical constraints by developing a widely-applicable genome engineering toolset for Gram-negative bacteria. The challenge is addressed by tailoring a CRISPR base editor that enables single-nucleotide resolution manipulations (C·G → T·A) with >90% efficiency. Furthermore, incorporating Cas6-mediated processing of guide RNAs in a streamlined protocol for plasmid assembly supports multiplex base editing with >85% efficiency. The toolset is adopted to construct and deconstruct complex phenotypes in the soil bacterium Pseudomonas putida. Single-step engineering of an aromatic-compound production phenotype and multi-step deconstruction of the intricate redox metabolism illustrate the versatility of multiplex base editing afforded by our toolbox. Hence, this approach overcomes typical limitations of previous technologies and empowers engineering programs in Gram-negative bacteria that were out of reach thus far. Rapid engineering of bacterial genomes is a requisite for both fundamental and applied studies. Here the authors develop an enhanced, broad-host-range cytidine base editor that enables multiplexed and efficient genome editing of Gram-negative bacteria.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Román A Martino
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ekaterina Kozaeva
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andrea M Smania
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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40
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Puhm M, Hendrikson J, Kivisaar M, Teras R. Pseudomonas putida Biofilm Depends on the vWFa-Domain of LapA in Peptides-Containing Growth Medium. Int J Mol Sci 2022; 23:ijms23115898. [PMID: 35682576 PMCID: PMC9180339 DOI: 10.3390/ijms23115898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
The biofilm of Pseudomonas putida is complexly regulated by several intercellular and extracellular factors. The cell surface adhesin LapA of this bacterium is a central factor for the biofilm and, consequently, the regulation of lapA expression, for example, by Fis. It has been recently shown that peptides in growth media enhance the formation of P. putida biofilm, but not as a source of carbon and nitrogen. Moreover, the peptide-dependent biofilm appeared especially clearly in the fis-overexpression strain, which also has increased LapA. Therefore, we investigate here whether there is a relationship between LapA and peptide-dependent biofilm. The P. putida strains with inducible lapA expression and LapA without the vWFa domain, which is described as a domain similar to von Willebrand factor domain A, were constructed. Thereafter, the biofilm of these strains was assessed in growth media containing extracellular peptides in the shape of tryptone and without it. We show that the vWFa domain in LapA is necessary for biofilm enhancement by the extracellular peptides in the growth medium. The importance of vWFa in LapA was particularly evident for the fis-overexpression strain F15. The absence of the vWFa domain diminished the positive effect of Fis on the F15 biofilm.
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41
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Yue SJ, Huang P, Li S, Cai YY, Wang W, Zhang XH, Nikel PI, Hu HB. Developing a CRISPR-assisted base-editing system for genome engineering of Pseudomonas chlororaphis. Microb Biotechnol 2022; 15:2324-2336. [PMID: 35575623 PMCID: PMC9437888 DOI: 10.1111/1751-7915.14075] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
Pseudomonas chlororaphis is a non‐pathogenic, plant growth‐promoting rhizobacterium that secretes phenazine compounds with broad‐spectrum antibiotic activity. Currently available genome‐editing methods for P. chlororaphis are based on homologous recombination (HR)‐dependent allelic exchange, which requires both exogenous DNA repair proteins (e.g. λ‐Red–like systems) and endogenous functions (e.g. RecA) for HR and/or providing donor DNA templates. In general, these procedures are time‐consuming, laborious and inefficient. Here, we established a CRISPR‐assisted base‐editing (CBE) system based on the fusion of a rat cytidine deaminase (rAPOBEC1), enhanced‐specificity Cas9 nickase (eSpCas9ppD10A) and uracil DNA glycosylase inhibitor (UGI). This CBE system converts C:G into T:A without DNA strands breaks or any donor DNA template. By engineering a premature STOP codon in target spacers, the hmgA and phzO genes of P. chlororaphis were successfully interrupted at high efficiency. The phzO‐inactivated strain obtained by base editing exhibited identical phenotypic features as compared with a mutant obtained by HR‐based allelic exchange. The use of this CBE system was extended to other P. chlororaphis strains (subspecies LX24 and HT66) and also to P. fluorescens 10586, with an equally high editing efficiency. The wide applicability of this CBE method will accelerate bacterial physiology research and metabolic engineering of non‐traditional bacterial hosts.
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Affiliation(s)
- Sheng-Jie Yue
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peng Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Song Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu-Yuan Cai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xue-Hong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
| | - Hong-Bo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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42
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Lv X, Hueso-Gil A, Bi X, Wu Y, Liu Y, Liu L, Ledesma-Amaro R. New synthetic biology tools for metabolic control. Curr Opin Biotechnol 2022; 76:102724. [PMID: 35489308 DOI: 10.1016/j.copbio.2022.102724] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/28/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
In industrial bioprocesses, microbial metabolism dictates the product yields, and therefore, our capacity to control it has an enormous potential to help us move towards a bio-based economy. The rapid development of multiomics data has accelerated our systematic understanding of complex metabolic regulatory mechanisms, which allow us to develop tools to manipulate them. In the last few years, machine learning-based metabolic modeling, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) derived synthetic biology tools, and synthetic genetic circuits have been widely used to control the metabolism of microorganisms, manipulate gene expression, and build synthetic pathways for bioproduction. This review describes the latest developments for metabolic control, and focuses on the trends and challenges of metabolic engineering strategies.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Angeles Hueso-Gil
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK
| | - Xinyu Bi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW72AZ, UK.
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Gurdo N, Volke DC, Nikel PI. Merging automation and fundamental discovery into the design–build–test–learn cycle of nontraditional microbes. Trends Biotechnol 2022; 40:1148-1159. [DOI: 10.1016/j.tibtech.2022.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 12/29/2022]
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Gabed N, Verret F, Peticca A, Kryvoruchko I, Gastineau R, Bosson O, Séveno J, Davidovich O, Davidovich N, Witkowski A, Kristoffersen JB, Benali A, Ioannou E, Koutsaviti A, Roussis V, Gâteau H, Phimmaha S, Leignel V, Badawi M, Khiar F, Francezon N, Fodil M, Pasetto P, Mouget JL. What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age. Mar Drugs 2022; 20:md20040234. [PMID: 35447907 PMCID: PMC9033121 DOI: 10.3390/md20040234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).
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Affiliation(s)
- Noujoud Gabed
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Oran High School of Biological Sciences (ESSBO), Cellular and Molecular Biology Department, Oran 31000, Algeria
- Laboratoire d’Aquaculture et Bioremediation AquaBior, Université d’Oran 1, Oran 31000, Algeria
| | - Frédéric Verret
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Correspondence: ; Tel.: +30-2810-337-852
| | - Aurélie Peticca
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Igor Kryvoruchko
- Department of Biology, United Arab Emirates University (UAEU), Al Ain P.O. Box 15551, United Arab Emirates;
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
| | - Orlane Bosson
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Julie Séveno
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Olga Davidovich
- Karadag Scientific Station, Natural Reserve of the Russian Academy of Sciences, Kurortnoe, 98188 Feodosiya, Russia;
| | - Nikolai Davidovich
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
- Karadag Scientific Station, Natural Reserve of the Russian Academy of Sciences, Kurortnoe, 98188 Feodosiya, Russia;
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
| | - Jon Bent Kristoffersen
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
| | - Amel Benali
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Laboratoire d’Aquaculture et Bioremediation AquaBior, Université d’Oran 1, Oran 31000, Algeria
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de la Technologie d’Oran Mohamed BOUDIAF-USTO-MB, BP 1505, El M’naouer, Oran 31000, Algeria
| | - Efstathia Ioannou
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Aikaterini Koutsaviti
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Vassilios Roussis
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Hélène Gâteau
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Suliya Phimmaha
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Vincent Leignel
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Myriam Badawi
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Feriel Khiar
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Nellie Francezon
- Institut des Molécules et Matériaux du Mans, UMR CNRS 6283, Le Mans Université, Avenue Olivier Messiaen, 2085 Le Mans, France; (N.F.); (P.P.)
| | - Mostefa Fodil
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Pamela Pasetto
- Institut des Molécules et Matériaux du Mans, UMR CNRS 6283, Le Mans Université, Avenue Olivier Messiaen, 2085 Le Mans, France; (N.F.); (P.P.)
| | - Jean-Luc Mouget
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
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Wang W, Peng X, Jin Y, Pan JA, Guo D. Reverse genetics systems for SARS-CoV-2. J Med Virol 2022; 94:3017-3031. [PMID: 35324008 PMCID: PMC9088479 DOI: 10.1002/jmv.27738] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/18/2022] [Indexed: 11/29/2022]
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID‐19) has caused severe public health crises and heavy economic losses. Limited knowledge about this deadly virus impairs our capacity to set up a toolkit against it. Thus, more studies on severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) biology are urgently needed. Reverse genetics systems, including viral infectious clones and replicons, are powerful platforms for viral research projects, spanning many aspects such as the rescues of wild‐type or mutant viral particles, the investigation of viral replication mechanism, the characterization of viral protein functions, and the studies on viral pathogenesis and antiviral drug development. The operations on viral infectious clones are strictly limited in the Biosafety Level 3 (BSL3) facilities, which are insufficient, especially during the pandemic. In contrast, the operation on the noninfectious replicon can be performed in Biosafety Level 2 (BSL2) facilities, which are widely available. After the outbreak of COVID‐19, many reverse genetics systems for SARS‐CoV‐2, including infectious clones and replicons are developed and given plenty of options for researchers to pick up according to the requirement of their research works. In this review, we summarize the available reverse genetics systems for SARS‐CoV‐2, by highlighting the features of these systems, and provide a quick guide for researchers, especially those without ample experience in operating viral reverse genetics systems.
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Affiliation(s)
- Wenhao Wang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
| | - Xiaoxue Peng
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
| | - Yunyun Jin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
| | - Deyin Guo
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong, 518107, China
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Jeske A, Arce-Rodriguez A, Thöming JG, Tomasch J, Häussler S. Evolution of biofilm-adapted gene expression profiles in lasR-deficient clinical Pseudomonas aeruginosa isolates. NPJ Biofilms Microbiomes 2022; 8:6. [PMID: 35165270 PMCID: PMC8844440 DOI: 10.1038/s41522-022-00268-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
The overall success of a pathogenic microbe depends on its ability to efficiently adapt to challenging conditions in the human host. Long-term evolution experiments track and predict adaptive trajectories and have contributed significantly to our understanding of the driving forces of bacterial adaptation. In this study, we conducted a cross-sectional study instead of long-term longitudinal evolution experiments. We analyzed the transcriptional profiles as well as genomic sequence variations of a large number of clinical Pseudomonas aeruginosa isolates that have been recovered from different infected human sites. Convergent changes in gene expression patterns were found in different groups of clinical isolates. The majority of repeatedly observed expression patterns could be attributed to a defective lasR gene, which encodes the major quorum-sensing regulator LasR. Strikingly, the gene expression pattern of the lasR-defective strains appeared to reflect a transcriptional response that evolves in a direction consistent with growth within a biofilm. In a process of genetic assimilation, lasR-deficient P. aeruginosa isolates appear to constitutively express a biofilm-adapted transcriptional profile and no longer require a respective environmental trigger. Our results demonstrate that profiling the functional consequences of pathoadaptive mutations in clinical isolates reveals long-term evolutionary pathways and may explain the success of lasR mutants in the opportunistic pathogen P. aeruginosa in a clinical context.
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Affiliation(s)
- Alexander Jeske
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
| | - Alejandro Arce-Rodriguez
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, 2100, Copenhagen, Denmark
| | - Jürgen Tomasch
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30265, Hannover, Germany.
- Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, 2100, Copenhagen, Denmark.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30265, Hannover, Germany.
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Wang P, Wang W, Peng X, Ruan F, Yang S. Protective effect of vasostatin-1 plasmid-like nanoparticles on aortic aneurysm and its mechanism. Bioengineered 2022; 13:544-559. [PMID: 34968165 PMCID: PMC8805933 DOI: 10.1080/21655979.2021.2009978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/18/2021] [Indexed: 11/23/2022] Open
Abstract
Vasostatin 1 (VS-1) plays an important role in the regulation of various tissue injury and repair processes, but its role in aortic aneurysm remains unclear. The plasmid-like nanoparticles containing the vasostatin-1 gene Pul-PGEA-pCas-sgVs-1 were constructed, and their guarantee, safety, hemolysis, and particle size were analyzed. Eighty-four eight-week-old male ApoE-mice were randomly divided into blank group (without any treatment), model group (Ang II aortic aneurysm model + tail injection of PBS), control group (modeling + tail injection of Pul-PGEA-pCas9), and experimental group (modeling + tail injection of Pul-PGEA-pCas-sgVs-1), with 21 rats in each group. The incidence, mortality, and maximum diameter of abdominal aortic aneurysm (AAA) and the contents of high sensitivity C-reactive protein (HS-CRP), soluble intercellular adhesion molecule-1 (ICAM-1), soluble vascular cell adhesion molecule-1 (VCAM-1), and TNF-a in serum were compared in different groups of mice. The results showed that Pul-PGEA-pCas-sgVs-1 had good biosafety and transfection ability. The maximum diameter of abdominal aorta, incidence of abdominal aortic aneurysm, mortality, and the expression levels of HS-CRP, ICAM-1, VCAM-1, and TNF-a in the experimental group were lower than those in the model group (P< 0.05). These results indicated that the plasmid-like nanoparticles Pul-PGEA-pCas-sgVs-1 can inhibit the development of aorta by down-regulating the expression of inflammatory factors, which played a good protective role on the aorta.
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Affiliation(s)
- Pingshan Wang
- Department of Cardiovascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Province, China
| | - Wei Wang
- Department of Cardiovascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Province, China
| | - Xingxing Peng
- Department of Cardiovascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Province, China
| | - Fugui Ruan
- Department of Cardiovascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Province, China
| | - Shiyao Yang
- Department of Cardiovascular Surgery, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi Province, China
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Wirth NT, Nikel PI. Combinatorial pathway balancing provides biosynthetic access to 2-fluoro- cis, cis-muconate in engineered Pseudomonas putida. CHEM CATALYSIS 2021; 1:1234-1259. [PMID: 34977847 PMCID: PMC8711041 DOI: 10.1016/j.checat.2021.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/15/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022]
Abstract
The wealth of bio-based building blocks produced by engineered microorganisms seldom include halogen atoms. Muconate is a platform chemical with a number of industrial applications that could be broadened by introducing fluorine atoms to tune its physicochemical properties. The soil bacterium Pseudomonas putida naturally assimilates benzoate via the ortho-cleavage pathway with cis,cis-muconate as intermediate. Here, we harnessed the native enzymatic machinery (encoded within the ben and cat gene clusters) to provide catalytic access to 2-fluoro-cis,cis-muconate (2-FMA) from fluorinated benzoates. The reactions in this pathway are highly imbalanced, leading to accumulation of toxic intermediates and limited substrate conversion. By disentangling regulatory patterns of ben and cat in response to fluorinated effectors, metabolic activities were adjusted to favor 2-FMA biosynthesis. After implementing this combinatorial approach, engineered P. putida converted 3-fluorobenzoate to 2-FMA at the maximum theoretical yield. Hence, this study illustrates how synthetic biology can expand the diversity of nature's biochemical catalysis.
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Affiliation(s)
- Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Patinios C, Creutzburg SCA, Arifah AQ, Adiego-Pérez B, Gyimah E, Ingham C, Kengen SWM, van der Oost J, Staals RHJ. Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas. Nucleic Acids Res 2021; 49:11392-11404. [PMID: 34614191 PMCID: PMC8565351 DOI: 10.1093/nar/gkab893] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas is a powerful tool for genome editing in bacteria. However, its efficacy is dependent on host factors (such as DNA repair pathways) and/or exogenous expression of recombinases. In this study, we mitigated these constraints by developing a simple and widely applicable genome engineering tool for bacteria which we termed SIBR-Cas (Self-splicing Intron-Based Riboswitch-Cas). SIBR-Cas was generated from a mutant library of the theophylline-dependent self-splicing T4 td intron that allows for tight and inducible control over CRISPR-Cas counter-selection. This control delays CRISPR-Cas counter-selection, granting more time for the editing event (e.g. by homologous recombination) to occur. Without the use of exogenous recombinases, SIBR-Cas was successfully applied to knock-out several genes in three wild-type bacteria species (Escherichia coli MG1655, Pseudomonas putida KT2440 and Flavobacterium IR1) with poor homologous recombination systems. Compared to other genome engineering tools, SIBR-Cas is simple, tightly regulated and widely applicable for most (non-model) bacteria. Furthermore, we propose that SIBR can have a wider application as a simple gene expression and gene regulation control mechanism for any gene or RNA of interest in bacteria.
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Affiliation(s)
- Constantinos Patinios
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Sjoerd C A Creutzburg
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Adini Q Arifah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Belén Adiego-Pérez
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Evans A Gyimah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Colin J Ingham
- Hoekmine Besloten Vennootschap, Kenniscentrum Technologie en Innovatie, Hogeschool Utrecht, 3584 CS, Utrecht, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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50
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Manfrão‐Netto JHC, Lund F, Muratovska N, Larsson EM, Parachin NS, Carlquist M. Metabolic engineering of Pseudomonas putida for production of vanillylamine from lignin-derived substrates. Microb Biotechnol 2021; 14:2448-2462. [PMID: 33533574 PMCID: PMC8601178 DOI: 10.1111/1751-7915.13764] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
Whole-cell bioconversion of technical lignins using Pseudomonas putida strains overexpressing amine transaminases (ATAs) has the potential to become an eco-efficient route to produce phenolic amines. Here, a novel cell growth-based screening method to evaluate the in vivo activity of recombinant ATAs towards vanillylamine in P. putida KT2440 was developed. It allowed the identification of the native enzyme Pp-SpuC-II and ATA from Chromobacterium violaceum (Cv-ATA) as highly active towards vanillylamine in vivo. Overexpression of Pp-SpuC-II and Cv-ATA in the strain GN442ΔPP_2426, previously engineered for reduced vanillin assimilation, resulted in 94- and 92-fold increased specific transaminase activity, respectively. Whole-cell bioconversion of vanillin yielded 0.70 ± 0.20 mM and 0.92 ± 0.30 mM vanillylamine, for Pp-SpuC-II and Cv-ATA, respectively. Still, amine production was limited by a substantial re-assimilation of the product and formation of the by-products vanillic acid and vanillyl alcohol. Concomitant overexpression of Cv-ATA and alanine dehydrogenase from Bacillus subtilis increased the production of vanillylamine with ammonium as the only nitrogen source and a reduction in the amount of amine product re-assimilation. Identification and deletion of additional native genes encoding oxidoreductases acting on vanillin are crucial engineering targets for further improvement.
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Affiliation(s)
| | - Fredrik Lund
- Division of Applied MicrobiologyDepartment of ChemistryFaculty of EngineeringLund UniversityPO Box 124Lund221 00Sweden
- Present address:
Applied MicrobiologyLund UniversityKemicentrum, Naturvetarvägen 14Lund22100Sweden
| | - Nina Muratovska
- Division of Applied MicrobiologyDepartment of ChemistryFaculty of EngineeringLund UniversityPO Box 124Lund221 00Sweden
- Present address:
Applied MicrobiologyLund UniversityKemicentrum, Naturvetarvägen 14Lund22100Sweden
| | - Elin M. Larsson
- Division of Applied MicrobiologyDepartment of ChemistryFaculty of EngineeringLund UniversityPO Box 124Lund221 00Sweden
- Department of BioengineeringCalifornia Institute of Technology1200 East California BlvdPasadenaCA91125USA
- Present address:
Applied MicrobiologyLund UniversityKemicentrum, Naturvetarvägen 14Lund22100Sweden
| | - Nádia Skorupa Parachin
- Grupo Engenharia de BiocatalisadoresInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
- Present address:
Ginkgo Bioworks27 Drydock AveBostonMA02210USA
| | - Magnus Carlquist
- Division of Applied MicrobiologyDepartment of ChemistryFaculty of EngineeringLund UniversityPO Box 124Lund221 00Sweden
- Present address:
Applied MicrobiologyLund UniversityKemicentrum, Naturvetarvägen 14Lund22100Sweden
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