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Michaelis C, Grohmann E. Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms. Antibiotics (Basel) 2023; 12:antibiotics12020328. [PMID: 36830238 PMCID: PMC9952180 DOI: 10.3390/antibiotics12020328] [Citation(s) in RCA: 68] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.
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Characterization of highly ferulate-tolerant Acinetobacter baylyi ADP1 isolates by a rapid reverse-engineering method. Appl Environ Microbiol 2021; 88:e0178021. [PMID: 34788063 DOI: 10.1128/aem.01780-21] [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
Adaptive laboratory evolution (ALE) is a powerful approach for improving phenotypes of microbial hosts. Evolved strains typically contain numerous mutations that can be revealed by whole-genome sequencing. However, determining the contribution of specific mutations to new phenotypes is typically challenging and laborious. This task is complicated by factors such as the mutation type, the genomic context, and the interplay between different mutations. Here, a novel approach was developed to identify the significance of mutations in strains evolved from Acinetobacter baylyi ADP1. This method, termed Rapid Advantageous Mutation ScrEening and Selection (RAMSES), was used to analyze mutants that emerged from stepwise adaptation to, and consumption of, high levels of ferulate, a common lignin-derived aromatic compound. After whole-genome sequence analysis, RAMSES allowed rapid determination of effective mutations and seamless introduction of the beneficial mutations into the chromosomes of new strains with different genetic backgrounds. This simple approach to reverse-engineering exploits the natural competence and high recombination efficiency of ADP1. Mutated DNA, added directly to growing cells, replaces homologous chromosomal regions to generate transformants that will become enriched if there is selective benefit. Thus, advantageous mutations can be rapidly identified. Here, the growth advantage of transformants under selective pressure revealed key mutations in genes related to aromatic transport, including hcaE, hcaK, and vanK, and a gene, ACIAD0482, which is associated with lipopolysaccharide synthesis. This study provides insights into enhanced utilization of industrially relevant aromatic substrates and demonstrates the use of A. baylyi ADP1 as a convenient platform for strain development and evolution studies. Importance Microbial conversion of lignin-enriched streams is a promising approach for lignin valorization. However, the lignin-derived aromatic compounds are toxic to cells at relevant concentrations. Although adaptive laboratory evolution (ALE) is a powerful approach to develop more tolerant strains, it is typically laborious to identify the mechanisms underlying phenotypic improvement. We employed Acinetobacter baylyi ADP1, an aromatic compound degrading strain that may be useful for biotechnology. The natural competence and high recombination efficiency of this strain can be exploited for critical applications such as the breakdown of lignin and plastics, abundant polymers composed of aromatic subunits. The natural transformability of this bacterium enabled us to develop a novel approach for rapid screening of advantageous mutations from ALE-derived aromatic-tolerant ADP1-derived strains. We clarified the mechanisms and genetic targets for improved tolerance towards common lignin-derived aromatic compounds. This study facilitates metabolic engineering for lignin valorization.
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Acinetobacter baylyi ADP1-naturally competent for synthetic biology. Essays Biochem 2021; 65:309-318. [PMID: 33769448 DOI: 10.1042/ebc20200136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 02/02/2023]
Abstract
Acinetobacter baylyi ADP1 is a non-pathogenic soil bacterium known for its metabolic diversity and high natural transformation and recombination efficiency. For these features, A. baylyi ADP1 has been long exploited in studying bacterial genetics and metabolism. The large pool of information generated in the fundamental studies has facilitated the development of a broad range of sophisticated and robust tools for the genome and metabolic engineering of ADP1. This mini-review outlines and describes the recent advances in ADP1 engineering and tool development, exploited in, for example, pathway and enzyme evolution, genome reduction and stabilization, and for the production of native and non-native products in both pure and rationally designed multispecies cultures. The rapidly expanding toolbox together with the unique features of A. baylyi ADP1 provide a strong base for a microbial cell factory excelling in synthetic biology applications where evolution meets rational engineering.
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Jiang X, Palazzotto E, Wybraniec E, Munro LJ, Zhang H, Kell DB, Weber T, Lee SY. Automating Cloning by Natural Transformation. ACS Synth Biol 2020; 9:3228-3235. [PMID: 33231069 DOI: 10.1021/acssynbio.0c00240] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Affordable and automated cloning platforms are essential to many synthetic biology studies. However, the traditional E. coli-based cloning is a major bottleneck as it requires heat shock or electroporation implemented in the robotic workflows. To overcome this problem, we explored bacterial natural transformation for automatic DNA cloning and engineering. Recombinant plasmids are efficiently generated from Gibson or overlap extension PCR (OE-PCR) products by simply adding the DNA into Acinetobacter baylyi ADP1 cultures. No DNA purification, competence induction, or special equipment is required. Up to 10,000 colonies were obtained per microgram of DNA, while the number of false positive colonies was low. We cloned and engineered 21 biosynthetic gene clusters (BGCs) of various types, with length from 1.5 to 19 kb and GC content from 35% to 72%. One of them, a nucleoside BGC, showed antibacterial activity. Furthermore, the method was easily transferred to a low-cost benchtop robot with consistent cloning efficiency. Thus, this automatic natural transformation (ANT) cloning provides an easy, robust, and affordable platform for high throughput DNA engineering.
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Affiliation(s)
- Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Emilia Palazzotto
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ewa Wybraniec
- Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lachlan Jake Munro
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Haibo Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, P. R. China
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Biochemistry and Systems Biology,Institute of Systems, Molecular and Integrative Biology, Biosciences Building, University of Liverpool, LiverpoolL69 7ZB, UK
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Li HZ, Zhang D, Yang K, An XL, Pu Q, Lin SM, Su JQ, Cui L. Phenotypic Tracking of Antibiotic Resistance Spread via Transformation from Environment to Clinic by Reverse D 2O Single-Cell Raman Probing. Anal Chem 2020; 92:15472-15479. [PMID: 33169970 DOI: 10.1021/acs.analchem.0c03218] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The rapid spread of antibiotic resistance threatens our fight against bacterial infections. Environments are an abundant reservoir of potentially transferable resistance to pathogens. However, the trajectory of antibiotic resistance genes (ARGs) spreading from environment to clinic and the associated risk remain poorly understood. Here, single-cell Raman spectroscopy combined with reverse D2O labeling (Raman-rD2O) was developed as a sensitive and rapid phenotypic tool to track the spread of plasmid-borne ARGs from soil to clinical bacteria via transformation. Based on the activity of bacteria in assimilating H to substitute prelabeled D under antibiotic treatment, Raman-rD2O sensitively discerned a small minority of phenotypically resistant transformants from a large pool of recipient cells. Its single-cell level detection greatly facilitated the direct calculation of spread efficiency. Raman-rD2O was further employed to study the transfer of complex soil resistant plasmids to pathogenic bacteria. Soil plasmid ARG-dependent transformability against five clinically relevant antibiotics was revealed and used to assess the spreading risk of different soil ARGs, i.e., ampicillin > cefradine and ciprofloxacin > meropenem and vancomycin. The developed single-cell phenotypic method can track the fate and risk of environmental ARGs to pathogenic bacteria and may guide developing new strategies to prevent the spread of high-risk ARGs.
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Affiliation(s)
- Hong-Zhe Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - DanDan Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiang Pu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Shao-Min Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
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Poikulainen E, Tienaho J, Sarjala T, Santala V. A panel of bioluminescent whole-cell bacterial biosensors for the screening for new antibacterial substances from natural extracts. J Microbiol Methods 2020; 178:106083. [PMID: 33068680 DOI: 10.1016/j.mimet.2020.106083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 01/14/2023]
Abstract
Whole-cell bacterial biosensors can be applied for the screening of antibacterial properties of extracts. We constructed a biosensor panel consisting of four different bacterial biosensor strains: Escherichia, Staphylococcus, Acinetobacter and Pseudomonas for expanded screening potential. The functionality of the panel was first evaluated with known antibacterial compounds: ethanol, naphthoquinones (juglone, lawsone, plumbagin) and a flavonoid (quercetin). Natural extracts comprise a vast source of potential new antibacterials for diverse functional purposes. To demonstrate the utilization of the panel for screening of a demanding sample material, round-leaved sundew (Drosera rotundifolia) extracts were used as an example. Differences between field- and laboratory originating sundew extracts could be detected. This demonstrates the efficiency of the developed biosensor panel in the rapid screening of the antibacterial properties of plant extracts.
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Affiliation(s)
- Emmi Poikulainen
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, 33720 Tampere, Finland.
| | - Jenni Tienaho
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, 33720 Tampere, Finland; Natural Resources Institute Finland, Kaironiementie 15, 39700 Parkano, Finland
| | - Tytti Sarjala
- Natural Resources Institute Finland, Kaironiementie 15, 39700 Parkano, Finland
| | - Ville Santala
- Faculty of Engineering and Natural Sciences, Tampere University, Hervanta campus, Korkeakoulunkatu 8, 33720 Tampere, Finland
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Nikitina AA, Ulasevich SA, Kassirov IS, Bryushkova EA, Koshel EI, Skorb EV. Nanostructured Layer-by-Layer Polyelectrolyte Containers to Switch Biofilm Fluorescence. Bioconjug Chem 2018; 29:3793-3799. [PMID: 30350577 DOI: 10.1021/acs.bioconjchem.8b00648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The development of stimuli-responsive nanocontainers is an issue of utmost importance for many applications such as targeted drug delivery, regulation of the cell and tissue behavior, making bacteria have useful functions and here converting light. The present work shows a new contribution to the design of polyelectrolyte (PE) containers based on surface modified mesoporous titania particles with deposited Ag nanoparticles to achieve chemical light upconversion via biofilms. The PE shell allows slowing down the kinetics of a release of loaded l-arabinose and switching the bacteria luminescence in a certain time. The hybrid TiO2/Ag/PE containers activated at 980 nm (IR) illumination demonstrate 10 times faster release of l-arabinose as opposed to non-activated containers. Fast IR-released l-arabinose switch bacteria fluorescence which we monitor at 510 nm. The approach described herein can be used in many applications where the target and delayed switching and light upconversion are required.
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Affiliation(s)
- Anna A Nikitina
- ITMO University , St. Petersburg 191002 , Russian Federation
| | | | - Ilia S Kassirov
- ITMO University , St. Petersburg 191002 , Russian Federation
| | | | - Elena I Koshel
- ITMO University , St. Petersburg 191002 , Russian Federation
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Santala S, Efimova E, Santala V. Dynamic decoupling of biomass and wax ester biosynthesis in Acinetobacter baylyi by an autonomously regulated switch. Metab Eng Commun 2018; 7:e00078. [PMID: 30271720 PMCID: PMC6158957 DOI: 10.1016/j.mec.2018.e00078] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/13/2018] [Accepted: 09/16/2018] [Indexed: 01/09/2023] Open
Abstract
For improving the microbial production of fuels and chemicals, gene knock-outs and overexpression are routinely applied to intensify the carbon flow from substrate to product. However, their possibilities in dynamic control of the flux between the biomass and product synthesis are limited, whereas dynamic metabolic switches can be used for optimizing the distribution of carbon and resources. The production of single cell oils is especially challenging, as the synthesis is strictly regulated, competes directly with biomass, and requires defined conditions, such as nitrogen limitation. Here, we engineered a metabolic switch for redirecting carbon flow from biomass to wax ester production in Acinetobacter baylyi ADP1 using acetate as a carbon source. Isocitrate lyase, an essential enzyme for growth on acetate, was expressed under an arabinose inducible promoter. The autonomous downregulation of the expression is based on the gradual oxidation of the arabinose inducer by a glucose dehydrogenase gcd. The depletion of the inducer, occurring simultaneously to acetate consumption, switches the cells from a biomass mode to a lipid synthesis mode, enabling the efficient channelling of carbon to wax esters in a simple batch culture. In the engineered strain, the yield and titer of wax esters were improved by 3.8 and 3.1 folds, respectively, over the control strain. In addition, the engineered strain accumulated wax esters 19% of cell dry weight, being the highest reported among microbes. The study provides important insights into the dynamic engineering of the biomass-dependent synthesis pathways for the improved production of biocompounds from low-cost and sustainable substrates. Efficient conversion of acetate to storage lipids (wax ester) is demonstrated. AraC-pBAD promoter coupled with glucose dehydrogenase was used as a dynamic switch. The autonomous switch allowed dynamic shift from biomass to lipid synthesis mode. Wax ester yield and titer were improved by 3–4 folds over the wild type strain. The highest amount of wax esters produced in microbes, 19% of CDW, was achieved.
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Affiliation(s)
- Suvi Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, FI-33720, Tampere, Finland
| | - Elena Efimova
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, FI-33720, Tampere, Finland
| | - Ville Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, Korkeakoulunkatu 8, FI-33720, Tampere, Finland
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