101
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Wongpayak P, Meesungnoen O, Saejang S, Subsoontorn P. A highly effective and self-transmissible CRISPR antimicrobial for elimination of target plasmids without antibiotic selection. PeerJ 2021; 9:e11996. [PMID: 34567840 PMCID: PMC8428258 DOI: 10.7717/peerj.11996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023] Open
Abstract
The use of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein) for sequence-specific elimination of bacteria or resistance genes is a powerful tool for combating antibiotic resistance. However, this approach requires efficient delivery of CRISPR/Cas DNA cassette(s) into the targeted bacterial population. Compared to phage transduction, plasmid conjugation can deliver DNA to a broader host range but often suffers from low delivery efficiency. Here, we developed multi-plasmid conjugation systems for efficient CRISPR/Cas delivery, target DNA elimination and plasmid replacement. The CRISPR/Cas system, delivered via a broad-host-range R1162 mobilizable plasmid, specifically eliminated the targeted plasmid in recipient cells. A self-transmissible RK2 helper plasmid facilitated the spread of mobilizable CRISPR/Cas. The replacement of the target plasmid with another plasmid from the same compatibility group helped speed up target plasmid elimination especially when the target plasmid was also mobilizable. Together, we showed that up to 100% of target plasmid from the entire recipient population could be replaced even at a low (1:180) donor-to-recipient ratio and in the absence of transconjugant selection. Such an ability to modify genetic content of microbiota efficiently in the absence of selection will be critical for future development of CRISPR antimicrobials as well as genetic tools for in situ microbiome engineering.
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Affiliation(s)
- Panjaporn Wongpayak
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
| | | | - Somchai Saejang
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
| | - Pakpoom Subsoontorn
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
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102
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Yubero P, Poyatos JF. Dissecting the Fitness Costs of Complex Mutations. Mol Biol Evol 2021; 38:4520-4531. [PMID: 34175930 PMCID: PMC8476139 DOI: 10.1093/molbev/msab193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The fitness cost of complex pleiotropic mutations is generally difficult to assess. On the one hand, it is necessary to identify which molecular properties are directly altered by the mutation. On the other, this alteration modifies the activity of many genetic targets with uncertain consequences. Here, we examine the possibility of addressing these challenges by identifying unique predictors of these costs. To this aim, we consider mutations in the RNA polymerase (RNAP) in Escherichia coli as a model of complex mutations. Changes in RNAP modify the global program of transcriptional regulation, with many consequences. Among others is the difficulty to decouple the direct effect of the mutation from the response of the whole system to such mutation. A problem that we solve quantitatively with data of a set of constitutive genes, those on which the global program acts most directly. We provide a statistical framework that incorporates the direct effects and other molecular variables linked to this program as predictors, which leads to the identification that some genes are more suitable to determine costs than others. Therefore, we not only identified which molecular properties best anticipate fitness, but we also present the paradoxical result that, despite pleiotropy, specific genes serve as more solid predictors. These results have connotations for the understanding of the architecture of robustness in biological systems.
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Affiliation(s)
- Pablo Yubero
- Logic of Genomic Systems Laboratory, CNB-CSIC, Madrid, Spain
| | - Juan F Poyatos
- Logic of Genomic Systems Laboratory, CNB-CSIC, Madrid, Spain
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103
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Pseudomonas aeruginosa mexR and mexEF Antibiotic Efflux Pump Variants Exhibit Increased Virulence. Antibiotics (Basel) 2021; 10:antibiotics10101164. [PMID: 34680745 PMCID: PMC8532662 DOI: 10.3390/antibiotics10101164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 11/18/2022] Open
Abstract
Antibiotic-resistant Pseudomonas aeruginosa infections are the primary cause of mortality in people with cystic fibrosis (CF). Yet, it has only recently become appreciated that resistance mutations can also increase P. aeruginosa virulence, even in the absence of antibiotics. Moreover, the mechanisms by which resistance mutations increase virulence are poorly understood. In this study we tested the hypothesis that mutations affecting efflux pumps can directly increase P. aeruginosa virulence. Using genetics, physiological assays, and model infections, we show that efflux pump mutations can increase virulence. Mutations of the mexEF efflux pump system increased swarming, rhamnolipid production, and lethality in a mouse infection model, while mutations in mexR that increased expression of the mexAB-oprM efflux system increased virulence during an acute murine lung infection without affecting swarming or rhamnolipid gene expression. Finally, we show that an efflux pump inhibitor, which represents a proposed novel treatment approach for P. aeruginosa, increased rhamnolipid gene expression in a dose-dependent manner. This finding is important because rhamnolipids are key virulence factors involved in dissemination through epithelial barriers and cause neutrophil necrosis. Together, these data show how current and proposed future anti-Pseudomonal treatments may unintentionally make infections worse by increasing virulence. Therefore, treatments that target efflux should be pursued with caution.
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104
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Round JW, Robeck LD, Eltis LD. An Integrative Toolbox for Synthetic Biology in Rhodococcus. ACS Synth Biol 2021; 10:2383-2395. [PMID: 34428025 DOI: 10.1021/acssynbio.1c00292] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of microbial cell factories requires robust synthetic biology tools to reduce design uncertainty and accelerate the design-build-test-learn process. Herein, we developed a suite of integrative genetic tools to facilitate the engineering of Rhodococcus, a genus of bacteria with considerable biocatalytic potential. We first created pRIME, a modular, copy-controlled integrative-vector, to provide a robust platform for strain engineering and characterizing genetic parts. This vector was then employed to benchmark a series of strong promoters. We found PM6 to be the strongest constitutive rhodococcal promoter, 2.5- to 3-fold stronger than the next in our study, while overall promoter activities ranged 23-fold between the weakest and strongest promoters during exponential growth. Next, we used an optimized variant of PM6 to develop hybrid-promoters and integrative vectors to allow for tetracycline-inducible gene expression in Rhodococcus. The best of the resulting hybrid-promoters maintained a maximal activity of ∼50% of PM6 and displayed an induction factor of ∼40-fold. Finally, we developed and implemented a uLoop-derived Golden Gate assembly strategy for high-throughput DNA assembly in Rhodococcus. To demonstrate the utility of our approaches, pRIME was used to engineer Rhodococcus jostii RHA1 to grow on vanillin at concentrations 10-fold higher than what the wild-type strain tolerated. Overall, this study provides a suite of tools that will accelerate the engineering of Rhodococcus for various biocatalytic applications, including the sustainable production of chemicals from lignin-derived aromatics.
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Affiliation(s)
- James W. Round
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Logan D. Robeck
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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105
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Felletti M, Romilly C, Wagner EGH, Jonas K. A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability. eLife 2021; 10:71611. [PMID: 34524083 PMCID: PMC8443254 DOI: 10.7554/elife.71611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/15/2021] [Indexed: 01/01/2023] Open
Abstract
The ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes; nevertheless, the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability in Caulobacter crescentus. By performing a detailed biochemical and genetic analysis of the dnaA mRNA, we identified a sequence downstream of the dnaA start codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, is critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that translation regulation by nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.
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Affiliation(s)
- Michele Felletti
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Cédric Romilly
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Kristina Jonas
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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106
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Wasselin V, Staerck C, Rincé I, Léger L, Budin-Verneuil A, Hartke A, Benachour A, Riboulet-Bisson E. Characterisation of the manganese superoxide dismutase of Enterococcus faecium. Res Microbiol 2021; 172:103876. [PMID: 34474124 DOI: 10.1016/j.resmic.2021.103876] [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: 06/08/2021] [Revised: 07/29/2021] [Accepted: 08/24/2021] [Indexed: 11/29/2022]
Abstract
The manganese superoxide dismutase (SodA) of E. faecium strain AUS0004 has been characterised. It is most closely related to Enterococcus hirae, Enterococcus durans, Enterococcus villorium, and Enterococcus mundtii with 100%, 91,55%, 90,85%, and 90,58% homology, respectively, but more distant from SodA of E. faecalis (81.68%). A sodA deletion mutant has been constructed. Compared to the parental strain, the ΔsodA mutant was affected in aerobic growth and more sensitive to hydrogen peroxide (H2O2), cumene hydroperoxide (CuOOH), and the superoxide anion (O2•-) generator menadione. The E. faecium strain AUS0004 is part of those bacteria accumulating H2O2 to high concentrations (around 5 mM) starting from late exponential growth phase. Accumulation of the peroxide was around 25% less in the mutant suggesting that this part of H2O2 is due to the dismutation of O2•- by SodA. The sodA gene of E. faecium AUS0004 was induced by oxygen, peroxides and menadione but the corresponding regulator remains hitherto unknown. Finally, we showed that SodA activity is important for virulence in the Galleria mellonella model.
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Affiliation(s)
- Valentin Wasselin
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France.
| | - Cindy Staerck
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France.
| | - Isabelle Rincé
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France.
| | - Loïc Léger
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France.
| | - Aurélie Budin-Verneuil
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France.
| | - Axel Hartke
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France.
| | - Abdellah Benachour
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France.
| | - Eliette Riboulet-Bisson
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France.
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107
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Ko HJ, Song H, Choi IG. Development of a Novel Cell Surface Attachment System to Display Multi-Protein Complex Using the Cohesin-Dockerin Binding Pair. J Microbiol Biotechnol 2021; 31:1183-1189. [PMID: 34226404 PMCID: PMC9705933 DOI: 10.4014/jmb.2105.05022] [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: 05/18/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022]
Abstract
Autodisplay of a multimeric protein complex on a cell surface is limited by intrinsic factors such as the types and orientations of anchor modules. Moreover, improper folding of proteins to be displayed often hinders functional cell surface display. While overcoming these drawbacks, we ultimately extended the applicability of the autodisplay platform to the display of a protein complex. We designed and constructed a cell surface attachment (CSA) system that uses a noncovalent protein-protein interaction. We employed the high-affinity interaction mediated by an orthogonal cohesin-dockerin (Coh-Doc) pair from Archaeoglobus fulgidus to build the CSA system. Then, we validated the orthogonal Coh-Doc binding by attaching a monomeric red fluorescent protein to the cell surface. In addition, we evaluated the functional anchoring of proteins fused with the Doc module to the autodisplayed Coh module on the surface of Escherichia coli. The designed CSA system was applied to create a functional attachment of dimeric α-neoagarobiose hydrolase to the surface of E. coli cells.
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Affiliation(s)
- Hyeok-Jin Ko
- Food Biotech R&D Center, Samyang Corp., Seongnam 13488, Republic of Korea
| | - Heesang Song
- Department of Biochemistry and Molecular Biology, Chosun University School of Medicine, Gwangju 61452, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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108
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DeCero SA, Winslow CH, Coburn J. Method to Overcome Inefficiencies in Site-Directed Mutagenesis of A/T-Rich DNA. J Biomol Tech 2021; 31:94-99. [PMID: 32831656 DOI: 10.7171/jbt.20-3103-003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Site-directed mutagenesis (SDM) is an invaluable technique that enables the manipulation of DNA and therefore the primary structure and function of any encoded gene products. Commercial protocols for SDM have been optimized for Escherichia coli and mean A/T content but may hinder generation of desired products using other templates. Mutagenesis of A/T-rich DNA is often hindered by low oligodeoxynucleotide (oligo)-annealing temperatures, requiring oligos longer than manufacturer protocol recommendations. However, longer oligos can result in primer dimer formation and decreased SDM efficiencies. Commercially available kits proved inefficient at generating AT-rich mutants. We sought to generate a modified protocol that generated SDM products detectable using gel electrophoresis and that did not require an apparent limit on oligo length.
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Affiliation(s)
- Samuel A DeCero
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; and
| | - Christa H Winslow
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; and
| | - Jenifer Coburn
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Center for Infectious Disease Research, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; and.,Division of Infectious Diseases, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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109
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Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density. Proc Natl Acad Sci U S A 2021; 118:2021416118. [PMID: 34341116 PMCID: PMC8364103 DOI: 10.1073/pnas.2021416118] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Intracellular biomass density is an important variable for cellular physiology. It defines the crowded state of the cytoplasm and thus influences macromolecular interactions and transport. To control density during growth, bacteria must expand their cell volumes in synchrony with biomass. The regulation of volume growth and biomass density remain fundamentally not understood—in bacteria or any other organism. Using advanced microscopy, we demonstrate that cells control dry-mass density indirectly through two independent processes. First, cells expand surface area, rather than volume, in proportion with biomass growth. Second, cell width is controlled independently, with an important influence of turgor pressure. Our findings overturn a long-standing paradigm of mass-density constancy in bacteria and reveal fundamental determinants of dry-mass density and shape. During growth, cells must expand their cell volumes in coordination with biomass to control the level of cytoplasmic macromolecular crowding. Dry-mass density, the average ratio of dry mass to volume, is roughly constant between different nutrient conditions in bacteria, but it remains unknown whether cells maintain dry-mass density constant at the single-cell level and during nonsteady conditions. Furthermore, the regulation of dry-mass density is fundamentally not understood in any organism. Using quantitative phase microscopy and an advanced image-analysis pipeline, we measured absolute single-cell mass and shape of the model organisms Escherichia coli and Caulobacter crescentus with improved precision and accuracy. We found that cells control dry-mass density indirectly by expanding their surface, rather than volume, in direct proportion to biomass growth—according to an empirical surface growth law. At the same time, cell width is controlled independently. Therefore, cellular dry-mass density varies systematically with cell shape, both during the cell cycle or after nutrient shifts, while the surface-to-mass ratio remains nearly constant on the generation time scale. Transient deviations from constancy during nutrient shifts can be reconciled with turgor-pressure variations and the resulting elastic changes in surface area. Finally, we find that plastic changes of cell width after nutrient shifts are likely driven by turgor variations, demonstrating an important regulatory role of mechanical forces for width regulation. In conclusion, turgor-dependent cell width and a slowly varying surface-to-mass coupling constant are the independent variables that determine dry-mass density.
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110
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Emerging and population analysis of Grapevine Pinot gris virus isolates from Iran. 3 Biotech 2021; 11:368. [PMID: 34295608 DOI: 10.1007/s13205-021-02914-5] [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: 02/23/2021] [Accepted: 06/29/2021] [Indexed: 10/20/2022] Open
Abstract
Grapevine Pinot gris virus (GPGV) is a novel member of Trichovirus genus in Betaflexiviridae family. During 2018-2019, 114 leaf and green shoot samples were collected from the main vineyards in Iran Zanjan, Hamedan and East Azerbaijan provinces. After total RNA extraction and cDNA synthesis, the samples were tested by PCR assay using two pairs of specific primers corresponding to the coat protein (CP) and movement protein (MP) regions of GPGV, in which 6 out of 114 samples were found to be infected by GPGV. Population genetics analysis and molecular evolution of GPGV were done based on the CP and MP gene sequences of six new Iranian isolates and 53 additional isolates from several different countries in three continents: Asia, Europe, and America. The phylogenetic tree of GPGV isolates was clustered into two independent clades with significant F ST values (> 0.44). The ω values were calculated < 1 for the GPGV isolates for both genes. These findings demonstrated that the GPGV evolutionary selection pressure is under negative selection. To our knowledge, this is the first detailed study on the molecular characterization, phylogenetic analysis, and provide a better understanding of the population evolution of GPGV isolates from vineyards in Iran. The new Iranian isolates were lied in a new cluster near to European isolates. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02914-5.
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111
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Sakkos JK, Hernandez-Ortiz S, Osteryoung KW, Ducat DC. Orthogonal Degron System for Controlled Protein Degradation in Cyanobacteria. ACS Synth Biol 2021; 10:1667-1681. [PMID: 34232633 DOI: 10.1021/acssynbio.1c00035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Synechococcus elongatus PCC 7942 is a model cyanobacterium for study of the circadian clock, photosynthesis, and bioproduction of chemicals, yet nearly 40% of its gene identities and functions remain unknown, in part due to limitations of the existing genetic toolkit. While classical techniques for the study of genes (e.g., deletion or mutagenesis) can yield valuable information about the absence of a gene and its associated protein, there are limits to these approaches, particularly in the study of essential genes. Herein, we developed a tool for inducible degradation of target proteins in S. elongatus by adapting a method using degron tags from the Mesoplasma florum transfer-mRNA (tmRNA) system. We observed that M. florum lon protease can rapidly degrade exogenous and native proteins tagged with the cognate sequence within hours of induction. We used this system to inducibly degrade the essential cell division factor, FtsZ, as well as shell protein components of the carboxysome. Our results have implications for carboxysome biogenesis and the rate of carboxysome turnover during cell growth. Lon protease control of proteins offers an alternative approach for the study of essential proteins and protein dynamics in cyanobacteria.
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Affiliation(s)
- Jonathan K. Sakkos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
| | - Sergio Hernandez-Ortiz
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Katherine W. Osteryoung
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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112
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Ghosh T, Mondal A, Vamsi Bharadwaj SV, Mishra S. A naturally fluorescent protein C-phycoerythrin and graphene oxide bio-composite as a selective fluorescence 'turn off/on' probe for DNA quantification and characterization. Int J Biol Macromol 2021; 185:644-653. [PMID: 34217741 DOI: 10.1016/j.ijbiomac.2021.06.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
Highly specific graphene-DNA interactions have been at the forefront of graphene-based sensor design for various analytes, including DNA itself. However, in addition to its detection, DNA also needs to be characterized according to its size and concentration in a sample, which is an additional analytical step. Designing a highly sensitive and selective DNA sensing and characterization platform is, thus, of great interest. The present study demonstrates that a bio-derived, naturally fluorescent protein C-phycoerythrin (CPE) - graphene oxide (GO) bio-composite can be used to detect dsDNA in nanomolar quantities efficiently via fluorescent "turn off/on" mechanism. Interaction with GO temporarily quenches CPE fluorescence in a dose-dependent manner. Analytical characterization indicates an indirect charge transfer with a corresponding loss of crystalline GO structure. The fluorescence is regained with the addition of DNA, while other biomolecules do not pose any hinderance in the detection process. The extent of regain is DNA length dependent, and the corresponding calibration curve successfully quantifies the size of an unknown DNA. The incubation time for detection is ~3-5 min. The bio-composite platform also works successfully in a complex biomolecule matrix and cell lysate. However, the presence of serum albumin poses a hinderance in the serum sample. Particle size analysis proves that CPE displacement from GO surface by the incoming DNA is the reason for the 'turn on' response, and that the sensing process is exclusive to dsDNA. This new platform could be an exciting and rapid DNA sensing and characterization tool.
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Affiliation(s)
- Tonmoy Ghosh
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| | - Aniruddha Mondal
- Inorganic Materials and Catalysis Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - S V Vamsi Bharadwaj
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sandhya Mishra
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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113
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Engineering AraC to make it responsive to light instead of arabinose. Nat Chem Biol 2021; 17:817-827. [PMID: 33903769 DOI: 10.1038/s41589-021-00787-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023]
Abstract
The L-arabinose-responsive AraC and its cognate PBAD promoter underlie one of the most often used chemically inducible prokaryotic gene expression systems in microbiology and synthetic biology. Here, we change the sensing capability of AraC from L-arabinose to blue light, making its dimerization and the resulting PBAD activation light-inducible. We engineer an entire family of blue light-inducible AraC dimers in Escherichia coli (BLADE) to control gene expression in space and time. We show that BLADE can be used with pre-existing L-arabinose-responsive plasmids and strains, enabling optogenetic experiments without the need to clone. Furthermore, we apply BLADE to control, with light, the catabolism of L-arabinose, thus externally steering bacterial growth with a simple transformation step. Our work establishes BLADE as a highly practical and effective optogenetic tool with plug-and-play functionality-features that we hope will accelerate the broader adoption of optogenetics and the realization of its vast potential in microbiology, synthetic biology and biotechnology.
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114
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Wang Y, Sun S, Yu L, Hu S, Fan W, Leng F, Ma J. Optimization and mechanism exploration for Escherichia coli transformed with plasmid pUC19 by the combination with ultrasound treatment and chemical method. ULTRASONICS SONOCHEMISTRY 2021; 74:105552. [PMID: 33887660 PMCID: PMC8091046 DOI: 10.1016/j.ultsonch.2021.105552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
As a basic technique of molecular cloning, bio-transformation has been successfully used in the fields of biomedicine and food processing. In this study, we established a transformation system of exogenous DNA into E. coli cells mediated by ultrasound. Under the optimal conditions (i.e. 35 °C, 40 W, 25 s, OD600 = 0.4-0.6) optimized by RSM, the transformation efficiency reached at 1.006 × 107 CFU/μg DNA. The results of membrane permeability, macromolecular substance and cell structure analysis before and after ultrasound treatment showed that the damage of host cells induced by lower (40 W) ultrasound and shorter ultrasound time (25 s) was reversible, and the transformation efficiency and cell survival rate were not significantly affected under this condition. In brief, proper changes in cell membrane and cell wall were the basic conditions for host cells to uptake exogenous DNA, while, whether exogenous DNA could be replicated and expressed in cells depends on the viability of host cells.
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Affiliation(s)
- Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Shangchen Sun
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Linmiao Yu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Shu Hu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Wenguang Fan
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Jianzhong Ma
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
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115
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Hao N, Sullivan AE, Shearwin KE, Dodd IB. The loopometer: a quantitative in vivo assay for DNA-looping proteins. Nucleic Acids Res 2021; 49:e39. [PMID: 33511418 PMCID: PMC8053113 DOI: 10.1093/nar/gkaa1284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/22/2020] [Accepted: 01/20/2021] [Indexed: 12/24/2022] Open
Abstract
Proteins that can bring together separate DNA sites, either on the same or on different DNA molecules, are critical for a variety of DNA-based processes. However, there are no general and technically simple assays to detect proteins capable of DNA looping in vivo nor to quantitate their in vivo looping efficiency. Here, we develop a quantitative in vivo assay for DNA-looping proteins in Escherichia coli that requires only basic DNA cloning techniques and a LacZ assay. The assay is based on loop assistance, where two binding sites for the candidate looping protein are inserted internally to a pair of operators for the E. coli LacI repressor. DNA looping between the sites shortens the effective distance between the lac operators, increasing LacI looping and strengthening its repression of a lacZ reporter gene. Analysis based on a general model for loop assistance enables quantitation of the strength of looping conferred by the protein and its binding sites. We use this ‘loopometer’ assay to measure DNA looping for a variety of bacterial and phage proteins.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia.,CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia
| | - Adrienne E Sullivan
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Keith E Shearwin
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ian B Dodd
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA 5005, Australia
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116
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Duedu KO, Mends JQ, Ayivor-Djanie R, Essandoh PE, Nattah EM, Gyamfi J, Kpeli GS. Plasmidome AMR screening (PAMRS) workflow: a rapid screening workflow for phenotypic characterization of antibiotic resistance in plasmidomes. AAS Open Res 2021. [DOI: 10.12688/aasopenres.13111.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Phenotypic characterization of antimicrobial resistance (AMR) in bacteria has remained the gold standard for investigation and monitoring of what resistance is present in an organism. However, the process is laborious and not attractive for screening multiple plasmids from a microbial community (plasmidomes). Instead, genomic tools are used, but a major bottle neck that presence of genes does not always translate into phenotypes. Methods: We designed the plasmidome AMR screening (PAMRS) workflow to investigate the presence of antibiotic resistant phenotypes in a plasmidome using Escherichia coli as a host organism. Plasmidomes were extracted from the faecal matter of chicken, cattle and humans using commercial plasmid extraction kits. Competent E. coli cells were transformed and evaluated using disk diffusion. Thirteen antibiotic resistant phenotypes were screened. Results: Here, we show that multiple antibiotic resistant phenotypes encoded by plasmids can be rapidly screened simultaneously using the PAMRS workflow. E. coli was able to pick up to 7, 5 or 8 resistant phenotypes from a single plasmidome from chicken, cattle or humans, respectively. Resistance to ceftazidime was the most frequently picked up phenotype in humans (52.6%) and cattle (90.5%), whereas in chickens, the most picked up resistant phenotype was resistance to co-trimoxazole, ceftriaxone and ampicillin (18.4% each). Conclusions: This workflow is a novel tool that could facilitate studies to evaluate the occurrence and expression of plasmid-encoded antibiotic resistance in microbial communities and their associated plasmid-host ranges. It could find application in the screening of plasmid-encoded virulence genes.
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117
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Staerck C, Wasselin V, Budin-Verneuil A, Rincé I, Cacaci M, Weigel M, Giraud C, Hain T, Hartke A, Riboulet-Bisson E. Analysis of glycerol and dihydroxyacetone metabolism in Enterococcus faecium. FEMS Microbiol Lett 2021; 368:6232157. [PMID: 33864460 DOI: 10.1093/femsle/fnab043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
Glycerol (Gly) can be dissimilated by two pathways in bacteria. Either this sugar alcohol is first oxidized to dihydroxyacetone (DHA) and then phosphorylated or it is first phosphorylated to glycerol-3-phosphate (GlyP) followed by oxidation. Oxidation of GlyP can be achieved by NAD-dependent dehydrogenases or by a GlyP oxidase. In both cases, dihydroxyacetone phosphate is the product. Genomic analysis showed that Enterococcus faecium harbors numerous genes annotated to encode activities for the two pathways. However, our physiological analyses of growth on glycerol showed that dissimilation is limited to aerobic conditions and that despite the presence of genes encoding presumed GlyP dehydrogenases, the GlyP oxidase is essential in this process. Although E. faecium contains an operon encoding the phosphotransfer protein DhaM and DHA kinase, which are required for DHA phosphorylation, it is unable to grow on DHA. This operon is highly expressed in stationary phase but its physiological role remains unknown. Finally, data obtained from sequencing of a transposon mutant bank of E. faecium grown on BHI revealed that the GlyP dehydrogenases and a major intrinsic family protein have important but hitherto unknown physiological functions.
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Affiliation(s)
- Cindy Staerck
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Valentin Wasselin
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Aurélie Budin-Verneuil
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Isabelle Rincé
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Margherita Cacaci
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy.,Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Markus Weigel
- Institute of Medical Microbiology, Justus-Liebig-University Giessen, Biomedical Research Facility Seltersberg (BFS), Schubertstrasse 81, D-35392 Giessen, Germany
| | - Caroline Giraud
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
| | - Torsten Hain
- Institute of Medical Microbiology, Justus-Liebig-University Giessen, Biomedical Research Facility Seltersberg (BFS), Schubertstrasse 81, D-35392 Giessen, Germany.,German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Schubertstrasse 81, D-35392 Giessen, Germany
| | - Axel Hartke
- Normandie Univ, UNICAEN U2RM-Stress and Virulence, Esplanade de la Paix, 14032 Caen, France
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118
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A Pseudomonas aeruginosa Antimicrobial Affects the Biogeography but Not Fitness of Staphylococcus aureus during Coculture. mBio 2021; 12:mBio.00047-21. [PMID: 33785630 PMCID: PMC8092195 DOI: 10.1128/mbio.00047-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Many human infections result from the action of multispecies bacterial communities. Within these communities, bacteria have been proposed to directly interact via physical and chemical means, resulting in increased disease and antimicrobial tolerance. Pseudomonas aeruginosa and Staphylococcus aureus are two of the most common coinfecting bacteria in human infections, including the cystic fibrosis (CF) lung. There is emerging evidence that coinfection with these microbes enhances disease severity and antimicrobial tolerance through direct interactions. However, one of the challenges to studying microbial interactions relevant to human infection is the lack of experimental models with the versatility to investigate complex interaction dynamics while maintaining biological relevance. Here, we developed a model based on an in vitro medium that mimics human CF lung secretions (synthetic CF sputum medium [SCFM2]) and allows time-resolved assessment of fitness and community spatial structure at the micrometer scale. Our results reveal that P. aeruginosa and S. aureus coexist as spatially structured communities in SCFM2 under static growth conditions, with S. aureus enriched at a distance of 3.5 μm from P. aeruginosa. Multispecies aggregates were rare, and aggregate (biofilm) sizes resembled those in human CF sputum. Elimination of P. aeruginosa’s ability to produce the antistaphylococcal small molecule HQNO (2-heptyl-4-hydroxyquinoline N-oxide) had no effect on bacterial fitness but altered the spatial structure of the community by increasing the distance of S. aureus from P. aeruginosa to 7.6 μm. Lastly, we show that coculture with P. aeruginosa sensitizes S. aureus to killing by the antibiotic tobramycin compared to monoculture growth despite HQNO enhancing tolerance during coculture. Our findings reveal that SCFM2 is a powerful model for studying P. aeruginosa and S. aureus and that HQNO alters S. aureus biogeography and antibiotic susceptibility without affecting fitness.
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119
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Joint Universal Modular Plasmids: A Flexible Platform for Golden Gate Assembly in Any Microbial Host. Methods Mol Biol 2021; 2205:255-273. [PMID: 32809204 DOI: 10.1007/978-1-0716-0908-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Modular cloning standards based on Golden Gate DNA assembly allow for construction of complex DNA constructs over several rounds of assembly. Despite being reliable and automation-friendly, each standard uses a specific set of vectors, requiring researchers to generate new tool kits for novel hosts and cloning applications. JUMP vectors (Valenzuela-Ortega and French, bioRxiv 799585, 2019) combine the robustness of modular cloning standards with the Standard European Vector Architecture and a flexible design that allows researchers to easily modify the vector backbone via secondary cloning sites. This flexibility allows for JUMP vectors to be used in a wide variety of applications and hosts.
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120
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Manna S, Truong J, Hammond MC. Guanidine Biosensors Enable Comparison of Cellular Turn-on Kinetics of Riboswitch-Based Biosensor and Reporter. ACS Synth Biol 2021; 10:566-578. [PMID: 33646758 PMCID: PMC7985839 DOI: 10.1021/acssynbio.0c00583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Indexed: 12/30/2022]
Abstract
Cell-based sensors are useful for many synthetic biology applications, including regulatory circuits, metabolic engineering, and diagnostics. While considerable research efforts have been made toward recognizing new target ligands and increasing sensitivity, the analysis and optimization of turn-on kinetics is often neglected. For example, to our knowledge there has been no systematic study that compared the performance of a riboswitch-based biosensor versus reporter for the same ligand. In this study, we show the development of RNA-based fluorescent (RBF) biosensors for guanidine, a common chaotropic agent that is a precursor to both fertilizer and explosive compounds. Guanidine is cell permeable and nontoxic to E. coli at millimolar concentrations, which in contrast to prior studies enabled direct activation of the riboswitch-based biosensor and corresponding reporter with ligand addition to cells. Our results reveal that the biosensors activate fluorescence in the cell within 4 min of guanidine treatment, which is at least 15 times faster than a reporter derived from the same riboswitch, and this rapid sensing activity is maintained for up to 1.6 weeks. Together, this study describes the design of two new biosensor topologies and showcases the advantages of RBF biosensors for monitoring dynamic processes in cell biology, biotechnology, and synthetic biology.
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Affiliation(s)
- Sudeshna Manna
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Johnny Truong
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ming C. Hammond
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
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121
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Tesfagaber W, Wang L, Tsegay G, Hagoss YT, Zhang Z, Zhang J, Huangfu H, Xi F, Li F, Sun E, Bu Z, Zhao D. Characterization of Anti-p54 Monoclonal Antibodies and Their Potential Use for African Swine Fever Virus Diagnosis. Pathogens 2021; 10:pathogens10020178. [PMID: 33562314 PMCID: PMC7915713 DOI: 10.3390/pathogens10020178] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 01/01/2023] Open
Abstract
African swine fever (ASF) is a highly lethal hemorrhagic viral disease of domestic pigs caused by African swine fever virus (ASFV). Although a good advance has been made to understand the virus, a safe and effective vaccine against ASFV is still lacking and its eradication solely depends on its early and accurate diagnosis. Thus, improving the available diagnostic assays and adding some validated techniques are useful for a range of serological investigations. The aim of this study was to produce and characterize p54 monoclonal antibodies with an ultimate goal of developing a monoclonal antibody-based enzyme-linked immunosorbent assay (ELISA) for ASFV antibody detection. Five monoclonal antibodies against p54 protein expressed in Escherichia coli was generated and their characterizations were investigated. Furthermore, a competitive enzyme-linked immunosorbent assay (cELISA) based on a monoclonal antibody designated as 2A7 was developed. To evaluate the performance of the assay, a total of 365 pig serum samples (178 negative and 187 positive samples) were tested and a receiver-operating characteristic (ROC) analysis was applied to determine the cut-off value. Based on the ROC analysis, the area under the curve (AUC) was 0.982 (95% confidence interval: 96.9% to 99.4%), besides a sensitivity of 92.5% and a specificity of 98.9% was achieved when the percent inhibition of 20% was selected as a threshold. Moreover, the result showed an excellent agreement when compared to other commercially available blocking ELISA (kappa value = 0.912) and showed no reaction to other swine pathogens. Overall, the newly developed cELISA method offers a promising approach for a rapid and convenient ASFV serodiagnosis, which could be used as alternative to other serological assays for screening possible ASFV infection.
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Affiliation(s)
- Weldu Tesfagaber
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- Department of Veterinary Science, Hamelmalo Agricultural College, Keren 397, Eritrea
| | - Lulu Wang
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Ghebremedhin Tsegay
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- Department of Veterinary Science, Hamelmalo Agricultural College, Keren 397, Eritrea
| | - Yibrah Tekle Hagoss
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhenjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jiwen Zhang
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Haoyue Huangfu
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Fei Xi
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Fang Li
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Encheng Sun
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhigao Bu
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Dongming Zhao
- State Key Laboratory of Veterinary Biotechnology, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
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122
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Valenzuela-Ortega M, French C. Joint universal modular plasmids (JUMP): a flexible vector platform for synthetic biology. Synth Biol (Oxf) 2021; 6:ysab003. [PMID: 33623824 PMCID: PMC7889407 DOI: 10.1093/synbio/ysab003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 12/08/2020] [Accepted: 12/22/2020] [Indexed: 12/21/2022] Open
Abstract
Generation of new DNA constructs is an essential process in modern life science and biotechnology. Modular cloning systems based on Golden Gate cloning, using Type IIS restriction endonucleases, allow assembly of complex multipart constructs from reusable basic DNA parts in a rapid, reliable and automation-friendly way. Many such toolkits are available, with varying degrees of compatibility, most of which are aimed at specific host organisms. Here, we present a vector design which allows simple vector modification by using modular cloning to assemble and add new functions in secondary sites flanking the main insertion site (used for conventional modular cloning). Assembly in all sites is compatible with the PhytoBricks standard, and vectors are compatible with the Standard European Vector Architecture (SEVA) as well as BioBricks. We demonstrate that this facilitates the construction of vectors with tailored functions and simplifies the workflow for generating libraries of constructs with common elements. We have made available a collection of vectors with 10 different microbial replication origins, varying in copy number and host range, and allowing chromosomal integration, as well as a selection of commonly used basic parts. This design expands the range of hosts which can be easily modified by modular cloning and acts as a toolkit which can be used to facilitate the generation of new toolkits with specific functions required for targeting further hosts.
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Affiliation(s)
- Marcos Valenzuela-Ortega
- Centre for Systems and Synthetic Biology, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, UK
| | - Christopher French
- Centre for Systems and Synthetic Biology, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, UK.,Zhejiang University-University of Edinburgh Joint Research Centre for Engineering Biology, International Campus, Zhejiang University, Haining, Zhejiang 314400, China
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123
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Molecular characterization and population evolution analysis of Watermelon mosaic virus isolates on cucurbits of Northwest Iran. 3 Biotech 2021; 11:43. [PMID: 33489666 DOI: 10.1007/s13205-020-02609-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022] Open
Abstract
One of the destructive potyviruses which cause economic damage and serious yield losses to cucurbit crops around the world is Watermelon mosaic potyvirus. In 2016, 305 leaf samples from different cucurbit cultivars with deformation and reduction in leaf size, blistering, mild and severe mosaic symptoms were collected from different cucurbits-growing regions in Northwest of Iran. Total RNA and their cDNA were tested by RT-PCR assay using two sets of specific primers corresponding to the partial sequences of CP and P1 genomic regions, in which approximately 80 out of 305 samples were found to be infected by WMV. DNA fragments of about 780 bp and 545 bp in length were amplified that belonged to the CP and P1 genes, respectively. Phylogenetic trees of WMV isolates were clustered into three main independent groups with significant F ST values (> 0.50 and > 0.55) for CP and P1 genes, respectively. dN/dS ratios obtained less than one (< 1) for CP gene that showed the WMV populations have been under the negative selection, whereas for P1 gene, the dN/dS values were calculated > 1 for EM clade containing; China, France, and Italy populations and < 1 for CL and G2 clades; South Korea and Iran populations. This results demonstrated that the WMV evolutionary selection pressure on the P1 gene is dependent on conditions such as the variety of cultivars and the type of cultivation.
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124
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Peng J, Schachterle JK, Sundin GW. Orchestration of virulence factor expression and modulation of biofilm dispersal in Erwinia amylovora through activation of the Hfq-dependent small RNA RprA. MOLECULAR PLANT PATHOLOGY 2021; 22:255-270. [PMID: 33314618 PMCID: PMC7814967 DOI: 10.1111/mpp.13024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Erwinia amylovora is the causative agent of the devastating disease fire blight of pome fruit trees. After infection of host plant leaves at apple shoot tips, E. amylovora cells form biofilms in xylem vessels, restrict water flow, and cause wilting symptoms. Although E. amylovora is well known to be able to cause systemic infection, how biofilm cells of E. amylovora transit from the sessile mode of growth in xylem to the planktonic mode of growth in cortical parenchyma remains unknown. Increasing evidence has suggested the important modulatory roles of Hfq-dependent small RNAs (sRNAs) in the pathogenesis of E. amylovora. Here, we demonstrate that the sRNA RprA acts as a positive regulator of amylovoran exopolysaccharide production, the type III secretion system (T3SS), and flagellar-dependent motility, and as a negative regulator of levansucrase activity and cellulose production. We also show that RprA affects the promoter activity of multiple virulence factor genes and regulates hrpS, a critical T3SS regulator, at the posttranscriptional level. We determined that rprA expression can be activated by the Rcs phosphorelay, and that expression is active during T3SS-mediated host infection in an immature pear fruit infection model. We further showed that overexpression of rprA activated the in vitro dispersal of E. amylovora cells from biofilms. Thus, our investigation of the varied role of RprA in affecting E. amylovora virulence provides important insights into the functions of this sRNA in biofilm control and systemic infection.
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Affiliation(s)
- Jingyu Peng
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Jeffrey K. Schachterle
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
- Present address:
US National Arboretum – Floral and Nursery Plants Research UnitUSDA‐ARSBeltsvilleMarylandUSA
| | - George W. Sundin
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
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125
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Yang Y, Wang T, Yu Q, Liu H, Xun L, Xia Y. The pathway of recombining short homologous ends in Escherichia coli revealed by the genetic study. Mol Microbiol 2021; 115:1309-1322. [PMID: 33372330 DOI: 10.1111/mmi.14677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
The recombination of short homologous ends in Escherichia coli has been known for 30 years, and it is often used for both site-directed mutagenesis and in vivo cloning. For cloning, a plasmid and target DNA fragments were converted into linear DNA fragments with short homologous ends, which are joined via recombination inside E. coli after transformation. Here this mechanism of joining homologous ends in E. coli was determined by a linearized plasmid with short homologous ends. Two 3'-5' exonucleases ExoIII and ExoX with nonprocessive activity digested linear dsDNA to generate 5' single-strand overhangs, which annealed with each other. The polymerase activity of DNA polymerase I (Pol I) was exclusively employed to fill in the gaps. The strand displacement activity and the 5'-3' exonuclease activity of Pol I were also required, likely to generate 5' phosphate termini for subsequent ligation. Ligase A (LigA) joined the nicks to finish the process. The model involving 5' single-stranded overhangs is different from established recombination pathways that all generate 3' single-stranded overhangs. This recombination is likely common in bacteria since the involved enzymes are ubiquitous.
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Affiliation(s)
- Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.,Institute of Marine Science and Technology, Shandong University, Qingdao, People's Republic of China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.,School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
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126
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Tagomori BY, dos Santos FC, Barbosa-Tessmann IP. Recombinant expression, purification, and characterization of an α-amylase from Massilia timonae. 3 Biotech 2021; 11:13. [PMID: 33442512 DOI: 10.1007/s13205-020-02505-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/24/2020] [Indexed: 10/22/2022] Open
Abstract
This work reports the amy1 gene cloning from Massilia timonae CTI-57, and its successful expression in Escherichia coli Rosetta™ (DE3) from the pTRCHis2B plasmid. The recombinant AMY1 protein had 47 kDa, and its modeled structure showed a monomer composed of three domains. An N-terminal domain with the characteristic (β/α)8-barrel structure of α-amylases, which contained the catalytic amino acid residues. The second domain was small, and the C-terminal domain was similar to those found in the barley α-amylase. A phylogenetic analysis demonstrated a high sequence identity of the studied protein with bacterial and plant α-amylases from the GH13_6 subfamily. This is the first characterized bacterial α-amylase from this glucoside hydrolase subfamily. Besides starch, the enzyme was also active against maltodextrin, amylopectin, and blocked p-nitrophenyl α-d-maltoheptaoside, but could not use β-cyclodextrin or 4-nitrophenyl α-d-glucopyranoside. The K M for highly pure grade soluble starch from potato and V max values were 0.79 mg/mL and 0.04 mg/min, respectively. The calcium ion showed to be essential for the purified enzyme's activity, while EDTA, molybdenum, cobalt, and mercury were strong inhibitors. The enzyme was almost fully active in SDS presence. The enzyme's optimal pH and temperature were 6.0 and 60 °C, respectively, and its denaturation T m was 79 °C. A TLC analysis revealed that glucose and maltose are products of the enzyme's action on starch. In conclusion, this work described the M. timonae GH13_6 subfamily α-amylase, which showed to be thermostable and anionic detergent-resistant.
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127
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Löwe H, Beentjes M, Pflüger-Grau K, Kremling A. Trehalose production by Cupriavidus necator from CO 2 and hydrogen gas. BIORESOURCE TECHNOLOGY 2021; 319:124169. [PMID: 33254445 DOI: 10.1016/j.biortech.2020.124169] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 06/12/2023]
Abstract
In this work, the hydrogen-oxidizing bacterium Cupriavidus necator H16 was engineered for trehalose production from gaseous substrates. First, it could be shown that C. necator is a natural producer of trehalose when stressed with sodium chloride. Bioinformatic investigations revealed a so far unknown mode of trehalose and glycogen metabolism in this organism. Next, it was found that expression of the sugar efflux transporter A (setA) from Escherichia coli lead to a trehalose leaky phenotype of C. necator. Finally, the strain was characterized under autotrophic conditions using a H2/CO2/O2-mixture and other substrates reaching titers of up to 0.47 g L-1 and yields of around 0.1 g g-1. Taken together, this process represents a new way to produce sugars with high areal efficiency. With further metabolic engineering, an application of this technology for the renewable production of trehalose and other sugars, as well as for the synthesis of 13C-labeled sugars seems promising.
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Affiliation(s)
- Hannes Löwe
- Systems Biotechnology, Technical University of Munich, Germany
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128
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Abstract
Genetic studies in Borrelia require special consideration of the highly segmented genome, complex growth requirements and evolutionary distance of spirochetes from other genetically tractable bacteria. Despite these challenges, a robust molecular genetic toolbox has been constructed to investigate the biology and pathogenic potential of these important human pathogens. In this review we summarize the tools and techniques that are currently available for the genetic manipulation of Borrelia, including the relapsing fever spirochetes, viewing them in the context of their utility and shortcomings. Our primary objective is to help researchers discern what is feasible and what is not practical when thinking about potential genetic experiments in Borrelia. We have summarized published methods and highlighted their critical elements, but we are not providing detailed protocols. Although many advances have been made since B. burgdorferi was first transformed over 25 years ago, some standard genetic tools remain elusive for Borrelia. We mention these limitations and why they persist, if known. We hope to encourage investigators to explore what might be possible, in addition to optimizing what currently can be achieved, through genetic manipulation of Borrelia.
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Affiliation(s)
- Patricia A. Rosa
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St. Hamilton, MT 59840 USA
| | - Mollie W. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 6900 Lake Nona Blvd, Orlando, FL 32827 USA
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129
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Identification of two fnr genes and characterisation of their role in the anaerobic switch in Sphingopyxis granuli strain TFA. Sci Rep 2020; 10:21019. [PMID: 33273546 PMCID: PMC7713065 DOI: 10.1038/s41598-020-77927-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/17/2020] [Indexed: 11/16/2022] Open
Abstract
Sphingopyxis granuli strain TFA is able to grow on the organic solvent tetralin as the only carbon and energy source. The aerobic catabolic pathway for tetralin, the genes involved and their regulation have been fully characterised. Unlike most of the bacteria belonging to the sphingomonads group, this strain is able to grow in anoxic conditions by respiring nitrate, though not nitrite, as the alternative electron acceptor. In this work, two fnr-like genes, fnrN and fixK, have been identified in strain TFA. Both genes are functional in E. coli and Sphingopyxis granuli although fixK, whose expression is apparently activated by FnrN, seems to be much less effective than fnrN in supporting anaerobic growth. Global transcriptomic analysis of a ΔfnrN ΔfixK double mutant and identification of Fnr boxes have defined a minimal Fnr regulon in this bacterium. However, expression of a substantial number of anaerobically regulated genes was not affected in the double mutant. Additional regulators such regBA, whose expression is also activated by Fnr, might also be involved in the anaerobic response. Anaerobically induced stress response genes were not regulated by Fnr but apparently induced by stress conditions inherent to anaerobic growth, probably due to accumulation of nitrite and nitric oxide.
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130
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Tülek A, Özdemir FI, Ramadhan SS. Cloning, Expression and Characterization of Membrane Bound FtsH Protease of Geobacillus kaustophilus. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820060186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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131
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Huang HM, Stephan P, Kries H. Engineering DNA-Templated Nonribosomal Peptide Synthesis. Cell Chem Biol 2020; 28:221-227.e7. [PMID: 33238159 DOI: 10.1016/j.chembiol.2020.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022]
Abstract
Diffusive escape of intermediates limits the rate enhancement that nanocontainers or macromolecular scaffolds can provide for artificial biocatalytic cascades. Nonribosomal peptide synthetases (NRPSs) naturally form gigantic assembly lines and prevent escape by covalently tethering intermediates. Here, we have built DNA-templated NRPS (DT-NRPS) by adding zinc-finger tags to split NRPS modules. The zinc fingers direct the NRPS modules to 9-bp binding sites on a DNA strand, where they form a catalytically active enzyme cascade. Geometric constraints of the DT-NRPSs were investigated using the template DNA as a molecular ruler. Up to four DT-NRPS modules were assembled on DNA to synthesize peptides. DT-NRPSs outperform previously reported DNA-templated enzyme cascades in terms of DNA acceleration, which demonstrates that covalent intermediate channeling is possible along the DNA template. Attachment of assembly line enzymes to a DNA scaffold is a promising catalytic strategy for the sequence-controlled biosynthesis of nonribosomal peptides and other polymers.
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Affiliation(s)
- Hsin-Mei Huang
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany.
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132
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Van Brempt M, Clauwaert J, Mey F, Stock M, Maertens J, Waegeman W, De Mey M. Predictive design of sigma factor-specific promoters. Nat Commun 2020; 11:5822. [PMID: 33199691 PMCID: PMC7670410 DOI: 10.1038/s41467-020-19446-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
To engineer synthetic gene circuits, molecular building blocks are developed which can modulate gene expression without interference, mutually or with the host's cell machinery. As the complexity of gene circuits increases, automated design tools and tailored building blocks to ensure perfect tuning of all components in the network are required. Despite the efforts to develop prediction tools that allow forward engineering of promoter transcription initiation frequency (TIF), such a tool is still lacking. Here, we use promoter libraries of E. coli sigma factor 70 (σ70)- and B. subtilis σB-, σF- and σW-dependent promoters to construct prediction models, capable of both predicting promoter TIF and orthogonality of the σ-specific promoters. This is achieved by training a convolutional neural network with high-throughput DNA sequencing data from fluorescence-activated cell sorted promoter libraries. This model functions as the base of the online promoter design tool (ProD), providing tailored promoters for tailored genetic systems.
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Affiliation(s)
- Maarten Van Brempt
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Jim Clauwaert
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Friederike Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Willem Waegeman
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, 9000, Ghent, Belgium.
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133
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Goyal G, Elsbree N, Fero M, Hillson NJ, Linshiz G. Repurposing a microfluidic formulation device for automated DNA construction. PLoS One 2020; 15:e0242157. [PMID: 33175889 PMCID: PMC7657503 DOI: 10.1371/journal.pone.0242157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022] Open
Abstract
Microfluidic applications have expanded greatly over the past decade. For the most part, however, each microfluidics platform is developed with a specific task in mind, rather than as a general-purpose device with a wide-range of functionality. Here, we show how a microfluidic system, originally developed to investigate protein phase behavior, can be modified and repurposed for another application, namely DNA construction. We added new programable controllers to direct the flow of reagents across the chip. We designed the assembly of a combinatorial Golden Gate DNA library using TeselaGen DESIGN software and used the repurposed microfluidics platform to assemble the designed library from off-chip prepared DNA assembly pieces. Further experiments verified the sequences and function of the on-chip assembled DNA constructs.
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Affiliation(s)
- Garima Goyal
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Nick Elsbree
- TeselaGen Biotechnology, San Francisco, California, United States of America
| | - Michael Fero
- TeselaGen Biotechnology, San Francisco, California, United States of America
| | - Nathan J. Hillson
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Gregory Linshiz
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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134
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Vahidinasab M, Lilge L, Reinfurt A, Pfannstiel J, Henkel M, Morabbi Heravi K, Hausmann R. Construction and description of a constitutive plipastatin mono-producing Bacillus subtilis. Microb Cell Fact 2020; 19:205. [PMID: 33167976 PMCID: PMC7654001 DOI: 10.1186/s12934-020-01468-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/29/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Plipastatin is a potent Bacillus antimicrobial lipopeptide with the prospect to replace conventional antifungal chemicals for controlling plant pathogens. However, the application of this lipopeptide has so far been investigated in a few cases, principally because of the yield in low concentration and unknown regulation of biosynthesis pathways. B. subtilis synthesizes plipastatin by a non-ribosomal peptide synthetase encoded by the ppsABCDE operon. In this study, B. subtilis 3NA (a non-sporulation strain) was engineered to gain more insights about plipastatin mono-production. RESULTS The 4-phosphopantetheinyl transferase Sfp posttranslationally converts non-ribosomal peptide synthetases from inactive apoforms into their active holoforms. In case of 3NA strain, sfp gene is inactive. Accordingly, the first step was an integration of a repaired sfp version in 3NA to construct strain BMV9. Subsequently, plipastatin production was doubled after integration of a fully expressed degQ version from B. subtilis DSM10T strain (strain BMV10), ensuring stimulation of DegU-P regulatory pathway that positively controls the ppsABSDE operon. Moreover, markerless substitution of the comparably weak native plipastatin promoter (Ppps) against the strong constitutive promoter Pveg led to approximately fivefold enhancement of plipastatin production in BMV11 compared to BMV9. Intriguingly, combination of both repaired degQ expression and promoter exchange (Ppps::Pveg) did not increase the plipastatin yield. Afterwards, deletion of surfactin (srfAA-AD) operon by the retaining the regulatory comS which is located within srfAB and is involved in natural competence development, resulted in the loss of plipastatin production in BMV9 and significantly decreased the plipastatin production of BMV11. We also observed that supplementation of ornithine as a precursor for plipastatin formation caused higher production of plipastatin in mono-producer strains, albeit with a modified pattern of plipastatin composition. CONCLUSIONS This study provides evidence that degQ stimulates the native plipastatin production. Moreover, a full plipastatin production requires surfactin synthetase or some of its components. Furthermore, as another conclusion of this study, results point towards ornithine provision being an indispensable constituent for a plipastatin mono-producer B. subtilis strain. Therefore, targeting the ornithine metabolic flux might be a promising strategy to further investigate and enhance plipastatin production by B. subtilis plipastatin mono-producer strains.
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Affiliation(s)
- Maliheh Vahidinasab
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering (150K), University of Hohenheim, Fruwirthstraße 12, 70599, Stuttgart, Germany
| | - Lars Lilge
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering (150K), University of Hohenheim, Fruwirthstraße 12, 70599, Stuttgart, Germany.
| | - Aline Reinfurt
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering (150K), University of Hohenheim, Fruwirthstraße 12, 70599, Stuttgart, Germany
| | - Jens Pfannstiel
- Core Facility Hohenheim, Mass Spectrometry Unit, University of Hohenheim, August-von-Hartmann-Str. 3, 70599, Stuttgart, Germany
| | - Marius Henkel
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering (150K), University of Hohenheim, Fruwirthstraße 12, 70599, Stuttgart, Germany
| | - Kambiz Morabbi Heravi
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering (150K), University of Hohenheim, Fruwirthstraße 12, 70599, Stuttgart, Germany
| | - Rudolf Hausmann
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering (150K), University of Hohenheim, Fruwirthstraße 12, 70599, Stuttgart, Germany
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135
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Kot W, Olsen NS, Nielsen TK, Hutinet G, de Crécy-Lagard V, Cui L, Dedon PC, Carstens AB, Moineau S, Swairjo MA, Hansen LH. Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs. Nucleic Acids Res 2020; 48:10383-10396. [PMID: 32941607 PMCID: PMC7544227 DOI: 10.1093/nar/gkaa735] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/22/2022] Open
Abstract
In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.
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Affiliation(s)
- Witold Kot
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Nikoline S Olsen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Tue K Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL USA.,Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander B Carstens
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec City, PQ, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, PQ, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, PQ, Canada
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Lars H Hansen
- Department of Plant and Environmental Science, University of Copenhagen, Denmark
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136
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Dewi KS, Fuad AM. Improving the Expression of Human Granulocyte Colony Stimulating Factor in Escherichia coli by Reducing the GC-content and Increasing mRNA Folding Free Energy at 5'-Terminal End. Adv Pharm Bull 2020; 10:610-616. [PMID: 33072539 PMCID: PMC7539321 DOI: 10.34172/apb.2020.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/24/2019] [Accepted: 01/27/2020] [Indexed: 01/16/2023] Open
Abstract
Purpose: Strategy for improving the production of biopharmaceutical protein continues to develop due to increasing market demand. Human granulocyte colony stimulating factor (hG-CSF) is one of biopharmaceutical proteins that has many applications, and easily produced in Escherichia coli expression system. Previous studies reported that codon usage, rare codon, mRNA folding and GC-content at 5’-terminal end were crucial for protein production in E. coli. In the present study, the effect of reducing the GC-content and increasing the mRNA folding free energy at the 5’-terminal end on the expression level of hG-CSF proteins was investigated. Methods: Synonymous codon substitutions were performed to generate mutant variants of open reading frame (ORF) with lower GC-content at 5’-terminal ends. Oligoanalyzer tool was used to calculate the GC content of eight codons sequence after ATG. Whereas, mRNA folding free energy was predicted using KineFold and RNAfold tools. The template DNA was amplified using three variant forward primers and one same reverse primer. Those DNA fragments were individually cloned into pJexpress414 expression vector and were confirmed using restriction and DNA sequencing analyses. The confirmed constructs were transformed into E. coli NiCo21(DE3) host cells and the recombinant protein was expressed using IPTG-induction. Total protein obtained were characterized using SDS-PAGE, Western blot and ImageJ software analyses. Results: The result showed that the mutant variant with lower GC-content and higher mRNA folding free energy near the translation initiation region (TIR) could produce a higher amount of hG-CSF proteins compared to the original gene sequence. Conclusion: This study emphasized the important role of the nucleotide composition immediately downstream the start codon to achieve high-yield protein product on heterologous expression in E. coli.
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Affiliation(s)
- Kartika Sari Dewi
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, Bogor, Indonesia, 16911
| | - Asrul Muhamad Fuad
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, Bogor, Indonesia, 16911
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137
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Hubbard ATM, Mason J, Roberts P, Parry CM, Corless C, van Aartsen J, Howard A, Bulgasim I, Fraser AJ, Adams ER, Roberts AP, Edwards T. Piperacillin/tazobactam resistance in a clinical isolate of Escherichia coli due to IS26-mediated amplification of bla TEM-1B. Nat Commun 2020; 11:4915. [PMID: 33004811 PMCID: PMC7530762 DOI: 10.1038/s41467-020-18668-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
A phenotype of Escherichia coli and Klebsiella pneumoniae, resistant to piperacillin/tazobactam (TZP) but susceptible to carbapenems and 3rd generation cephalosporins, has emerged. The resistance mechanism associated with this phenotype has been identified as hyperproduction of the β-lactamase TEM. However, the mechanism of hyperproduction due to gene amplification is not well understood. Here, we report a mechanism of gene amplification due to a translocatable unit (TU) excising from an IS26-flanked pseudo-compound transposon, PTn6762, which harbours blaTEM-1B. The TU re-inserts into the chromosome adjacent to IS26 and forms a tandem array of TUs, which increases the copy number of blaTEM-1B, leading to TEM-1B hyperproduction and TZP resistance. Despite a significant increase in blaTEM-1B copy number, the TZP-resistant isolate does not incur a fitness cost compared to the TZP-susceptible ancestor. This mechanism of amplification of blaTEM-1B is an important consideration when using genomic data to predict susceptibility to TZP.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Anti-Bacterial Agents/therapeutic use
- Chromosomes, Bacterial/genetics
- DNA Transposable Elements/genetics
- DNA, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/genetics
- Drug Therapy, Combination/methods
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/isolation & purification
- Escherichia coli Infections/drug therapy
- Escherichia coli Infections/microbiology
- Escherichia coli Proteins/genetics
- Gene Amplification
- Gene Expression Regulation, Bacterial
- Genome, Bacterial/genetics
- Humans
- Microbial Sensitivity Tests
- Piperacillin/pharmacology
- Piperacillin/therapeutic use
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- Tazobactam/pharmacology
- Tazobactam/therapeutic use
- Whole Genome Sequencing
- beta-Lactamases/genetics
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Affiliation(s)
- Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Jenifer Mason
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Paul Roberts
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
- Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Building MA, Wulfruna Street, Wolverhampton, WV1 1LY, UK
| | - Christopher M Parry
- Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, L12 2AP, UK
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, L69 7BE, UK
- Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- School of Tropical Medicine and Global Health, University of Nagasaki, Nagasaki, Japan
| | - Caroline Corless
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Jon van Aartsen
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Alex Howard
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Issra Bulgasim
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Alice J Fraser
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Emily R Adams
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Thomas Edwards
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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138
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Hobmeier K, Goëss MC, Sehr C, Schwaminger S, Berensmeier S, Kremling A, Kunte HJ, Pflüger-Grau K, Marin-Sanguino A. Anaplerotic Pathways in Halomonas elongata: The Role of the Sodium Gradient. Front Microbiol 2020; 11:561800. [PMID: 33101236 PMCID: PMC7545133 DOI: 10.3389/fmicb.2020.561800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2022] Open
Abstract
Salt tolerance in the γ-proteobacterium Halomonas elongata is linked to its ability to produce the compatible solute ectoine. The metabolism of ectoine production is of great interest since it can shed light on the biochemical basis of halotolerance as well as pave the way for the improvement of the biotechnological production of such compatible solute. Ectoine belongs to the biosynthetic family of aspartate-derived amino-acids. Aspartate is formed from oxaloacetate, thereby connecting ectoine production to the anaplerotic reactions that refill carbon into the tricarboxylic acid cycle (TCA cycle). This places a high demand on these reactions and creates the need to regulate them not only in response to growth but also in response to extracellular salt concentration. In this work, we combine modeling and experiments to analyze how these different needs shape the anaplerotic reactions in H. elongata. First, the stoichiometric and thermodynamic factors that condition the flux distributions are analyzed, then the optimal patterns of operation for oxaloacetate production are calculated. Finally, the phenotype of two deletion mutants lacking potentially relevant anaplerotic enzymes: phosphoenolpyruvate carboxylase (Ppc) and oxaloacetate decarboxylase (Oad) are experimentally characterized. The results show that the anaplerotic reactions in H. elongata are indeed subject to evolutionary pressures that differ from those faced by other gram-negative bacteria. Ectoine producing halophiles must meet a higher metabolic demand for oxaloacetate and the reliance of many marine bacteria on the Entner-Doudoroff pathway compromises the anaplerotic efficiency of Ppc, which is usually one of the main enzymes fulfilling this role. The anaplerotic flux in H. elongata is contributed not only by Ppc but also by Oad, an enzyme that has not yet been shown to play this role in vivo. Ppc is necessary for H. elongata to grow normally at low salt concentrations but it is not required to achieve near maximal growth rates as long as there is a steep sodium gradient. On the other hand, the lack of Oad presents serious difficulties to grow at high salt concentrations. This points to a shared role of these two enzymes in guaranteeing the supply of oxaloacetate for biosynthetic reactions.
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Affiliation(s)
- Karina Hobmeier
- Professorship for Systems Biotechnology, Technical University of Munich, Munich, Germany
| | - Marie C. Goëss
- Professorship for Systems Biotechnology, Technical University of Munich, Munich, Germany
| | - Christiana Sehr
- Professorship for Systems Biotechnology, Technical University of Munich, Munich, Germany
| | - Sebastian Schwaminger
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich, Munich, Germany
| | - Sonja Berensmeier
- Bioseparation Engineering Group, Department of Mechanical Engineering, Technical University of Munich, Munich, Germany
| | - Andreas Kremling
- Professorship for Systems Biotechnology, Technical University of Munich, Munich, Germany
| | - Hans Jörg Kunte
- Division of Biodeterioration and Reference Organisms, Bundesanstalt Für Materialforschung und -Prüfung (BAM), Berlin, Germany
| | - Katharina Pflüger-Grau
- Professorship for Systems Biotechnology, Technical University of Munich, Munich, Germany
| | - Alberto Marin-Sanguino
- Professorship for Systems Biotechnology, Technical University of Munich, Munich, Germany
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139
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Johnson GE, Lalanne JB, Peters ML, Li GW. Functionally uncoupled transcription-translation in Bacillus subtilis. Nature 2020; 585:124-128. [PMID: 32848247 PMCID: PMC7483943 DOI: 10.1038/s41586-020-2638-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/22/2020] [Indexed: 11/10/2022]
Abstract
Tight coupling of transcription and translation is considered a defining feature of bacterial gene expression1,2. The pioneering ribosome can both physically associate and kinetically coordinate with RNA polymerase (RNAP)3-11, forming a signal-integration hub for co-transcriptional regulation that includes translation-based attenuation12,13 and RNA quality control2. However, it remains unclear whether transcription-translation coupling-together with its broad functional consequences-is indeed a fundamental characteristic of bacteria other than Escherichia coli. Here we show that RNAPs outpace pioneering ribosomes in the Gram-positive model bacterium Bacillus subtilis, and that this 'runaway transcription' creates alternative rules for both global RNA surveillance and translational control of nascent RNA. In particular, uncoupled RNAPs in B. subtilis explain the diminished role of Rho-dependent transcription termination, as well as the prevalence of mRNA leaders that use riboswitches and RNA-binding proteins. More broadly, we identified widespread genomic signatures of runaway transcription in distinct phyla across the bacterial domain. Our results show that coupled RNAP-ribosome movement is not a general hallmark of bacteria. Instead, translation-coupled transcription and runaway transcription constitute two principal modes of gene expression that determine genome-specific regulatory mechanisms in prokaryotes.
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Affiliation(s)
- Grace E Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michelle L Peters
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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140
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Landberg J, Wright NR, Wulff T, Herrgård MJ, Nielsen AT. CRISPR interference of nucleotide biosynthesis improves production of a single-domain antibody in Escherichia coli. Biotechnol Bioeng 2020; 117:3835-3848. [PMID: 32808670 PMCID: PMC7818426 DOI: 10.1002/bit.27536] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/13/2020] [Accepted: 08/14/2020] [Indexed: 12/23/2022]
Abstract
Growth decoupling can be used to optimize the production of biochemicals and proteins in cell factories. Inhibition of excess biomass formation allows for carbon to be utilized efficiently for product formation instead of growth, resulting in increased product yields and titers. Here, we used CRISPR interference to increase the production of a single‐domain antibody (sdAb) by inhibiting growth during production. First, we screened 21 sgRNA targets in the purine and pyrimidine biosynthesis pathways and found that the repression of 11 pathway genes led to the increased green fluorescent protein production and decreased growth. The sgRNA targets pyrF, pyrG, and cmk were selected and further used to improve the production of two versions of an expression‐optimized sdAb. Proteomics analysis of the sdAb‐producing pyrF, pyrG, and cmk growth decoupling strains showed significantly decreased RpoS levels and an increase of ribosome‐associated proteins, indicating that the growth decoupling strains do not enter stationary phase and maintain their capacity for protein synthesis upon growth inhibition. Finally, sdAb production was scaled up to shake‐flask fermentation where the product yield was improved 2.6‐fold compared to the control strain with no sgRNA target sequence. An sdAb content of 14.6% was reached in the best‐performing pyrG growth decoupling strain.
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Affiliation(s)
- Jenny Landberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Naia Risager Wright
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tune Wulff
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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141
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Wang Y, Wang X, Yu L, Tian Y, Li S, Leng F, Ma J, Chen J. Effects of Sr 2 + on the preparation of Escherchia coli DH5α competent cells and plasmid transformation. PeerJ 2020. [DOI: 10.7717/peerj.9480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial gene transformation used with Escherichia coli as a desired microorganism is one of the important techniques in genetic engineering. In this study, the preparation of E. coli DH5α competent cells treated with SrCl2 and transformation by heat-shock with pUC19 plasmid was optimized by Response Surface Methodology (RSM). Other five E. coli strains including BL21 (DE3), HB-101, JM109, TOP10 and TG1, three different sizes plasmids (pUC19, pET32a, pPIC9k) were used to verify the protocol, respectively. The transformation mechanism was explored by scanning electron microscope combined with energy dispersive spectrometer (SEM-EDS), atomic absorption spectroscopy (AAS) and Fourier-transform infrared spectroscopy (FT-IR). An equation of regression model was obtained, and the ideal parameters were Sr2 + ions of 90 mM, heat-shock time of 90 s and 9 ng of plasmid. Under this conditions, the transformation efficiency could almost reach to 106 CFU/µg DNA. A small change of the cell surface structure has been observed between E. coli DH5α strain and competent cells by abovementioned spectrum technologies, which implied that a strict regulation mechanism involved in the formation of competent cells and transformation of plasmids. An equation of regression model for the competent cells preparation and plasmid transformation could be applied in gene cloning technology
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Affiliation(s)
- Yonggang Wang
- School of Energy and Power Engineering, Lanzhou University of Technology, Lan Zhou, Gansu, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Xinjian Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Linmiao Yu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Yuan Tian
- Lhasa National Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Shaowei Li
- Lhasa National Ecological Research Station, Key Laboratory of Ecosystem Network Observation and Modelling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Jianzhong Ma
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
| | - Jixiang Chen
- School of Energy and Power Engineering, Lanzhou University of Technology, Lan Zhou, Gansu, China
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, Gansu, China
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142
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Caccamo PD, Jacq M, VanNieuwenhze MS, Brun YV. A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex. Curr Biol 2020; 30:3908-3922.e4. [PMID: 32795444 DOI: 10.1016/j.cub.2020.07.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 05/22/2020] [Accepted: 07/20/2020] [Indexed: 12/31/2022]
Abstract
Bacteria come in an array of shapes and sizes, but the mechanisms underlying diverse morphologies are poorly understood. The peptidoglycan (PG) cell wall is the primary determinant of cell shape. At the molecular level, morphological variation often results from the regulation of enzymes involved in cell elongation and division. These enzymes are spatially controlled by cytoskeletal scaffolding proteins, which both recruit and organize the PG synthesis complex. How then do cells define alternative morphogenic processes that are distinct from cell elongation and division? To address this, we have turned to the specific morphotype of Alphaproteobacterial stalks. Stalk synthesis is a specialized form of zonal growth, which requires PG synthesis in a spatially constrained zone to extend a thin cylindrical projection of the cell envelope. The morphogen SpmX defines the site of stalk PG synthesis, but SpmX is a PG hydrolase. How then does a non-cytoskeletal protein, SpmX, define and constrain PG synthesis to form stalks? Here, we report that SpmX and the bactofilin BacA act in concert to regulate stalk synthesis in Asticcacaulis biprosthecum. We show that SpmX recruits BacA to the site of stalk synthesis. BacA then serves as a stalk-specific topological organizer for PG synthesis activity, including its recruiter SpmX, at the base of the stalk. In the absence of BacA, cells produce "pseudostalks" that are the result of unconstrained PG synthesis. Therefore, the protein responsible for recruitment of a morphogenic PG remodeling complex, SpmX, is distinct from the protein that topologically organizes the complex, BacA.
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Affiliation(s)
- Paul D Caccamo
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA; School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, USA
| | - Maxime Jacq
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Pavillon Roger-Gaudry, C.P. 6128, Succursale Centreville, Montréal, Canada
| | - Michael S VanNieuwenhze
- Department of Molecular and Cellular Biochemistry, 212 S. Hawthorne Drive, Indiana University, Bloomington, IN 47405, USA; Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Yves V Brun
- Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Pavillon Roger-Gaudry, C.P. 6128, Succursale Centreville, Montréal, Canada.
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143
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Tang H, Zhu J, Wu S, Niu H. Identification and characterization of an actin filament-associated Anaplasma phagocytophilum protein. Microb Pathog 2020; 147:104439. [PMID: 32768516 DOI: 10.1016/j.micpath.2020.104439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 10/23/2022]
Abstract
Anaplasma phagocytophilum, the aetiologic agent of human granulocytic anaplasmosis (HGA) is an obligate intracellular Gram-negative bacterium. During intracellular replication, A. phagocytophilum interacts with many host cell components including actin cytoskeleton. However the bacterial factors contributing to the interaction between A. phagocytophilum and actin filaments remain unknown. In this study we identified a novel type IV secretion system substrate of A. phagocytophilum by employing TEM-1 β-lactamase based protein translocation assay, and found it is an actin filament-associated protein. Here, we name this protein as an actin filament-associated Anaplasma phagocytophilumprotein (AFAP). Further analysis showed that the middle region of AFAP harboring four tandem repeats is involved in its interaction with actin filaments. The identification and characterization of an actin filament-associated A. phagocytophilum protein in this study may help understand the interaction between A. phagocytophilum and actin cytoskeleton of its host cells, facilitating the elucidation of HGA pathogenesis.
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Affiliation(s)
- Hongcheng Tang
- Department of Microbiology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Jiafeng Zhu
- Department of Microbiology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Shuyan Wu
- Department of Microbiology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Hua Niu
- Department of Microbiology, School of Biology & Basic Medical Sciences, Soochow University, Suzhou, Jiangsu Province, 215123, China.
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144
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Hubbard ATM, Bulgasim I, Roberts AP. A novel hemA mutation is responsible for a small-colony-variant phenotype in Escherichia coli. MICROBIOLOGY-SGM 2020; 167. [PMID: 32762803 DOI: 10.1099/mic.0.000962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We identified a small colony variant (SCV) of an amoxicillin/clavulanic acid-resistant derivative of a clinical isolate of Escherichia coli from Malawi, which was selected for in vitro in a subinhibitory concentration of gentamicin. The SCV was auxotrophic for hemin and had impaired biofilm formation compared to the ancestral isolates. A single novel nucleotide polymorphism (SNP) in hemA, which encodes a glutamyl-tRNA reductase that catalyses the initial step of porphyrin biosynthesis leading to the production of haem, was responsible for the SCV phenotype. We showed the SNP in hemA resulted in a significant fitness cost to the isolate, which persisted even in the presence of hemin. However, the phenotype quickly reverted during sequential sub-culturing in liquid growth media. As hemA is not found in mammalian cells, and disruption of the gene results in a significant fitness cost, it represents a potential target for novel drug development specifically for the treatment of catheter-associated urinary tract infections caused by E. coli.
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Affiliation(s)
- Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Issra Bulgasim
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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145
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Baumschlager A, Rullan M, Khammash M. Exploiting natural chemical photosensitivity of anhydrotetracycline and tetracycline for dynamic and setpoint chemo-optogenetic control. Nat Commun 2020; 11:3834. [PMID: 32737309 PMCID: PMC7395757 DOI: 10.1038/s41467-020-17677-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 07/02/2020] [Indexed: 01/02/2023] Open
Abstract
The transcriptional inducer anhydrotetracycline (aTc) and the bacteriostatic antibiotic tetracycline (Tc) are commonly used in all fields of biology for control of transcription or translation. A drawback of these and other small molecule inducers is the difficulty of their removal from cell cultures, limiting their application for dynamic control. Here, we describe a simple method to overcome this limitation, and show that the natural photosensitivity of aTc/Tc can be exploited to turn them into highly predictable optogenetic transcriptional- and growth-regulators. This new optogenetic class uniquely features both dynamic and setpoint control which act via population-memory adjustable through opto-chemical modulation. We demonstrate this method by applying it for dynamic gene expression control and for enhancing the performance of an existing optogenetic system. We then expand the utility of the aTc system by constructing a new chemical bandpass filter that increases its aTc response range. The simplicity of our method enables scientists and biotechnologists to use their existing systems employing aTc/Tc for dynamic optogenetic experiments without genetic modification.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Marc Rullan
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
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146
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Duprey A, Groisman EA. FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo. mBio 2020; 11:e01053-20. [PMID: 32723920 PMCID: PMC7387798 DOI: 10.1128/mbio.01053-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/24/2020] [Indexed: 11/20/2022] Open
Abstract
DNA supercoiling (DS) is essential for life because it controls critical processes, including transcription, replication, and recombination. Current methods to measure DNA supercoiling in vivo are laborious and unable to examine single cells. Here, we report a method for high-throughput measurement of bacterial DNA supercoiling in vivoFluorescent evaluation of DNA supercoiling (FEDS) utilizes a plasmid harboring the gene for a green fluorescent protein transcribed by a discovered promoter that responds exclusively to DNA supercoiling and the gene for a red fluorescent protein transcribed by a constitutive promoter as the internal standard. Using FEDS, we uncovered single-cell heterogeneity in DNA supercoiling and established that, surprisingly, population-level decreases in DNA supercoiling result from a low-mean/high-variance DNA supercoiling subpopulation rather than from a homogeneous shift in supercoiling of the whole population. In addition, we identified a regulatory loop in which a gene that decreases DNA supercoiling is transcriptionally repressed when DNA supercoiling increases.IMPORTANCE DNA represents the chemical support of genetic information in all forms of life. In addition to its linear sequence of nucleotides, it bears critical information in its structure. This information, called DNA supercoiling, is central to all fundamental DNA processes, such as transcription and replication, and defines cellular physiology. Unlike reading of a nucleotide sequence, DNA supercoiling determinations have been laborious. We have now developed a method for rapid measurement of DNA supercoiling and established its utility by identifying a novel regulator of DNA supercoiling in the bacterium Salmonella enterica as well as behaviors that could not have been discovered with current methods.
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Affiliation(s)
- Alexandre Duprey
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Microbial Sciences Institute, West Haven, Connecticut, USA
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147
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Marshall RL, Bavro VN. Mutations in the TolC Periplasmic Domain Affect Substrate Specificity of the AcrAB-TolC Pump. Front Mol Biosci 2020; 7:166. [PMID: 32850959 PMCID: PMC7396618 DOI: 10.3389/fmolb.2020.00166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/01/2020] [Indexed: 01/08/2023] Open
Abstract
TolC and the other members of the outer membrane factor (OMF) family are outer membrane proteins forming trimeric channels that serve as a conduit for most actively effluxed substrates in Gram-negative bacteria by providing a key component in a multitude of tripartite efflux-pumps. Current models of tripartite pump assembly ascribe substrate selection to the inner-membrane transporter and periplasmic-adapter protein (PAP) assembly, suggesting that TolC is a passive, non-selective channel. While the membrane-embedded portion of the protein adopts a porin-like fold, the periplasmic domain of TolC presents a unique "alpha-barrel" architecture. This alpha-barrel consists of pseudo-continuous α-helices forming curved coiled-coils, whose tips form α-helical hairpins, relaxation of which results in a transition of TolC from a closed to an open-aperture state allowing effective efflux of substrates through its channel. Here, we analyzed the effects of site-directed mutations targeting the alpha-barrel of TolC, of the principal tripartite efflux-pump Escherichia coli AcrAB-TolC, on the activity and specificity of efflux. Live-cell functional assays with these TolC mutants revealed that positions both at the periplasmic tip of, and partway up the TolC coiled-coil alpha-barrel domain are involved in determining the functionality of the complex. We report that mutations affecting the electrostatic properties of the channel, particularly the D371V mutation, significantly impact growth even in the absence of antibiotics, causing hyper-susceptibility to all tested efflux-substrates. These results suggest that inhibition of TolC functionality is less well-tolerated than deletion of tolC, and such inhibition may have an antibacterial effect. Significantly and unexpectedly, we identified antibiotic-specific phenotypes associated with novel TolC mutations, suggesting that substrate specificity may not be determined solely by the transporter protein or the PAP, but may reside at least partially with the TolC-channel. Furthermore, some of the effects of mutations are difficult to reconcile with the currently prevalent tip-to-tip model of PAP-TolC interaction due to their location higher-up on the TolC alpha-barrel relative to the proposed PAP-docking sites. Taken together our results suggest a possible new role for TolC in vetting of efflux substrates, alongside its established role in tripartite complex assembly.
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Affiliation(s)
- Robert L. Marshall
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Vassiliy N. Bavro
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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148
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Hanaoka Y, Kimoto H, Yoshimume K, Hara I, Matsuyama H, Yumoto I. Relationship Between Main Channel Structure of Catalases and the Evolutionary Direction in Cold-Adapted Hydrogen Peroxide-Tolerant Exiguobacteium and Psychrobacter. Indian J Microbiol 2020; 60:353-362. [PMID: 32647394 DOI: 10.1007/s12088-020-00878-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
Catalase has crucial role in adaptive response to H2O2. Main channel structure responsible for substrate selectivity was estimated to understand the relationship between the evolutionary direction of catalases from Exiguobacterium oxidotolerans and Psychrobacter piscatorii which survive in cold and high concentration of hydrogen peroxide, and their catalytic property. E. oxidotolerans catalase (EKTA) exhibited a higher ratio of compound I formation rate using peracetic acid (a substrate lager than H2O2)/catalase activity using H2O2 as the substrate than P. piscatori catalase (PKTA). It was considered that the ratio was attributed to the size of the amino acid residues locating at the bottle neck structure in the main channel. The differences in the ratio of the compound I formation rate with peracetic acid to catalase activity with H2O2 between the deeper branches in the phylogenetic tree in both EKTA and PKTA were large. This indicates that catalases from the hydrogen peroxide-tolerant bacteria have evolved in different directions, exhibiting effective catalytic activity and allowing broader substrates size or H2O2-specific substrate acceptability in EKTA and PKTA, respectively. It is considered that the main channel structure reflected the difference in the evolutionary direction of clade 1 and clade 3 catalases.
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Affiliation(s)
- Yoshiko Hanaoka
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
| | - Hideyuki Kimoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan.,School of Biological Science and Engineering, Tokai University, Sapporo, Japan
| | | | | | - Hidetoshi Matsuyama
- School of Biological Science and Engineering, Tokai University, Sapporo, Japan
| | - Isao Yumoto
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
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149
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Genetic dominance governs the evolution and spread of mobile genetic elements in bacteria. Proc Natl Acad Sci U S A 2020; 117:15755-15762. [PMID: 32571917 PMCID: PMC7355013 DOI: 10.1073/pnas.2001240117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mobile genetic elements (MGEs), such as plasmids, promote bacterial evolution through horizontal gene transfer (HGT). However, the rules governing the repertoire of traits encoded on MGEs remain unclear. In this study, we uncovered the central role of genetic dominance shaping genetic cargo in MGEs, using antibiotic resistance as a model system. MGEs are typically present in more than one copy per host bacterium, and as a consequence, genetic dominance favors the fixation of dominant mutations over recessive ones. In addition, genetic dominance also determines the phenotypic effects of horizontally acquired MGE-encoded genes, silencing recessive alleles if the recipient bacterium already carries a wild-type copy of the gene. The combination of these two effects governs the catalog of genes encoded on MGEs. Our results help to understand how MGEs evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. Moreover, our findings offer a framework to forecast the spread and evolvability of MGE-encoded genes, which encode traits of key human interest, such as virulence or antibiotic resistance.
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150
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Fino C, Vestergaard M, Ingmer H, Pierrel F, Gerdes K, Harms A. PasT of Escherichia coli sustains antibiotic tolerance and aerobic respiration as a bacterial homolog of mitochondrial Coq10. Microbiologyopen 2020; 9:e1064. [PMID: 32558363 PMCID: PMC7424257 DOI: 10.1002/mbo3.1064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 12/22/2022] Open
Abstract
Antibiotic‐tolerant persisters are often implicated in treatment failure of chronic and relapsing bacterial infections, but the underlying molecular mechanisms have remained elusive. Controversies revolve around the relative contribution of specific genetic switches called toxin–antitoxin (TA) modules and global modulation of cellular core functions such as slow growth. Previous studies on uropathogenic Escherichia coli observed impaired persister formation for mutants lacking the pasTI locus that had been proposed to encode a TA module. Here, we show that pasTI is not a TA module and that the supposed toxin PasT is instead the bacterial homolog of mitochondrial protein Coq10 that enables the functionality of the respiratory electron carrier ubiquinone as a “lipid chaperone.” Consistently, pasTI mutants show pleiotropic phenotypes linked to defective electron transport such as decreased membrane potential and increased sensitivity to oxidative stress. We link impaired persister formation of pasTI mutants to a global distortion of cellular stress responses due to defective respiration. Remarkably, the ectopic expression of human coq10 largely complements the respiratory defects and decreased persister levels of pasTI mutants. Our work suggests that PasT/Coq10 has a central role in respiratory electron transport that is conserved from bacteria to humans and sustains bacterial tolerance to antibiotics.
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Affiliation(s)
- Cinzia Fino
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | - Martin Vestergaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Hanne Ingmer
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Fabien Pierrel
- CNRS, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France
| | - Kenn Gerdes
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Harms
- Department of Biology, Centre for Bacterial Stress Response and Persistence, University of Copenhagen, Copenhagen, Denmark.,Focal Area of Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
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