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Choi S, Kim B, Kim S, Lee Y, Shin Y, Oh J, Bhatia SK, Seo SO, Park SH, Park K, Yang YH. Establishment of efficient 5-hydroxyvaleric acid production system by regenerating alpha-ketoglutaric acid and its application in poly(5-hydroxyvaleric acid) production. J Biotechnol 2024; 387:12-22. [PMID: 38522773 DOI: 10.1016/j.jbiotec.2024.03.007] [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: 01/17/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
5-hydroxyvaleric acid (5-HV) is a versatile C5 intermediate of bio-based high-value chemical synthesis pathways. However, 5-HV production faces a few shortcomings involving the supply of cofactors, especially α-ketoglutaric acid (α-KG). Herein, we established a two-cell biotransformation system by introducing L-glutamate oxidase (GOX) to regenerate α-KG. Additionally, the catalase KatE was adapted to inhibit α-KG degradation by the H2O2 produced during GOX reaction. We searched for the best combination of genes and vectors and optimized the biotransformation conditions to maximize GOX effectiveness. Under the optimized conditions, 5-HV pathway with GOX showed 1.60-fold higher productivity than that of without GOX, showing 11.3 g/L titer. Further, the two-cell system with GOX and KatE was expanded to produce poly(5-hydroxyvaleric acid) (P(5HV)), and it reached at 412 mg/L of P(5HV) production and 20.5% PHA contents when using the biotransformation supernatant. Thus, the two-cell biotransformation system with GOX can potentially give the practical and economic alternative of 5-HV production using bio-based methods. We also propose direct utilization of 5-HV from bioconversion for P(5HV) production.
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Affiliation(s)
- Suhye Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Byungchan Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Suwon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Yeda Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Yuni Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jinok Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul, Republic of Korea
| | - Seung-Oh Seo
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - See-Hyoung Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong, Republic of Korea
| | - Kyungmoon Park
- Department of Biological and Chemical Engineering, Hongik University, Sejong, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul, Republic of Korea.
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2
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Schulte M, Grotheer L, Hensel M. Bright individuals: Applications of fluorescent protein-based reporter systems in single-cell cellular microbiology. Mol Microbiol 2024; 121:605-617. [PMID: 38234267 DOI: 10.1111/mmi.15227] [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: 07/18/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Activation and function of virulence functions of bacterial pathogens are highly dynamic in time and space, and can show considerable heterogeneity between individual cells in pathogen populations. To investigate the complex events in host-pathogen interactions, single cell analyses are required. Fluorescent proteins (FPs) are excellent tools to follow the fate of individual bacterial cells during infection, and can also be deployed to use the pathogen as a sensor for its specific environment in host cells or host organisms. This Resources describes design and applications of dual fluorescence reporters (DFR) in cellular microbiology. DFR feature constitutively expressed FPs for detection of bacterial cells, and FPs expressed by an environmentally regulated promoter for interrogation of niche-specific cues or nutritional parameters. Variations of the basic design allow the generation of DFR that can be used to analyze, on single cell level, bacterial proliferation during infection, subcellular localization of intracellular bacteria, stress response, or persister state. We describe basic considerations for DFR design and review recent applications of DFR in cellular microbiology.
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Affiliation(s)
- Marc Schulte
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs-Center of Cellular Nanoanalytics Osnabrück, Universität Osnabrück, Osnabrück, Germany
| | - Luisa Grotheer
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- CellNanOs-Center of Cellular Nanoanalytics Osnabrück, Universität Osnabrück, Osnabrück, Germany
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3
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Brülisauer L, León-Sampedro R, Hall AR. Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro. Plasmid 2023; 128:102706. [PMID: 37652194 DOI: 10.1016/j.plasmid.2023.102706] [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: 03/01/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain-dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.
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Affiliation(s)
- Laura Brülisauer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
| | - Ricardo León-Sampedro
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland; Centro de Investigación Biológica en Red, Epidemiología y Salud Pública- CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Alex R Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
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4
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Mohler K, Moen JM, Rogulina S, Rinehart J. System-wide optimization of an orthogonal translation system with enhanced biological tolerance. Mol Syst Biol 2023; 19:e10591. [PMID: 37477096 PMCID: PMC10407733 DOI: 10.15252/msb.202110591] [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: 07/20/2021] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023] Open
Abstract
Over the past two decades, synthetic biological systems have revolutionized the study of cellular physiology. The ability to site-specifically incorporate biologically relevant non-standard amino acids using orthogonal translation systems (OTSs) has proven particularly useful, providing unparalleled access to cellular mechanisms modulated by post-translational modifications, such as protein phosphorylation. However, despite significant advances in OTS design and function, the systems-level biology of OTS development and utilization remains underexplored. In this study, we employ a phosphoserine OTS (pSerOTS) as a model to systematically investigate global interactions between OTS components and the cellular environment, aiming to improve OTS performance. Based on this analysis, we design OTS variants to enhance orthogonality by minimizing host process interactions and reducing stress response activation. Our findings advance understanding of system-wide OTS:host interactions, enabling informed design practices that circumvent deleterious interactions with host physiology while improving OTS performance and stability. Furthermore, our study emphasizes the importance of establishing a pipeline for systematically profiling OTS:host interactions to enhance orthogonality and mitigate mechanisms underlying OTS-mediated host toxicity.
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Affiliation(s)
- Kyle Mohler
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI)University of California, San FranciscoSan FranciscoCAUSA
- 2QBI Coronavirus Research Group (QCRG)San FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Svetlana Rogulina
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
| | - Jesse Rinehart
- Department of Cellular & Molecular PhysiologyYale School of MedicineNew HavenCTUSA
- Systems Biology InstituteYale UniversityNew HavenCTUSA
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5
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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6
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Diep P, Leo Shen H, Wiesner JA, Mykytczuk N, Papangelakis V, Yakunin AF, Mahadevan R. Engineered nickel bioaccumulation in Escherichia coli by NikABCDE transporter and metallothionein overexpression. Eng Life Sci 2023; 23:2200133. [PMID: 37408871 PMCID: PMC10317975 DOI: 10.1002/elsc.202200133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/24/2023] [Indexed: 07/07/2023] Open
Abstract
Mine wastewater often contains dissolved metals at concentrations too low to be economically extracted by existing technologies, yet too high for environmental discharge. The most common treatment is chemical precipitation of the dissolved metals using limestone and subsequent disposal of the sludge in tailing impoundments. While it is a cost-effective solution to meet regulatory standards, it represents a lost opportunity. In this study, we engineered Escherichia coli to overexpress its native NikABCDE transporter and a heterologous metallothionein to capture nickel at concentrations in local effluent streams. We found the engineered strain had a 7-fold improvement in the bioaccumulation performance for nickel compared to controls, but also observed a drastic decrease in cell viability due to metabolic burden or inducer (IPTG) toxicity. Growth kinetic analysis revealed the IPTG concentrations used based on past studies lead to growth inhibition, thus delineating future avenues for optimization of the engineered strain and its growth conditions to perform in more complex environments.
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Affiliation(s)
- Patrick Diep
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
| | - Heping Leo Shen
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
| | | | | | - Vladimiros Papangelakis
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
| | - Alexander F. Yakunin
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
- Centre for Environmental BiotechnologySchool of Natural SciencesUniversity of BangorWalesUK
| | - Radhakrishnan Mahadevan
- BioZone – Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoCanada
- Institute of Biomedical EngineeringUniversity of TorontoTorontoCanada
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7
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Mayo-Muñoz D, Pinilla-Redondo R, Birkholz N, Fineran PC. A host of armor: Prokaryotic immune strategies against mobile genetic elements. Cell Rep 2023; 42:112672. [PMID: 37347666 DOI: 10.1016/j.celrep.2023.112672] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
Prokaryotic adaptation is strongly influenced by the horizontal acquisition of beneficial traits via mobile genetic elements (MGEs), such as viruses/bacteriophages and plasmids. However, MGEs can also impose a fitness cost due to their often parasitic nature and differing evolutionary trajectories. In response, prokaryotes have evolved diverse immune mechanisms against MGEs. Recently, our understanding of the abundance and diversity of prokaryotic immune systems has greatly expanded. These defense systems can degrade the invading genetic material, inhibit genome replication, or trigger abortive infection, leading to population protection. In this review, we highlight these strategies, focusing on the most recent discoveries. The study of prokaryotic defenses not only sheds light on microbial evolution but also uncovers novel enzymatic activities with promising biotechnological applications.
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Affiliation(s)
- David Mayo-Muñoz
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Rafael Pinilla-Redondo
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Bioprotection Aotearoa, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
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8
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Ahmad M, Prensky H, Balestrieri J, ElNaggar S, Gomez-Simmonds A, Uhlemann AC, Traxler B, Singh A, Lopatkin AJ. Tradeoff between lag time and growth rate drives the plasmid acquisition cost. Nat Commun 2023; 14:2343. [PMID: 37095096 PMCID: PMC10126158 DOI: 10.1038/s41467-023-38022-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Conjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.
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Affiliation(s)
- Mehrose Ahmad
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | - Hannah Prensky
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | | | - Shahd ElNaggar
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | - Angela Gomez-Simmonds
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, 10032, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, 10032, USA
| | - Beth Traxler
- Department Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, 19717, USA
| | - Allison J Lopatkin
- Department of Biology, Barnard College, New York, NY, 10027, USA.
- Department Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, 10027, USA.
- Data Science Institute, Columbia University, New York, NY, 10027, USA.
- Department of Chemical Engineering, University of Rochester, Rochester, NY, 14627, USA.
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14627, USA.
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9
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Jiang Z, Lu J, Tong Y, Yang H, Feng S. Enhancement of acid tolerance of Escherichia coli by introduction of molecule chaperone CbpA from extremophile. World J Microbiol Biotechnol 2023; 39:158. [PMID: 37046107 DOI: 10.1007/s11274-023-03613-4] [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: 02/24/2023] [Accepted: 04/08/2023] [Indexed: 04/14/2023]
Abstract
Molecular chaperone CbpA from extreme acidophile Acidithiobacillus caldus was applied to improve acid tolerance of Escherichia coli via CRISPR/Cas9. Cell growth and viability of plasmid complementary strain indicated the importance of cbpAAc for bacteria acid tolerance. With in situ gene replacement by CRISPR/Cas9 system, colony formation unit (CFU) of genome recombinant strain BL21-ΔcbpA/AccbpA showed 7.7 times higher cell viability than deficient strain BL21-ΔcbpA and 2.3 times higher than wild type. Cell morphology observation using Field Emission Scanning Electron Microscopy (FESEM) revealed cell breakage of BL21-ΔcbpA and significant recovery of BL21-ΔcbpA/AccbpA. The intracellular ATP level of all strains gradually decreased along with the increased stress time. Particularly, the value of recombinant strain was 56.0% lower than that of deficient strain after 5 h, indicating that the recombinant strain consumed a lot of energy to resist acid stress. The arginine concentration in BL21-ΔcbpA/AccbpA was double that of BL21-ΔcbpA, while the aspartate and glutamate contents were 14.8% and 6.2% higher, respectively, compared to that of wild type. Moreover, RNA-Seq analysis examined 93 genes down-regulated in BL21-ΔcbpA compared to wild type strain, while 123 genes were up-regulated in BL21-ΔcbpA/AccbpA compared to BL21-ΔcbpA, with an emphasis on energy metabolism, transport, and cell components. Finally, the working model in response to acid stress of cbpA from A. caldus was developed. This study constructed a recombinant strain resistant to acid stress and also provided a reference for enhancing microorganisms' robustness to various conditions.
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Affiliation(s)
- Zhenming Jiang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jie Lu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, China
| | - Hailin Yang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Shoushuai Feng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
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10
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Kosiorek K, Koryszewska-Bagińska A, Skoneczny M, Stasiak-Różańska L, Aleksandrzak-Piekarczyk T. The Presence of Plasmids in Lactococcus lactis IL594 Determines Changes in the Host Phenotype and Expression of Chromosomal Genes. Int J Mol Sci 2023; 24:ijms24010793. [PMID: 36614234 PMCID: PMC9821262 DOI: 10.3390/ijms24010793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
The L. lactis IL594 strain contains seven plasmids (pIL1 to pIL7) and is the parental strain of the plasmid-free L. lactis IL1403, one of the most studied lactic acid bacteria (LAB) strain. The genetic sequences of pIL1 to pIL7 plasmids have been recently described, however the knowledge of global changes in host phenotype and transcriptome remains poor. In the present study, global phenotypic analyses were combined with transcriptomic studies to evaluate a potential influence of plasmidic genes on overall gene expression in industrially important L. lactis strains. High-throughput screening of phenotypes differences revealed pronounced phenotypic differences in favor of IL594 during the metabolism of some C-sources, including lactose and β-glucosides. A plasmids-bearing strain presented increased resistance to unfavorable growth conditions, including the presence of heavy metal ions and antimicrobial compounds. Global comparative transcriptomic study of L. lactis strains revealed variation in the expression of over 370 of chromosomal genes caused by plasmids presence. The general trend presented upregulated energy metabolism and biosynthetic genes, differentially expressed regulators, prophages and cell resistance proteins. Our findings suggest that plasmids maintenance leads to significant perturbation in global gene regulation that provides change in central metabolic pathways and adaptive properties of the IL594 cells.
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Affiliation(s)
- Katarzyna Kosiorek
- Institute of Biochemistry and Biosciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | | | - Marek Skoneczny
- Institute of Biochemistry and Biosciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Lidia Stasiak-Różańska
- Department of Food Technology and Assessment, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159C St., 02-787 Warsaw, Poland
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11
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Kairamkonda M, Sharma M, Gupta P, Poluri KM. Overexpression of bacteriophage T4 and T7 endolysins differentially regulate the metabolic fingerprint of host Escherichia coli. Int J Biol Macromol 2022; 221:212-223. [PMID: 36075302 DOI: 10.1016/j.ijbiomac.2022.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 12/21/2022]
Abstract
Bioactive proteins are often overexpressed in different host systems for biotechnological/biomedical applications. Endolysins are natural bactericidal proteins that cleave the bacterial peptidoglycan membrane, and have the potential to be the next-generation enzybiotics. Therefore, the present study aims to elucidate the impact of two endolysins (T4L, T7L) overexpression on metabolic fingerprint of E. coli using NMR spectroscopy. The 1H NMR-based metabolomics analysis revealed global metabolite profiles of E. coli in response to endolysins. The study has identified nearly 75 metabolites, including organic acids, amino acids, sugars and nucleic acids. RNA Polymerase (RNAP) has been considered as reference protein for marking the specific alterations in metabolic pathways. The data suggested downregulation of central carbon metabolic pathway in both endolysins overexpression, but to a different extent. Also, the endolysin overexpression have highlighted the enhanced metabolic load and stress generation in the host cells, thus leading to the activation of osmoregulatory pathways. The overall changes in metabolic fingerprint of E. coli highlights the enhanced perturbations during the overexpression of T4L as compared to T7L. These untargeted metabolic studies shed light on the regulation of molecular pathways during the heterologous overexpression of these lytic enzymes that are lethal to the host.
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Affiliation(s)
- Manikyaprabhu Kairamkonda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Meenakshi Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Payal Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
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12
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Cheng SY, Lin TH, Chen PT. Integration of Multiple Phage Attachment Sites System to Create the Chromosomal T7 System for Protein Production in Escherichia coli Nissle 1917. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10239-10247. [PMID: 35960546 DOI: 10.1021/acs.jafc.2c04614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Escherichia coli Nissle 1917 (EcN) is a probiotic used to treat gastrointestinal diseases. The probiotic and endotoxin-free characteristics of EcN support its potential to be developed into a microbial expression system. With this aim, in this study, the powerful T7 expression system was constructed in the cryptic plasmid-free EcN (EcNP) to generate the T7 expression host ENL6P. The concept of multiple copies of gene expression cassettes regulated by the chromosomal T7 promoter was promoted due to plasmid instability issues with protein production in ENL6P. The integration of multiple phage attachment sites (IMPACT) system, which combined Cre-lox72, CRIM, and lambda red recombinase systems, was designed to simplify the manipulation and achieve the multiple φ80 bacterial attachment sites (attB) in ENL6P to generate the new strain ENL6PP4 with four φ80 attB sites. The strain can simultaneously integrate four copies of gene expression cassettes in the chromosome to produce recombinant proteins. The IMPACT systems incorporated several tools in gene editing to rapidly achieve more robust and stable microbial strains for research and various industrial applications.
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Affiliation(s)
- Shu-Yun Cheng
- Department of Biotechnology and Food Technology, Southern Taiwan University of Science and Technology, Tainan 710, Taiwan
| | - Tzu-Han Lin
- Department of Biotechnology and Food Technology, Southern Taiwan University of Science and Technology, Tainan 710, Taiwan
| | - Po-Ting Chen
- Department of Biotechnology and Food Technology, Southern Taiwan University of Science and Technology, Tainan 710, Taiwan
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13
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Abstract
Plasmids are one of the most commonly used platforms for genetic engineering and recombinant gene expression in bacteria. The range of available copy numbers for cloning vectors is largely restricted to the handful of Origins of Replication (ORIs) that have been isolated from plasmids found in nature. Here, we introduce two systems that allow for the continuous, finely-tuned control of plasmid copy number between 1 and 800 copies per cell: a plasmid with an anhydrotetracycline-controlled copy number, and a parallelized assay that is used to generate a continuous spectrum of 1194 ColE1-based copy number variants. Using these systems, we investigate the effects of plasmid copy number on cellular growth rates, gene expression, biosynthesis, and genetic circuit performance. We perform single-cell timelapse measurements to characterize plasmid loss, runaway plasmid replication, and quantify the impact of plasmid copy number on the variability of gene expression. Using our assay, we find that each plasmid imposes a 0.063% linear metabolic burden on their hosts, hinting at a simple relationship between metabolic burdens and plasmid DNA synthesis. Our systems enable the precise control of gene expression, and our results highlight the importance of tuning plasmid copy number as a powerful tool for the optimization of synthetic biological systems.
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14
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Chen Q, Dharmaraj T, Cai PC, Burgener EB, Haddock NL, Spakowitz AJ, Bollyky PL. Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics. Pharmaceutics 2022; 14:1425. [PMID: 35890320 PMCID: PMC9318951 DOI: 10.3390/pharmaceutics14071425] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophages, viruses that infect and replicate within bacteria, impact bacterial responses to antibiotics in complex ways. Recent studies using lytic bacteriophages to treat bacterial infections (phage therapy) demonstrate that phages can promote susceptibility to chemical antibiotics and that phage/antibiotic synergy is possible. However, both lytic and lysogenic bacteriophages can contribute to antimicrobial resistance. In particular, some phages mediate the horizontal transfer of antibiotic resistance genes between bacteria via transduction and other mechanisms. In addition, chronic infection filamentous phages can promote antimicrobial tolerance, the ability of bacteria to persist in the face of antibiotics. In particular, filamentous phages serve as structural elements in bacterial biofilms and prevent the penetration of antibiotics. Over time, these contributions to antibiotic tolerance favor the selection of resistance clones. Here, we review recent insights into bacteriophage contributions to antibiotic susceptibility, resistance, and tolerance. We discuss the mechanisms involved in these effects and address their impact on bacterial fitness.
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Affiliation(s)
- Qingquan Chen
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Tejas Dharmaraj
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Pamela C. Cai
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA;
| | - Elizabeth B. Burgener
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; (E.B.B.); (A.J.S.)
| | - Naomi L. Haddock
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
| | - Andy J. Spakowitz
- Center for Excellence in Pulmonary Biology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; (E.B.B.); (A.J.S.)
| | - Paul L. Bollyky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Beckman Center, 279 Campus Drive, Stanford, CA 94305, USA; (T.D.); (N.L.H.); (P.L.B.)
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15
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Davenport BI, Tica J, Isalan M. Reducing metabolic burden in the PACEmid evolver system by remastering high-copy phagemid vectors. ENGINEERING BIOLOGY 2022; 6:50-61. [PMID: 36969104 PMCID: PMC9996709 DOI: 10.1049/enb2.12021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 01/12/2023] Open
Abstract
Orthogonal or non-cross-reacting transcription factors are used in synthetic biology as components of genetic circuits. Brödel et al. (2016) engineered 12 such cIλ transcription factor variants using a directed evolution 'PACEmid' system. The variants operate as dual activator/repressors and expand gene circuit construction possibilities. However, the high-copy phagemid vectors carrying the cIλ variants imposed high metabolic burden upon cells. Here, the authors 'remaster' the phagemid backbones to relieve their burden substantially, exhibited by a recovery in Escherichia coli growth. The remastered phagemids' ability to function within the PACEmid evolver system is maintained, as is the cIλ transcription factors' activity within these vectors. The low-burden phagemid versions are more suitable for use in PACEmid experiments and synthetic gene circuits; the authors have, therefore, replaced the original high-burden phagemids on the Addgene repository. The authors' work emphasises the importance of understanding metabolic burden and incorporating it into design steps in future synthetic biology ventures.
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Affiliation(s)
- Beth India Davenport
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
| | - Jure Tica
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
| | - Mark Isalan
- Department of Life SciencesImperial College LondonSouth Kensington CampusLondonUK
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16
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Hydrodynamic Effects on Biofilm Development and Recombinant Protein Expression. Microorganisms 2022; 10:microorganisms10050931. [PMID: 35630375 PMCID: PMC9145004 DOI: 10.3390/microorganisms10050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Hydrodynamics play an important role in the rate of cell attachment and nutrient and oxygen transfer, which can affect biofilm development and the level of recombinant protein production. In the present study, the effects of different flow conditions on the development of Escherichia coli biofilms and the expression of a model recombinant protein (enhanced green fluorescent protein, eGFP) were examined. Planktonic and biofilm cells were grown at two different flow rates in a recirculating flow cell system for 7 days: 255 and 128 L h−1 (corresponding to a Reynolds number of 4600 and 2300, respectively). The fluorometric analysis showed that the specific eGFP production was higher in biofilms than in planktonic cells under both hydrodynamic conditions (3-fold higher for 255 L h−1 and 2-fold higher for 128 L h−1). In the biofilm cells, the percentage of eGFP-expressing cells was on average 52% higher at a flow rate of 255 L h−1. Furthermore, a higher plasmid copy number (PCN) was obtained for the highest flow rate for both planktonic (244 PCN/cell versus 118 PCN/cell) and biofilm cells (43 PCN/cell versus 29 PCN/cell). The results suggested that higher flow velocities promoted eGFP expression in E. coli biofilms.
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17
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Persistence of plasmids targeted by CRISPR interference in bacterial populations. Proc Natl Acad Sci U S A 2022; 119:e2114905119. [PMID: 35394860 PMCID: PMC9169639 DOI: 10.1073/pnas.2114905119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
RNA-guided CRISPR-Cas nucleases efficiently protect bacterial cells from phage infection and plasmid transformation. Yet, the efficiency of CRISPR-Cas defense is not absolute. Mutations in either CRISPR-Cas components of the host or mobile genetic elements regions targeted by CRISPR-Cas inactivate the defensive action. Here, we show that even at conditions of active CRISPR-Cas and unaltered targeted plasmids, a kinetic equilibrium between CRISPR-Cas nucleases action and plasmid replication processes allows for existence of a small subpopulation of plasmid-bearing cells on the background of cells that have been cured from the plasmid. In nature, the observed diversification of phenotypes may allow rapid changes in the population structure to meet the demands of the environment. CRISPR-Cas systems provide prokaryotes with an RNA-guided defense against foreign mobile genetic elements (MGEs) such as plasmids and viruses. A common mechanism by which MGEs avoid interference by CRISPR consists of acquisition of escape mutations in regions targeted by CRISPR. Here, using microbiological, live microscopy and microfluidics analyses we demonstrate that plasmids can persist for multiple generations in some Escherichia coli cell lineages at conditions of continuous targeting by the type I-E CRISPR-Cas system. We used mathematical modeling to show how plasmid persistence in a subpopulation of cells mounting CRISPR interference is achieved due to the stochastic nature of CRISPR interference and plasmid replication events. We hypothesize that the observed complex dynamics provides bacterial populations with long-term benefits due to continuous maintenance of mobile genetic elements in some cells, which leads to diversification of phenotypes in the entire community and allows rapid changes in the population structure to meet the demands of a changing environment.
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18
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Walter de Walthoffen S. Penicillinase plasmid Australia type in Neisseria gonorrhoeae isolated in Poland. Arch Microbiol 2022; 204:130. [PMID: 34999997 PMCID: PMC8743264 DOI: 10.1007/s00203-021-02623-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 11/29/2022]
Abstract
Purpose Neisseria gonorrhoeae is an etiological agent of gonorrhea which remains a major public health problem the mechanisms that determine resistance to drugs of the beta-lactam class, which are recommended for the treatment of gonorrhea, are currently the most important problem in its treatment. Chromosomal mutations are responsible for resistance to ceftriaxone and cefepime. The possibility of mutations in the gene encoding beta-lactamase (blaTEM) in the penicillinase plasmid may also turn out to be a serious threat. Methods The occurrence of resistance encoded on penicillinase plasmid has been investigated. For this purpose, the susceptibility of bacteria was determined and the gene for resistance to beta-lactams as well as the plasmids themselves was typed. Results Of the 333 strains tested, 21 (6.3%) had the beta-lactamase gene and produced penicillinase. Two of the beta-lactamase: TEM-1 and TEM-135 occurred among the tested strains of N. gonorrhoeae. Most of the known penicillinase plasmid types of N. gonorrhoeae were demonstrated: the Asian, the African, the Toronto/Rio plasmids and Australian variants. Conclusions In the first 3 years, TEM-1 beta-lactamases dominated in N. gonorrhoeae, which were replaced by TEM-135 in the following years of the study. Not all molecular methods are capable of varying the types of penicillinase plasmids. A particularly noteworthy observation is the fact that the Australia-type of penicillinase plasmid (3270 bp) was identified for the first time in Europe, and the second time in the world. Electronic supplementary material The online version of this article (10.1007/s00203-021-02623-w) contains supplementary material, which is available to authorized users.
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19
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Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution. J Bacteriol 2021; 203:e0017721. [PMID: 34370561 PMCID: PMC8508098 DOI: 10.1128/jb.00177-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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20
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Huleani S, Roberts MR, Beales L, Papaioannou EH. Escherichia coli as an antibody expression host for the production of diagnostic proteins: significance and expression. Crit Rev Biotechnol 2021; 42:756-773. [PMID: 34470557 DOI: 10.1080/07388551.2021.1967871] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
This review article concerns the production of recombinant antibody fragments for applications mainly in the diagnostic sector. The so-called "point of care diagnostics" is very important for timely diagnosis and treatment, thus being able to save lives and resources. There is intense pressure for more accurate and less expensive rapid diagnostic tests, with a value preferably <$1. Thus, the large-scale cost-effective production of recombinant antibodies is vital. The importance of Escherichia coli toward the production of inexpensive rapid tests will be explained in this review paper. Details about the different strains of E. coli, the strategies used for the insertion and the expression of recombinant proteins, and the challenges that still exist are provided. Afterward, the importance of the expression scale and culture parameters in the final yield of the antibodies are examined. From this analysis, it appears that for good yields of recombinant antibodies, aside from appropriate gene transfer and expression, the culturing parameters are of paramount importance. Larger scale production is more favorable, mainly due to the higher cell densities that can be achieved. Yields of functional Fab fragments in the range of 10-20 mg/L are considered good in shake flasks, whereas in bioreactors can be up to 1-2 g/L. An amount of 10-500 mg of such antibody per million rapid tests is required. Despite the substantial importance of the production of the antibodies and their fragments, their downstream processing should be appropriately considered from the beginning for achieving the target value of the final rapid diagnostic tests.
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Affiliation(s)
- Sergiu Huleani
- Engineering Building, Lancaster University, Lancaster, UK
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21
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Unrath N, McCabe E, Macori G, Fanning S. Application of Whole Genome Sequencing to Aid in Deciphering the Persistence Potential of Listeria monocytogenes in Food Production Environments. Microorganisms 2021; 9:1856. [PMID: 34576750 PMCID: PMC8464834 DOI: 10.3390/microorganisms9091856] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 01/26/2023] Open
Abstract
Listeria monocytogenes is the etiological agent of listeriosis, a foodborne illness associated with high hospitalizations and mortality rates. This bacterium can persist in food associated environments for years with isolates being increasingly linked to outbreaks. This review presents a discussion of genomes of Listeria monocytogenes which are commonly regarded as persisters within food production environments, as well as genes which are involved in mechanisms aiding this phenotype. Although criteria for the detection of persistence remain undefined, the advent of whole genome sequencing (WGS) and the development of bioinformatic tools have revolutionized the ability to find closely related strains. These advancements will facilitate the identification of mechanisms responsible for persistence among indistinguishable genomes. In turn, this will lead to improved assessments of the importance of biofilm formation, adaptation to stressful conditions and tolerance to sterilizers in relation to the persistence of this bacterium, all of which have been previously associated with this phenotype. Despite much research being published around the topic of persistence, more insights are required to further elucidate the nature of true persistence and its implications for public health.
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Affiliation(s)
- Natalia Unrath
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
- Department of Microbiology, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland
| | - Guerrino Macori
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
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22
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Sharma P, Sirohi R, Tong YW, Kim SH, Pandey A. Metal and metal(loids) removal efficiency using genetically engineered microbes: Applications and challenges. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125855. [PMID: 34492804 DOI: 10.1016/j.jhazmat.2021.125855] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
The environment is being polluted in different many with metal and metalloid pollution, mostly due to anthropogenic activity, which is directly affecting human and environmental health. Metals and metalloids are highly toxic at low concentrations and contribute primarily to the survival equilibrium of activities in the environment. However, because of non-degradable, they persist in nature and these metal and metalloids bioaccumulate in the food chain. Genetically engineered microorganisms (GEMs) mediated techniques for the removal of metals and metalloids are considered an environmentally safe and economically feasible strategy. Various forms of GEMs, including fungi, algae, and bacteria have been produced by recombinant DNA and RNA technologies, which have been used to eliminate metal and metalloids compounds from the polluted areas. Besides, GEMs have the potentiality to produce enzymes and other metabolites that are capable of tolerating metals stress and detoxify the pollutants. Thus, the aim of this review is to discuss the use of GEMs as advanced tools to produce metabolites, signaling molecules, proteins through genetic expression during metal and metalloids interaction, which help in the breakdown of persistent pollutants in the environment.
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Affiliation(s)
- Pooja Sharma
- Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea
| | - Yen Wah Tong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Sang Hyoun Kim
- Department of Chemical and Environmental Engineering, Yonsei University, Seoul, Republic of Korea
| | - Ashok Pandey
- Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India; Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, Uttar Pradesh, India.
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23
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Pilkiewicz KR, Mayo ML. Magnetic induction inspires a schematic theory for crosstalk-driven relaxation dynamics in cells. Phys Rev E 2021; 103:042417. [PMID: 34005977 DOI: 10.1103/physreve.103.042417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/19/2021] [Indexed: 11/07/2022]
Abstract
Establishing formal mathematical analogies between disparate physical systems can be a powerful tool, allowing for the well studied behavior of one system to be directly translated into predictions about the behavior of another that may be harder to probe. In this paper we lay the foundation for such an analogy between the macroscale electrodynamics of simple magnetic circuits and the microscale chemical kinetics of transcriptional regulation in cells. By artificially allowing the inductor coils of the former to elastically expand under the action of their Lorentz pressure, we introduce nonlinearities into the system that we interpret through the lens of our analogy as a schematic model for the impact of crosstalk on the rates of gene expression near steady state. Synthetic plasmids introduced into a cell must compete for a finite pool of metabolic and enzymatic resources against a maelstrom of crisscrossing biological processes, and our theory makes sensible predictions about how this noisy background might impact the expression profiles of synthetic constructs without explicitly modeling the kinetics of numerous interconnected regulatory interactions. We conclude the paper with a discussion of how our theory might be expanded to a broader class of plasmid circuits and how our predictions might be tested experimentally.
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Affiliation(s)
- Kevin R Pilkiewicz
- U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, USA
| | - Michael L Mayo
- U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi 39180, USA
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24
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Han JH, Jung ST, Oh MK. Improved Yield of Recombinant Protein via Flagella Regulator Deletion in Escherichia coli. Front Microbiol 2021; 12:655072. [PMID: 33790884 PMCID: PMC8005581 DOI: 10.3389/fmicb.2021.655072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Protein production requires a significant amount of intracellular energy. Eliminating the flagella has been proposed to help Escherichia coli improve protein production by reducing energy consumption. In this study, the gene encoding a subunit of FlhC, a master regulator of flagella assembly, was deleted to reduce the expression of flagella-related genes. FlhC knockout in the ptsG-deleted strain triggered significant growth retardation with increased ATP levels and a higher NADPH/NADP+ ratio. Metabolic flux analysis using a 13C-labeled carbon substrate showed increased fluxes toward the pentose phosphate and tricarboxylic acid cycle pathways in the flhC- and ptsG-deleted strains. Introduction of a high copy number plasmid or overexpression of the recombinant protein in this strain restored growth rate without increasing glucose consumption. These results suggest that the metabolic burden caused by flhC deletion was resolved by recombinant protein production. The recombinant enhanced green fluorescent protein yield per glucose consumption increased 1.81-fold in the flhC mutant strain. Thus, our study demonstrates that high-yield production of the recombinant protein was achieved with reduced flagella formation.
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Affiliation(s)
- Jae-Ho Han
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
| | - Sang Taek Jung
- BK21 Graduate Program, Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul, South Korea
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25
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Köstlbacher S, Collingro A, Halter T, Domman D, Horn M. Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria. Curr Biol 2021; 31:346-357.e3. [PMID: 33157023 PMCID: PMC7846284 DOI: 10.1016/j.cub.2020.10.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/30/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022]
Abstract
Plasmids are important in microbial evolution and adaptation to new environments. Yet, carrying a plasmid can be costly, and long-term association of plasmids with their hosts is poorly understood. Here, we provide evidence that the Chlamydiae, a phylum of strictly host-associated intracellular bacteria, have coevolved with their plasmids since their last common ancestor. Current chlamydial plasmids are amalgamations of at least one ancestral plasmid and a bacteriophage. We show that the majority of plasmid genes are also found on chromosomes of extant chlamydiae. The most conserved plasmid gene families are predominantly vertically inherited, while accessory plasmid gene families show significantly increased mobility. We reconstructed the evolutionary history of plasmid gene content of an entire bacterial phylum over a period of around one billion years. Frequent horizontal gene transfer and chromosomal integration events illustrate the pronounced impact of coevolution with these extrachromosomal elements on bacterial genome dynamics in host-dependent microbes.
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Affiliation(s)
- Stephan Köstlbacher
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, Vienna 1090, Austria
| | - Astrid Collingro
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, Vienna 1090, Austria
| | - Tamara Halter
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, Vienna 1090, Austria
| | - Daryl Domman
- Wellcome Sanger Institute, Parasites and Microbes Programme, Hinxton, Cambridge CB10 1SA, UK; Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Matthias Horn
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Althanstrasse 14, Vienna 1090, Austria.
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26
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Bohnenkamp AC, Kruis AJ, Mars AE, Wijffels RH, van der Oost J, Kengen SWM, Weusthuis RA. Multilevel optimisation of anaerobic ethyl acetate production in engineered Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:65. [PMID: 32280373 PMCID: PMC7137189 DOI: 10.1186/s13068-020-01703-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/25/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Ethyl acetate is a widely used industrial solvent that is currently produced by chemical conversions from fossil resources. Several yeast species are able to convert sugars to ethyl acetate under aerobic conditions. However, performing ethyl acetate synthesis anaerobically may result in enhanced production efficiency, making the process economically more viable. RESULTS We engineered an E. coli strain that is able to convert glucose to ethyl acetate as the main fermentation product under anaerobic conditions. The key enzyme of the pathway is an alcohol acetyltransferase (AAT) that catalyses the formation of ethyl acetate from acetyl-CoA and ethanol. To select a suitable AAT, the ethyl acetate-forming capacities of Atf1 from Saccharomyces cerevisiae, Eat1 from Kluyveromyces marxianus and Eat1 from Wickerhamomyces anomalus were compared. Heterologous expression of the AAT-encoding genes under control of the inducible LacI/T7 and XylS/Pm promoters allowed optimisation of their expression levels. CONCLUSION Engineering efforts on protein and fermentation level resulted in an E. coli strain that anaerobically produced 42.8 mM (3.8 g/L) ethyl acetate from glucose with an unprecedented efficiency, i.e. 0.48 C-mol/C-mol or 72% of the maximum pathway yield.
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Affiliation(s)
- Anna C. Bohnenkamp
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Aleksander J. Kruis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Astrid E. Mars
- Biobased Products, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Rene H. Wijffels
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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27
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Schäfer L, Karande R, Bühler B. Maximizing Biocatalytic Cyclohexane Hydroxylation by Modulating Cytochrome P450 Monooxygenase Expression in P. taiwanensis VLB120. Front Bioeng Biotechnol 2020; 8:140. [PMID: 32175317 PMCID: PMC7056670 DOI: 10.3389/fbioe.2020.00140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/11/2020] [Indexed: 01/31/2023] Open
Abstract
Cytochrome P450 monooxygenases (Cyps) effectively catalyze the regiospecific oxyfunctionalization of inert C-H bonds under mild conditions. Due to their cofactor dependency and instability in isolated form, oxygenases are preferably applied in living microbial cells with Pseudomonas strains constituting potent host organisms for Cyps. This study presents a holistic genetic engineering approach, considering gene dosage, transcriptional, and translational levels, to engineer an effective Cyp-based whole-cell biocatalyst, building on recombinant Pseudomonas taiwanensis VLB120 for cyclohexane hydroxylation. A lac-based regulation system turned out to be favorable in terms of orthogonality to the host regulatory network and enabled a remarkable specific whole-cell activity of 34 U gCDW -1. The evaluation of different ribosomal binding sites (RBSs) revealed that a moderate translation rate was favorable in terms of the specific activity. An increase in gene dosage did only slightly elevate the hydroxylation activity, but severely impaired growth and resulted in a large fraction of inactive Cyp. Finally, the introduction of a terminator reduced leakiness. The optimized strain P. taiwanensis VLB120 pSEVA_Cyp allowed for a hydroxylation activity of 55 U gCDW -1. Applying 5 mM cyclohexane, molar conversion and biomass-specific yields of 82.5% and 2.46 mmolcyclohexanol gbiomass -1 were achieved, respectively. The strain now serves as a platform to design in vivo cascades and bioprocesses for the production of polymer building blocks such as ε-caprolactone.
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Affiliation(s)
- Lisa Schäfer
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Rohan Karande
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research-UFZ, Leipzig, Germany
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Gomes L, Monteiro G, Mergulhão F. The Impact of IPTG Induction on Plasmid Stability and Heterologous Protein Expression by Escherichia coli Biofilms. Int J Mol Sci 2020; 21:ijms21020576. [PMID: 31963160 PMCID: PMC7013871 DOI: 10.3390/ijms21020576] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 11/30/2022] Open
Abstract
This work assesses the effect of chemical induction with isopropyl β-D-1-thiogalactopyranoside (IPTG) on the expression of enhanced green fluorescent protein (eGFP) by planktonic and biofilm cells of Escherichia coli JM109(DE3) transformed with a plasmid containing a T7 promoter. It was shown that induction negatively affected the growth and viability of planktonic cultures, and eGFP production did not increase. Heterologous protein production was not limited by gene dosage or by transcriptional activity. Results suggest that plasmid maintenance at high copy number imposes a metabolic burden that precludes high level expression of the heterologous protein. In biofilm cells, the inducer avoided the overall decrease in the amount of expressed eGFP, although this was not correlated with the gene dosage. Higher specific production levels were always attained with biofilm cells and it seems that while induction of biofilm cells shifts their metabolism towards the maintenance of heterologous protein concentration, in planktonic cells the cellular resources are directed towards plasmid replication and growth.
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Affiliation(s)
- Luciana Gomes
- LEPABE—Department of Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal;
| | - Gabriel Monteiro
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - Filipe Mergulhão
- LEPABE—Department of Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal;
- Correspondence: ; Tel.: +351-225081668
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Kruis AJ, Bohnenkamp AC, Nap B, Nielsen J, Mars AE, Wijffels RH, van der Oost J, Kengen SWM, Weusthuis RA. From Eat to trEat: engineering the mitochondrial Eat1 enzyme for enhanced ethyl acetate production in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:76. [PMID: 32328168 PMCID: PMC7168974 DOI: 10.1186/s13068-020-01711-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/04/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Genetic engineering of microorganisms has become a common practice to establish microbial cell factories for a wide range of compounds. Ethyl acetate is an industrial solvent that is used in several applications, mainly as a biodegradable organic solvent with low toxicity. While ethyl acetate is produced by several natural yeast species, the main mechanism of production has remained elusive until the discovery of Eat1 in Wickerhamomyces anomalus. Unlike other yeast alcohol acetyl transferases (AATs), Eat1 is located in the yeast mitochondria, suggesting that the coding sequence contains a mitochondrial pre-sequence. For expression in prokaryotic hosts such as E. coli, expression of heterologous proteins with eukaryotic signal sequences may not be optimal. RESULTS Unprocessed and synthetically truncated eat1 variants of Kluyveromyces marxianus and Wickerhamomyces anomalus have been compared in vitro regarding enzyme activity and stability. While the specific activity remained unaffected, half-life improved for several truncated variants. The same variants showed better performance regarding ethyl acetate production when expressed in E. coli. CONCLUSION By analysing and predicting the N-terminal pre-sequences of different Eat1 proteins and systematically trimming them, the stability of the enzymes in vitro could be improved, leading to an overall improvement of in vivo ethyl acetate production in E. coli. Truncated variants of eat1 could therefore benefit future engineering approaches towards efficient ethyl acetate production.
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Affiliation(s)
- Aleksander J. Kruis
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Anna C. Bohnenkamp
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bram Nap
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jochem Nielsen
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Astrid E. Mars
- Biobased Products, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Rene H. Wijffels
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Vecchione S, Fritz G. CRIMoClo plasmids for modular assembly and orthogonal chromosomal integration of synthetic circuits in Escherichia coli. J Biol Eng 2019; 13:92. [PMID: 31798686 PMCID: PMC6883643 DOI: 10.1186/s13036-019-0218-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/23/2019] [Indexed: 01/09/2023] Open
Abstract
Background Synthetic biology heavily depends on rapid and simple techniques for DNA engineering, such as Ligase Cycling Reaction (LCR), Gibson assembly and Golden Gate assembly, all of which allow for fast, multi-fragment DNA assembly. A major enhancement of Golden Gate assembly is represented by the Modular Cloning (MoClo) system that allows for simple library propagation and combinatorial construction of genetic circuits from reusable parts. Yet, one limitation of the MoClo system is that all circuits are assembled in low- and medium copy plasmids, while a rapid route to chromosomal integration is lacking. To overcome this bottleneck, here we took advantage of the conditional-replication, integration, and modular (CRIM) plasmids, which can be integrated in single copies into the chromosome of Escherichia coli and related bacteria by site-specific recombination at different phage attachment (att) sites. Results By combining the modularity of the MoClo system with the CRIM plasmids features we created a set of 32 novel CRIMoClo plasmids and benchmarked their suitability for synthetic biology applications. Using CRIMoClo plasmids we assembled and integrated a given genetic circuit into four selected phage attachment sites. Analyzing the behavior of these circuits we found essentially identical expression levels, indicating orthogonality of the loci. Using CRIMoClo plasmids and four different reporter systems, we illustrated a framework that allows for a fast and reliable sequential integration at the four selected att sites. Taking advantage of four resistance cassettes the procedure did not require recombination events between each round of integration. Finally, we assembled and genomically integrated synthetic ECF σ factor/anti-σ switches with high efficiency, showing that the growth defects observed for circuits encoded on medium-copy plasmids were alleviated. Conclusions The CRIMoClo system enables the generation of genetic circuits from reusable, MoClo-compatible parts and their integration into 4 orthogonal att sites into the genome of E. coli. Utilizing four different resistance modules the CRIMoClo system allows for easy, fast, and reliable multiple integrations. Moreover, utilizing CRIMoClo plasmids and MoClo reusable parts, we efficiently integrated and alleviated the toxicity of plasmid-borne circuits. Finally, since CRIMoClo framework allows for high flexibility, it is possible to utilize plasmid-borne and chromosomally integrated circuits simultaneously. This increases our ability to permute multiple genetic modules and allows for an easier design of complex synthetic metabolic pathways in E. coli.
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Affiliation(s)
- Stefano Vecchione
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, 35032 Marburg, Germany
| | - Georg Fritz
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, 35032 Marburg, Germany
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Sjöberg G, Guevara-Martínez M, van Maris AJA, Gustavsson M. Metabolic engineering applications of the Escherichia coli bacterial artificial chromosome. J Biotechnol 2019; 305:43-50. [PMID: 31505217 DOI: 10.1016/j.jbiotec.2019.09.002] [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: 05/02/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 11/25/2022]
Abstract
In metabolic engineering and synthetic biology, the number of genes expressed to achieve better production and pathway regulation in each strain is steadily increasing. The method of choice for expression in Escherichia coli is usually one or several multi-copy plasmids. Meanwhile, the industry standard for long-term, robust production is chromosomal integration of the desired genes. Despite recent advances, genetic manipulation of the bacterial chromosome remains more time consuming than plasmid construction. To allow screening of different metabolic engineering strategies at a level closer to industry while maintaining the molecular-biology advantages of plasmid-based expression, we have investigated the single-copy bacterial artificial chromosome (BAC) as a development tool for metabolic engineering. Using (R)-3-hydroxybutyrate as a model product, we show that BAC can outperform multi-copy plasmids in terms of yield, productivity and specific growth rate, with respective increases of 12%, 18%, and 5%. We both show that gene expression by the BAC simplifies pathway optimization and that the phenotype of pathway expression from BAC is very close to that of chromosomal expression. From these results, we conclude that the BAC can provide a simple platform for performing pathway design and optimization.
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Affiliation(s)
- Gustav Sjöberg
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mónica Guevara-Martínez
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden; Faculty of Science and Technology, Center of Biotechnology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Martin Gustavsson
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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Hingston P, Brenner T, Truelstrup Hansen L, Wang S. Comparative Analysis of Listeria monocytogenes Plasmids and Expression Levels of Plasmid-Encoded Genes during Growth under Salt and Acid Stress Conditions. Toxins (Basel) 2019; 11:toxins11070426. [PMID: 31330827 PMCID: PMC6669625 DOI: 10.3390/toxins11070426] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 01/31/2023] Open
Abstract
Listeria monocytogenes strains are known to harbour plasmids that confer resistance to sanitizers, heavy metals, and antibiotics; however, very little research has been conducted into how plasmids may influence L. monocytogenes’ ability to tolerate food-related stresses. To investigate this, a library (n = 93) of L. monocytogenes plasmid sequences were compared. Plasmid sequences were divided into two groups (G1 and G2) based on a repA phylogeny. Twenty-six unique plasmid types were observed, with 13 belonging to each of the two repA-based groups. G1 plasmids were significantly (p < 0.05) smaller than G2 plasmids but contained a larger diversity of genes. The most prevalent G1 plasmid (57,083 bp) was observed in 26 strains from both Switzerland and Canada and a variety of serotypes. Quantitative PCR (qPCR) revealed a >2-fold induction of plasmid-contained genes encoding an NADH peroxidase, cadmium ATPase, multicopper oxidase, and a ClpL chaperone protein during growth under salt (6% NaCl) and acid conditions (pH 5) and ProW, an osmolyte transporter, under salt stress conditions. No differences in salt and acid tolerance were observed between plasmid-cured and wildtype strains. This work highlights the abundance of specific plasmid types among food-related L. monocytogenes strains, the unique characteristics of G1 and G2 plasmids, and the possible contributions of plasmids to L. monocytogenes tolerance to food-related stresses.
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Affiliation(s)
- Patricia Hingston
- Department of Food, Nutrition and Health, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Thomas Brenner
- Department of Food, Nutrition and Health, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | | - Siyun Wang
- Department of Food, Nutrition and Health, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Mohamed ET, Mundhada H, Landberg J, Cann I, Mackie RI, Nielsen AT, Herrgård MJ, Feist AM. Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution. Microb Cell Fact 2019; 18:116. [PMID: 31255177 PMCID: PMC6599523 DOI: 10.1186/s12934-019-1165-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 06/22/2019] [Indexed: 01/01/2023] Open
Abstract
Background Sucrose is an attractive industrial carbon source due to its abundance and the fact that it can be cheaply generated from sources such as sugarcane. However, only a few characterized Escherichia coli strains are able to metabolize sucrose, and those that can are typically slow growing or pathogenic strains. Methods To generate a platform strain capable of efficiently utilizing sucrose with a high growth rate, adaptive laboratory evolution (ALE) was utilized to evolve engineered E. coli K-12 MG1655 strains containing the sucrose utilizing csc genes (cscB, cscK, cscA) alongside the native sucrose consuming E. coli W. Results Evolved K-12 clones displayed an increase in growth and sucrose uptake rates of 1.72- and 1.40-fold on sugarcane juice as compared to the original engineered strains, respectively, while E. coli W clones showed a 1.4-fold increase in sucrose uptake rate without a significant increase in growth rate. Whole genome sequencing of evolved clones and populations revealed that two genetic regions were frequently mutated in the K-12 strains; the global transcription regulatory genes rpoB and rpoC, and the metabolic region related to a pyrimidine biosynthetic deficiency in K-12 attributed to pyrE expression. These two mutated regions have been characterized to confer a similar benefit when glucose is the main carbon source, and reverse engineering revealed the same causal advantages on M9 sucrose. Additionally, the most prevalent mutation found in the evolved E. coli W lineages was the inactivation of the cscR gene, the transcriptional repression of sucrose uptake genes. Conclusion The generated K-12 and W platform strains, and the specific sets of mutations that enable their phenotypes, are available as valuable tools for sucrose-based industrial bioproduction in the facile E. coli chassis. Electronic supplementary material The online version of this article (10.1186/s12934-019-1165-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elsayed T Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Hemanshu Mundhada
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Jenny Landberg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Isaac Cann
- Department of Animal Sciences, Institute for Genomic Biology and Energy Biosciences Institute, University of Illinois, Urbana, IL, 61801, USA
| | - Roderick I Mackie
- Department of Animal Sciences, Institute for Genomic Biology and Energy Biosciences Institute, University of Illinois, Urbana, IL, 61801, USA
| | - Alex Toftgaard Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Lyngby, 2800 Kgs, Denmark. .,Department of Bioengineering, University of California, 9500 Gilman Drive La Jolla, San Diego, CA, 92093, USA.
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Folarin O, Nesbeth D, Ward JM, Keshavarz-Moore E. Application of Plasmid Engineering to Enhance Yield and Quality of Plasmid for Vaccine and Gene Therapy. Bioengineering (Basel) 2019; 6:bioengineering6020054. [PMID: 31248216 PMCID: PMC6631426 DOI: 10.3390/bioengineering6020054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 11/19/2022] Open
Abstract
There is an increased interest in plasmid DNA as therapeutics. This is evident in the number of ongoing clinical trials involving the use of plasmid DNA. In order to be an effective therapeutic, high yield and high level of supercoiling are required. From the bioprocessing point of view, the supercoiling level potentially has an impact on the ease of downstream processing. We approached meeting these requirements through plasmid engineering. A 7.2 kb plasmid was developed by the insertion of a bacteriophage Mu strong gyrase-binding sequence (Mu-SGS) to a 6.8 kb pSVβ-Gal and it was used to transform four different E. coli strains, and cultured in order to investigate the Mu-SGS effect and dependence on strain. There was an increase of over 20% in the total plasmid yield with pSVβ-Gal398 in two of the strains. The supercoiled topoisomer content was increased by 5% in both strains leading to a 27% increase in the overall yield. The extent of supercoiling was examined using superhelical density (σ) quantification with pSVβ-Gal398 maintaining a superhelical density of −0.022, and pSVβ-Gal −0.019, in both strains. This study has shown that plasmid modification with the Mu-phage SGS sequence has a beneficial effect on improving not only the yield of total plasmid but also the supercoiled topoisomer content of therapeutic plasmid DNA during bioprocessing.
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Affiliation(s)
- Olusegun Folarin
- Advanced Center for Biochemical Engineering, University College London, London WC1E 6BT, UK.
| | - Darren Nesbeth
- Advanced Center for Biochemical Engineering, University College London, London WC1E 6BT, UK.
| | - John M Ward
- Advanced Center for Biochemical Engineering, University College London, London WC1E 6BT, UK.
| | - Eli Keshavarz-Moore
- Advanced Center for Biochemical Engineering, University College London, London WC1E 6BT, UK.
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Long D, Zhu LL, Du FL, Xiang TX, Wan LG, Wei DD, Zhang W, Liu Y. Phenotypical profile and global transcriptomic profile of Hypervirulent Klebsiella pneumoniae due to carbapenemase-encoding plasmid acquisition. BMC Genomics 2019; 20:480. [PMID: 31185888 PMCID: PMC6558890 DOI: 10.1186/s12864-019-5705-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/16/2019] [Indexed: 12/13/2022] Open
Abstract
Background Plasmids play an vital role in driving the rapid global spread of antimicrobial resistance and adaptation to changing ambient conditions. It has been suggested that the presence of plasmids can pose tremendous impacts on the host physiology. However, little is known regarding the contributions of carbapenemase-encoding plasmid carriage on the physiology and pathogenicity of hypervirulent K. pneumoniae (hvKP). Results Here we performed a transcriptomic analysis of hvKP with or without carbapenemase-encoding plasmid p24835-NDM5. The results had shown 683 genes with differential expression (false discovery rate, ≤0.001; > 2-fold change), of which 107 were up-regulated and 576 were down-regulated. Gene groups with functions relating to carbohydrate metabolism and multidrug efflux system were increased in genes with increased expression, and those relating to capsule biosynthesis and virulence factors were increased in the genes with decreased expression. In agreement with these changes, survival rate of TfpNDM-hvKP in the presence of normal human serum decreased, and competitive index (CI values) indicated significant fitness defects in the plasmid-carrying hvKP strain when co-cultured with its plasmid-free isogenic ancestor and the ATCC control. Moreover, the p24835-NDM5-containing hvKP strain retained its high neutrophil-mediated phagocytosis and murine lethality. Conclusion These data indicate that hvKP responds to carbapenemase-encoding plasmid by altering the expression of genes involved in carbohydrate metabolism, antibiotic resistance, capsule biosynthesis and virulence expression. Apart from antibiotic resistance selective advantages, carbapenemase-encoding plasmid carriage may also lead to virulence change or adaption to specific habitats in hvKP strain. Electronic supplementary material The online version of this article (10.1186/s12864-019-5705-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dan Long
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Yong wai zheng jie No. 17, Nanchang, 330006, People's Republic of China
| | - Lan-Lan Zhu
- Department of Respiratory, First Affiliated Hospital of Nanchang University, Nanchang University, Yong wai zheng jie No. 17, Nanchang, 330006, People's Republic of China
| | - Fang-Ling Du
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Yong wai zheng jie No. 17, Nanchang, 330006, People's Republic of China
| | - Tian-Xin Xiang
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Yong wai zheng jie No. 17, Nanchang, 330006, People's Republic of China
| | - La-Gen Wan
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Yong wai zheng jie No. 17, Nanchang, 330006, People's Republic of China
| | - Dan-Dan Wei
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Yong wai zheng jie No. 17, Nanchang, 330006, People's Republic of China
| | - Wei Zhang
- Department of Respiratory, First Affiliated Hospital of Nanchang University, Nanchang University, Yong wai zheng jie No. 17, Nanchang, 330006, People's Republic of China
| | - Yang Liu
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Yong wai zheng jie No. 17, Nanchang, 330006, People's Republic of China.
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Boock JT, Freedman AJE, Tompsett GA, Muse SK, Allen AJ, Jackson LA, Castro-Dominguez B, Timko MT, Prather KLJ, Thompson JR. Engineered microbial biofuel production and recovery under supercritical carbon dioxide. Nat Commun 2019; 10:587. [PMID: 30718495 PMCID: PMC6361901 DOI: 10.1038/s41467-019-08486-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/11/2019] [Indexed: 12/16/2022] Open
Abstract
Culture contamination, end-product toxicity, and energy efficient product recovery are long-standing bioprocess challenges. To solve these problems, we propose a high-pressure fermentation strategy, coupled with in situ extraction using the abundant and renewable solvent supercritical carbon dioxide (scCO2), which is also known for its broad microbial lethality. Towards this goal, we report the domestication and engineering of a scCO2-tolerant strain of Bacillus megaterium, previously isolated from formation waters from the McElmo Dome CO2 field, to produce branched alcohols that have potential use as biofuels. After establishing induced-expression under scCO2, isobutanol production from 2-ketoisovalerate is observed with greater than 40% yield with co-produced isopentanol. Finally, we present a process model to compare the energy required for our process to other in situ extraction methods, such as gas stripping, finding scCO2 extraction to be potentially competitive, if not superior. End-product toxicity, culture contamination, and energy efficient product recovery are long-standing issues in bioprocessing. Here, the authors address these problems using a fermentation strategy that combines microbial production of branched alcohols with supercritical carbon dioxide extraction.
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Affiliation(s)
- Jason T Boock
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, OH, 45056, USA
| | - Adam J E Freedman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Geoffrey A Tompsett
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Sarah K Muse
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Audrey J Allen
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Luke A Jackson
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Bernardo Castro-Dominguez
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.,Department of Chemical Engineering, University of Bath, Bath, BA2 7AY, UK
| | - Michael T Timko
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Janelle R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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da Mota FF, Castro DP, Vieira CS, Gumiel M, de Albuquerque JP, Carels N, Azambuja P. In vitro Trypanocidal Activity, Genomic Analysis of Isolates, and in vivo Transcription of Type VI Secretion System of Serratia marcescens Belonging to the Microbiota of Rhodnius prolixus Digestive Tract. Front Microbiol 2019; 9:3205. [PMID: 30733713 PMCID: PMC6353840 DOI: 10.3389/fmicb.2018.03205] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Serratia marcescens is a bacterium with the ability to colonize several niches, including some eukaryotic hosts. S. marcescens have been recently found in the gut of hematophagous insects that act as parasite vectors, such as Anopheles, Rhodnius, and Triatoma. While some S. marcescens strains have been reported as symbiotic or pathogenic to other insects, the role of S. marcescens populations from the gut microbiota of Rhodnius prolixus, a vector of Chagas’ disease, remains unknown. Bacterial colonies from R. prolixus gut were isolated on BHI agar. After BOX-PCR fingerprinting, the genomic sequences of two isolates RPA1 and RPH1 were compared to others S. marcescens from the NCBI database in other to estimate their evolutionary divergence. The in vitro trypanolytic activity of these two bacterial isolates against Trypanosoma cruzi (DM28c clone and Y strain) was assessed by microscopy. In addition, the gene expression of type VI secretion system (T6SS) was detected in vivo by RT-PCR. Comparative genomics of RPA1 and RPH1 revealed, besides plasmid presence and genomic islands, genes related to motility, attachment, and quorum sensing in both genomes while genes for urea hydrolysis and type II secretion system (T2SS) were found only in the RPA1 genome. The in vitro trypanolytic activity of both S. marcescens strains was stronger in their stationary phases of growth than in their exponential ones, with 65–70 and 85–90% of epimastigotes (Dm28c clone and Y strain, respectively) being lysed after incubation with RPA1 or RPH1 in stationary phase. Although T6SS transcripts were detected in guts up to 40 days after feeding (DAF), R. prolixus morbidity or mortality did not appear to be affected. In this report, we made available two trypanolytic S. marcescens strains from R. prolixus gut to the scientific community together with their genomic sequences. Here, we describe their genomic features with the purpose of bringing new insights into the S. marcescens adaptations for colonization of the specific niche of triatomine guts. This study provides the basis for a better understanding of the role of S. marcescens in the microbiota of R. prolixus gut as a potential antagonist of T. cruzi in this complex system.
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Affiliation(s)
- Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil
| | - Daniele Pereira Castro
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil.,Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Cecilia Stahl Vieira
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Marcia Gumiel
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Julia Peixoto de Albuquerque
- Laboratório de Enteropatógenos, Microbiologia Veterinária e de Alimentos, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense (MIP/UFF), Rio de Janeiro, Brazil
| | - Nicolas Carels
- Laboratório de Modelagem de Sistemas Biológicos, National Institute for Science and Technology on Innovation in Neglected Diseases (INCT-IDN), Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz (CDTS/FIOCRUZ), Rio de Janeiro, Brazil
| | - Patricia Azambuja
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil.,Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
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38
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Meyer AJ, Segall-Shapiro TH, Glassey E, Zhang J, Voigt CA. Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors. Nat Chem Biol 2018; 15:196-204. [DOI: 10.1038/s41589-018-0168-3] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/05/2018] [Indexed: 11/09/2022]
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39
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Papić L, Rivas J, Toledo S, Romero J. Double-stranded RNA production and the kinetics of recombinant Escherichia coli HT115 in fed-batch culture. ACTA ACUST UNITED AC 2018; 20:e00292. [PMID: 30568886 PMCID: PMC6288044 DOI: 10.1016/j.btre.2018.e00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/28/2017] [Accepted: 10/29/2018] [Indexed: 12/28/2022]
Abstract
dsRNA production was growth-associated according to Luedeking-Piret model. dsRNA/biomass yield was 0.06 g g−1, the same value in bacth and fed-batch culture. dsRNA productivity was 37% higher in fed-batch fermentation. Production of dsRNA occurred while the bacteria were actively multiplying.
Double-stranded RNA can induce interference processes. The specificity of this system raises the possibility of using dsRNA for therapeutic applications targeting viral diseases. Escherichia coli HT115 (DE3) has been widely used to produce dsRNA; however, the kinetics of dsRNA production and the relationship between dsRNA and biomass remain unknown. Our aims were to study the kinetics of dsRNA production and to improve dsRNA productivity with fed-batch technology. The results revealed that the production of dsRNA was growth-associated. In batch fermentation, the dsRNA/biomass yield remained close to 0.06 g·g−1, with a maximum productivity of 11.1 mg l−1 h−1 at 10 h of culture. In fed-batch fermentation, the yield was 0.06 g g−1, with a maximum dsRNA productivity of 15.2 mg l−1 h−1 at the end of the feed (12 h). Therefore, to increase the production of dsRNA, it is necessary to enhance the biomass that produces the recombinant nucleic acid.
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Affiliation(s)
- Ljubomir Papić
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile. El Líbano 5524, Macul, Santiago, Chile
- Doctorado en Acuicultura, Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, Chile
| | - José Rivas
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile. El Líbano 5524, Macul, Santiago, Chile
| | - Soledad Toledo
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile. El Líbano 5524, Macul, Santiago, Chile
| | - Jaime Romero
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile. El Líbano 5524, Macul, Santiago, Chile
- Corresponding author.
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40
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Pontrelli S, Fricke RCB, Sakurai SSM, Putri SP, Fitz-Gibbon S, Chung M, Wu HY, Chen YJ, Pellegrini M, Fukusaki E, Liao JC. Directed strain evolution restructures metabolism for 1-butanol production in minimal media. Metab Eng 2018; 49:153-163. [PMID: 30107263 DOI: 10.1016/j.ymben.2018.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 06/30/2018] [Accepted: 08/10/2018] [Indexed: 01/02/2023]
Abstract
Engineering a microbial strain for production sometimes entails metabolic modifications that impair essential physiological processes for growth or production. Restoring these functions may require amending a variety of non-obvious physiological networks, and thus, rational design strategies may not be practical. Here we demonstrate that growth and production may be restored by evolution that repairs impaired metabolic function. Furthermore, we use genomics, metabolomics and proteomics to identify several underlying mutations and metabolic perturbations that allow metabolism to repair. Previously, high titers of butanol production were achieved by Escherichia coli using a growth-coupled, modified Clostridial CoA-dependent pathway after all native fermentative pathways were deleted. However, production was only observed in rich media. Native metabolic function of the host was unable to support growth and production in minimal media. We use directed cell evolution to repair this phenotype and observed improved growth, titers and butanol yields. We found a mutation in pcnB which resulted in decreased plasmid copy numbers and pathway enzymes to balance resource utilization. Increased protein abundance was measured for biosynthetic pathways, glycolytic enzymes have increased activity, and adenosyl energy charge was increased. We also found mutations in the ArcAB two-component system and integration host factor (IHF) that tune redox metabolism to alter byproduct formation. These results demonstrate that directed strain evolution can enable systematic adaptations to repair metabolic function and enhance microbial production. Furthermore, these results demonstrate the versatile repair capabilities of cell metabolism and highlight important aspects of cell physiology that are required for production in minimal media.
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Affiliation(s)
- Sammy Pontrelli
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles (UCLA), United States
| | - Riley C B Fricke
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles (UCLA), United States
| | | | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
| | - Sorel Fitz-Gibbon
- Institute of Genomics and Proteomics, University of California, Los Angeles, United States
| | - Matthew Chung
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles (UCLA), United States
| | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Matteo Pellegrini
- Institute of Genomics and Proteomics, University of California, Los Angeles, United States; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, United States
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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41
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Worsch A, Eggimann FK, Girhard M, von Bühler CJ, Tieves F, Czaja R, Vogel A, Grumaz C, Sohn K, Lütz S, Kittelmann M, Urlacher VB. A novel cytochrome P450 mono-oxygenase from Streptomyces platensis resembles activities of human drug metabolizing P450s. Biotechnol Bioeng 2018; 115:2156-2166. [PMID: 29943426 DOI: 10.1002/bit.26781] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/28/2018] [Accepted: 06/18/2018] [Indexed: 12/18/2022]
Abstract
Cytochrome P450 mono-oxygenases (P450) are versatile enzymes which play essential roles in C-source assimilation, secondary metabolism, and in degradations of endo- and exogenous xenobiotics. In humans, several P450 isoforms constitute the largest part of phase I metabolizing enzymes and catalyze oxidation reactions which convert lipophilic xenobiotics, including drugs, to more water soluble species. Recombinant human P450s and microorganisms are applied in the pharmaceutical industry for the synthesis of drug metabolites for pharmacokinetics and toxicity studies. Compared to the membrane-bound eukaryotic P450s, prokaryotic ones exhibit some advantageous features, such as high stability and generally easier heterologous expression. Here, we describe a novel P450 from Streptomyces platensis DSM 40041 classified as CYP107L that efficiently converts several commercial drugs of various size and properties. This P450 was identified by screening of actinobacterial strains for amodiaquine and ritonavir metabolizing activities, followed by genome sequencing and expression of the annotated S. platensis P450s in Escherichia coli. Performance of CYP107L in biotransformations of amodiaquine, ritonavir, amitriptyline, and thioridazine resembles activities of the main human metabolizing P450s, namely CYPs 3A4, 2C8, 2C19, and 2D6. For application in the pharmaceutical industry, an E. coli whole-cell biocatalyst expressing CYP107L was developed and evaluated for preparative amodiaquine metabolite production.
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Affiliation(s)
- Anne Worsch
- Heinrich Heine University Düsseldorf, Institute of Biochemistry, Düsseldorf, Germany
| | | | - Marco Girhard
- Heinrich Heine University Düsseldorf, Institute of Biochemistry, Düsseldorf, Germany
| | - Clemens J von Bühler
- Heinrich Heine University Düsseldorf, Institute of Biochemistry, Düsseldorf, Germany.,Present address: Bayer AG, Drug Discovery, Pharmaceuticals DM, Wuppertal, Germany
| | - Florian Tieves
- Heinrich Heine University Düsseldorf, Institute of Biochemistry, Düsseldorf, Germany.,Present address: Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | | | - Christian Grumaz
- Department of Molecular Biotechnology, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Kai Sohn
- Department of Molecular Biotechnology, Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Stephan Lütz
- Novartis Pharma AG, Basel, Switzerland.,Present address:, Technische Universität Dortmund, Bio- und Chemieingenieurwesen, Bioprozesstechnik, Dortmund, Germany
| | | | - Vlada B Urlacher
- Heinrich Heine University Düsseldorf, Institute of Biochemistry, Düsseldorf, Germany
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42
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Soares A, Gomes LC, Mergulhão FJ. Comparing the Recombinant Protein Production Potential of Planktonic and Biofilm Cells. Microorganisms 2018; 6:E48. [PMID: 29794993 PMCID: PMC6027475 DOI: 10.3390/microorganisms6020048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 11/17/2022] Open
Abstract
Recombinant protein production in bacterial cells is commonly performed using planktonic cultures. However, the natural state for many bacteria is living in communities attached to surfaces forming biofilms. In this work, a flow cell system was used to compare the production of a model recombinant protein (enhanced green fluorescent protein, eGFP) between planktonic and biofilm cells. The fluorometric analysis revealed that when the system was in steady state, the average specific eGFP production from Escherichia coli biofilm cells was 10-fold higher than in planktonic cells. Additionally, epifluorescence microscopy was used to determine the percentage of eGFP-expressing cells in both planktonic and biofilm populations. In steady state, the percentage of planktonic-expressing cells oscillated around 5%, whereas for biofilms eGFP-expressing cells represented on average 21% of the total cell population. Therefore, the combination of fluorometric and microscopy data allowed us to conclude that E. coli biofilm cells can have a higher recombinant protein production capacity when compared to their planktonic counterparts.
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Affiliation(s)
- Alexandra Soares
- LEPABE-Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
| | - Luciana Calheiros Gomes
- LEPABE-Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
| | - Filipe José Mergulhão
- LEPABE-Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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43
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Dietel AK, Kaltenpoth M, Kost C. Convergent Evolution in Intracellular Elements: Plasmids as Model Endosymbionts. Trends Microbiol 2018; 26:755-768. [PMID: 29650391 DOI: 10.1016/j.tim.2018.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/14/2018] [Accepted: 03/21/2018] [Indexed: 11/29/2022]
Abstract
Endosymbionts are organisms that live inside the cells of other species. This lifestyle is ubiquitous across the tree of life and is featured by unicellular eukaryotes, prokaryotes, and by extrachromosomal genetic elements such as plasmids. Given that all of these elements dwell in the cytoplasm of their host cell, they should be subject to similar selection pressures. Here we show that strikingly similar features have evolved in both bacterial endosymbionts and plasmids. Since host and endosymbiont are often metabolically tightly intertwined, they are difficult to disentangle experimentally. We propose that using plasmids as tractable model systems can help to solve this problem, thus allowing fundamental questions to be experimentally addressed about the ecology and evolution of endosymbiotic interactions.
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Affiliation(s)
- Anne-Kathrin Dietel
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Martin Kaltenpoth
- Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, 55128 Mainz, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Current address: Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49069 Osnabrück, Germany.
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44
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Ramees TP, Dhama K, Karthik K, Rathore RS, Kumar A, Saminathan M, Tiwari R, Malik YS, Singh RK. Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control - a comprehensive review. Vet Q 2017; 37:136-161. [PMID: 28438095 DOI: 10.1080/01652176.2017.1323355] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Arcobacter has emerged as an important food-borne zoonotic pathogen, causing sometimes serious infections in humans and animals. Newer species of Arcobacter are being incessantly emerging (presently 25 species have been identified) with novel information on the evolutionary mechanisms and genetic diversity among different Arcobacter species. These have been reported from chickens, domestic animals (cattle, pigs, sheep, horses, dogs), reptiles (lizards, snakes and chelonians), meat (poultry, pork, goat, lamb, beef, rabbit), vegetables and from humans in different countries. Arcobacters are implicated as causative agents of diarrhea, mastitis and abortion in animals, while causing bacteremia, endocarditis, peritonitis, gastroenteritis and diarrhea in humans. Three species including A. butzleri, A. cryaerophilus and A. skirrowii are predominantly associated with clinical conditions. Arcobacters are primarily transmitted through contaminated food and water sources. Identification of Arcobacter by biochemical tests is difficult and isolation remains the gold standard method. Current diagnostic advances have provided various molecular methods for efficient detection and differentiation of the Arcobacters at genus and species level. To overcome the emerging antibiotic resistance problem there is an essential need to explore the potential of novel and alternative therapies. Strengthening of the diagnostic aspects is also suggested as in most cases Arcobacters goes unnoticed and hence the exact epidemiological status remains uncertain. This review updates the current knowledge and many aspects of this important food-borne pathogen, namely etiology, evolution and emergence, genetic diversity, epidemiology, the disease in animals and humans, public health concerns, and advances in its diagnosis, prevention and control.
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Affiliation(s)
- Thadiyam Puram Ramees
- a Division of Veterinary Public Health , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Kuldeep Dhama
- b Division of Pathology , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Kumaragurubaran Karthik
- c Central University Laboratory , Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - Ramswaroop Singh Rathore
- a Division of Veterinary Public Health , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Ashok Kumar
- a Division of Veterinary Public Health , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Mani Saminathan
- b Division of Pathology , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Ruchi Tiwari
- d Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences , UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura , India
| | - Yashpal Singh Malik
- e Division of Biological Standardization , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Raj Kumar Singh
- f ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
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45
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Abstract
Bacteria gain antibiotic resistance genes by horizontal acquisition of mobile genetic elements (MGE) from other lineages. Newly acquired MGEs are often poorly adapted causing intragenomic conflicts, resolved by compensatory adaptation of the chromosome, the MGE or reciprocal coadaptation. The footprints of such intragenomic coevolution are present in bacterial genomes, suggesting an important role promoting genomic integration of horizontally acquired genes, but direct experimental evidence of the process is limited. Here we show adaptive modulation of tetracycline resistance via intragenomic coevolution between Escherichia coli and the multi-drug resistant (MDR) plasmid RK2. Tetracycline treatments, including monotherapy or combination therapies with ampicillin, favoured de novo chromosomal resistance mutations coupled with mutations on RK2 impairing the plasmid-encoded tetracycline efflux-pump. These mutations together provided increased tetracycline resistance at reduced cost. Additionally, the chromosomal resistance mutations conferred cross-resistance to chloramphenicol. Reciprocal coadaptation was not observed under ampicillin-only or no antibiotic selection. Intragenomic coevolution can create genomes comprised of multiple replicons that together provide high-level, low-cost resistance, but the resulting co-dependence may limit the spread of coadapted MGEs to other lineages.
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46
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Song Y, Li J, Shin HD, Liu L, Du G, Chen J. Tuning the transcription and translation of L-amino acid deaminase in Escherichia coli improves α-ketoisocaproate production from L-leucine. PLoS One 2017; 12:e0179229. [PMID: 28662040 PMCID: PMC5491005 DOI: 10.1371/journal.pone.0179229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/25/2017] [Indexed: 11/19/2022] Open
Abstract
α-Ketoisocaproate (KIC) is used widely in the pharmaceutical and nutraceutical industries. In previous studies, we achieved a one-step biosynthesis of KIC from l-leucine, using an Escherichia coli whole-cell biocatalyst expressing an l-amino acid deaminase (l-AAD) from Proteus vulgaris. Herein, we report the fine-tuning of l-AAD gene expression in E. coli BL21 (DE3) at the transcriptional and translational levels to improve the KIC titer. By optimizing the plasmid origin with different copy numbers, modulating messenger RNA structure downstream of the initiation codon, and designing the sequences at the ribosome binding site, we increased biocatalyst activity to 31.77%, 24.89%, and 30.20%, respectively, above that achieved with BL21/pet28a-lad. The highest KIC titers reached 76.47 g·L-1, 80.29 g·L-1, and 81.41 g·L-1, respectively. Additionally, the integration of these three engineering strategies achieved an even higher KIC production of 86.55 g·L-1 and a higher l-leucine conversion rate of 94.25%. The enzyme-engineering strategies proposed herein may be generally applicable to the construction of other biocatalysts.
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Affiliation(s)
- Yang Song
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
| | - Hyun-dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, United States of America
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
| | - Jian Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Synergetic Innovation of Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
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47
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Wang Y, Penkul P, Milstein JN. Quantitative Localization Microscopy Reveals a Novel Organization of a High-Copy Number Plasmid. Biophys J 2017; 111:467-479. [PMID: 27508432 DOI: 10.1016/j.bpj.2016.06.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 05/24/2016] [Accepted: 06/29/2016] [Indexed: 12/13/2022] Open
Abstract
The maintenance of high-copy number plasmids within bacteria had been commonly thought to result from free diffusion and random segregation. Recent microscopy experiments, however, observed high-copy number plasmids clustering into discrete foci, which seemed to contradict this model, and hinted at an undiscovered active mechanism, as often found in low-copy number plasmids. We recently investigated the cellular organization of a ColE1-derivative plasmid in Escherichia coli bacteria using quantitative superresolved microscopy based on single-molecule localization in combination with single-molecule fluorescence in situ hybridization (smFISH). We observed that many of the plasmids aggregated into large clusters, although most of the plasmids were randomly distributed throughout the bacteria, minus an excluded volume about the chromosomal DNA. Our results indicate that neither of the previous models completely encompasses the behavior of high-copy number plasmids. We also found many plasmids within the chromosomal volume, providing further evidence that the nucleoid does not fully exclude DNA and RNA.
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Affiliation(s)
- Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, Arkansas; Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Paul Penkul
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Joshua N Milstein
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
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48
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Rodriguez A, Martínez JA, Millard P, Gosset G, Portais JC, Létisse F, Bolivar F. Plasmid-encoded biosynthetic genes alleviate metabolic disadvantages while increasing glucose conversion to shikimate in an engineeredEscherichia colistrain. Biotechnol Bioeng 2017; 114:1319-1330. [DOI: 10.1002/bit.26264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/17/2017] [Accepted: 02/08/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Alberto Rodriguez
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | - Juan A. Martínez
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | - Pierre Millard
- LISBP, Université de Toulouse, CNRS, INRA; INSA; Toulouse France
| | - Guillermo Gosset
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | | | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA; INSA; Toulouse France
| | - Francisco Bolivar
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
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Hingston P, Chen J, Dhillon BK, Laing C, Bertelli C, Gannon V, Tasara T, Allen K, Brinkman FSL, Truelstrup Hansen L, Wang S. Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold, Salt, Acid, or Desiccation Stress. Front Microbiol 2017; 8:369. [PMID: 28337186 PMCID: PMC5340757 DOI: 10.3389/fmicb.2017.00369] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/22/2017] [Indexed: 01/11/2023] Open
Abstract
The human pathogen Listeria monocytogenes is a large concern in the food industry where its continuous detection in food products has caused a string of recalls in North America and Europe. Most recognized for its ability to grow in foods during refrigerated storage, L. monocytogenes can also tolerate several other food-related stresses with some strains possessing higher levels of tolerances than others. The objective of this study was to use a combination of phenotypic analyses and whole genome sequencing to elucidate potential relationships between L. monocytogenes genotypes and food-related stress tolerance phenotypes. To accomplish this, 166 L. monocytogenes isolates were sequenced and evaluated for their ability to grow in cold (4°C), salt (6% NaCl, 25°C), and acid (pH 5, 25°C) stress conditions as well as survive desiccation (33% RH, 20°C). The results revealed that the stress tolerance of L. monocytogenes is associated with serotype, clonal complex (CC), full length inlA profiles, and the presence of a plasmid which was identified in 55% of isolates. Isolates with full length inlA exhibited significantly (p < 0.001) enhanced cold tolerance relative to those harboring a premature stop codon (PMSC) in this gene. Similarly, isolates possessing a plasmid demonstrated significantly (p = 0.013) enhanced acid tolerance. We also identified nine new L. monocytogenes sequence types, a new inlA PMSC, and several connections between CCs and the presence/absence or variations of specific genetic elements. A whole genome single-nucleotide-variants phylogeny revealed sporadic distribution of tolerant isolates and closely related sensitive and tolerant isolates, highlighting that minor genetic differences can influence the stress tolerance of L. monocytogenes. Specifically, a number of cold and desiccation sensitive isolates contained PMSCs in σB regulator genes (rsbS, rsbU, rsbV). Collectively, the results suggest that knowing the sequence type of an isolate in addition to screening for the presence of full-length inlA and a plasmid, could help food processors and food agency investigators determine why certain isolates might be persisting in a food processing environment. Additionally, increased sequencing of L. monocytogenes isolates in combination with stress tolerance profiling, will enhance the ability to identify genetic elements associated with higher risk strains.
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Affiliation(s)
- Patricia Hingston
- Department of Food, Nutrition, and Health, University of British ColumbiaVancouver, BC, Canada
| | - Jessica Chen
- Department of Food, Nutrition, and Health, University of British ColumbiaVancouver, BC, Canada
| | - Bhavjinder K. Dhillon
- Department of Molecular Biology and Biochemistry, Simon Fraser UniversityBurnaby, BC, Canada
| | - Chad Laing
- Laboratory for Foodborne Zoonoses, Public Health Agency of CanadaLethbridge, AB, Canada
| | - Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser UniversityBurnaby, BC, Canada
| | - Victor Gannon
- Laboratory for Foodborne Zoonoses, Public Health Agency of CanadaLethbridge, AB, Canada
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Kevin Allen
- Department of Food, Nutrition, and Health, University of British ColumbiaVancouver, BC, Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser UniversityBurnaby, BC, Canada
| | - Lisbeth Truelstrup Hansen
- Division for Microbiology and Production, National Food Institute, Technical University of DenmarkKongens Lyngby, Denmark
| | - Siyun Wang
- Department of Food, Nutrition, and Health, University of British ColumbiaVancouver, BC, Canada
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Wang Y. Spatial distribution of high copy number plasmids in bacteria. Plasmid 2017; 91:2-8. [PMID: 28263761 DOI: 10.1016/j.plasmid.2017.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/27/2017] [Accepted: 02/27/2017] [Indexed: 11/26/2022]
Abstract
Plasmids play essential roles in bacterial metabolism, evolution, and pathogenesis. The maintenance of plasmids is of great importance both scientifically and practically. In this mini-review, I look at the problem from a slightly different point of view and focus on the spatial distribution of high copy number plasmids, for which no active segregation mechanism has been identified. I review several distribution models and summarize the direct and indirect evidence in the literature, including the most recent progress on measuring the spatial distribution of high copy number plasmids using emerging super-resolution fluorescence microscopy. It is concluded that many open questions remain in the field and that in-depth studies on the spatial distribution of plasmids could shed light on the understanding of the maintenance of plasmids in bacteria.
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Affiliation(s)
- Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, United States; Microelectronics and Photonics Program, University of Arkansas, Fayetteville, AR 72701, United States; Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, United States.
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