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Hernández-Beltrán JCR, San Millán A, Fuentes-Hernández A, Peña-Miller R. Mathematical Models of Plasmid Population Dynamics. Front Microbiol 2021; 12:606396. [PMID: 34803935 PMCID: PMC8600371 DOI: 10.3389/fmicb.2021.606396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/14/2021] [Indexed: 11/24/2022] Open
Abstract
With plasmid-mediated antibiotic resistance thriving and threatening to become a serious public health problem, it is paramount to increase our understanding of the forces that enable the spread and maintenance of drug resistance genes encoded in mobile genetic elements. The relevance of plasmids as vehicles for the dissemination of antibiotic resistance genes, in addition to the extensive use of plasmid-derived vectors for biotechnological and industrial purposes, has promoted the in-depth study of the molecular mechanisms controlling multiple aspects of a plasmids' life cycle. This body of experimental work has been paralleled by the development of a wealth of mathematical models aimed at understanding the interplay between transmission, replication, and segregation, as well as their consequences in the ecological and evolutionary dynamics of plasmid-bearing bacterial populations. In this review, we discuss theoretical models of plasmid dynamics that span from the molecular mechanisms of plasmid partition and copy-number control occurring at a cellular level, to their consequences in the population dynamics of complex microbial communities. We conclude by discussing future directions for this exciting research topic.
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Affiliation(s)
| | | | | | - Rafael Peña-Miller
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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2
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Gurbatri CR, Lia I, Vincent R, Coker C, Castro S, Treuting PM, Hinchliffe TE, Arpaia N, Danino T. Engineered probiotics for local tumor delivery of checkpoint blockade nanobodies. Sci Transl Med 2021; 12:12/530/eaax0876. [PMID: 32051224 DOI: 10.1126/scitranslmed.aax0876] [Citation(s) in RCA: 240] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 10/25/2019] [Accepted: 01/13/2020] [Indexed: 12/25/2022]
Abstract
Checkpoint inhibitors have revolutionized cancer therapy but only work in a subset of patients and can lead to a multitude of toxicities, suggesting the need for more targeted delivery systems. Because of their preferential colonization of tumors, microbes are a natural platform for the local delivery of cancer therapeutics. Here, we engineer a probiotic bacteria system for the controlled production and intratumoral release of nanobodies targeting programmed cell death-ligand 1 (PD-L1) and cytotoxic T lymphocyte-associated protein-4 (CTLA-4) using a stabilized lysing release mechanism. We used computational modeling coupled with experimental validation of lysis circuit dynamics to determine the optimal genetic circuit parameters for maximal therapeutic efficacy. A single injection of this engineered system demonstrated an enhanced therapeutic response compared to analogous clinically relevant antibodies, resulting in tumor regression in syngeneic mouse models. Supporting the potentiation of a systemic immune response, we observed a relative increase in activated T cells, an abscopal effect, and corresponding increases in systemic T cell memory populations in mice treated with probiotically delivered checkpoint inhibitors. Last, we leveraged the modularity of our platform to achieve enhanced therapeutic efficacy in a poorly immunogenic syngeneic mouse model through effective combinations with a probiotically produced cytokine, granulocyte-macrophage colony-stimulating factor (GM-CSF). Together, these results demonstrate that our engineered probiotic system bridges synthetic biology and immunology to improve upon checkpoint blockade delivery.
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Affiliation(s)
- Candice R Gurbatri
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Ioana Lia
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Rosa Vincent
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Courtney Coker
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Samuel Castro
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Piper M Treuting
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Taylor E Hinchliffe
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Nicholas Arpaia
- Department of Microbiology & Immunology, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10027, USA.,Data Science Institute, Columbia University, New York, NY 10027, USA
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3
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Fedorec AJH, Ozdemir T, Doshi A, Ho YK, Rosa L, Rutter J, Velazquez O, Pinheiro VB, Danino T, Barnes CP. Two New Plasmid Post-segregational Killing Mechanisms for the Implementation of Synthetic Gene Networks in Escherichia coli. iScience 2019; 14:323-334. [PMID: 30954530 PMCID: PMC6489366 DOI: 10.1016/j.isci.2019.03.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/29/2018] [Accepted: 03/18/2019] [Indexed: 11/03/2022] Open
Abstract
Plasmids are the workhorse of both industrial biotechnology and synthetic biology, but ensuring they remain in bacterial cells is a challenge. Antibiotic selection cannot be used to stabilize plasmids in most real-world applications, and inserting dynamical gene networks into the genome remains challenging. Plasmids have evolved several mechanisms for stability, one of which, post-segregational killing (PSK), ensures that plasmid-free cells do not survive. Here we demonstrate the plasmid-stabilizing capabilities of the axe/txe toxin-antitoxin system and the microcin-V bacteriocin system in the probiotic bacteria Escherichia coli Nissle 1917 and show that they can outperform the commonly used hok/sok. Using plasmid stability assays, automated flow cytometry analysis, mathematical models, and Bayesian statistics we quantified plasmid stability in vitro. Furthermore, we used an in vivo mouse cancer model to demonstrate plasmid stability in a real-world therapeutic setting. These new PSK systems, plus the developed Bayesian methodology, will have wide applicability in clinical and industrial biotechnology.
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Affiliation(s)
- Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK; Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology, University College London, London WC1E 6BT, UK.
| | - Tanel Ozdemir
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Anjali Doshi
- Department of Biomedical Engineering, Columbia University, New York City, NY 10027, USA
| | - Yan-Kay Ho
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Luca Rosa
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Jack Rutter
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Oscar Velazquez
- Department of Biomedical Engineering, Columbia University, New York City, NY 10027, USA
| | - Vitor B Pinheiro
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK; KU Leuven Rega Institute for Medical Research, Herestraat, 49 Box 1030, 3000 Leuven, Belgium
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York City, NY 10027, USA; Data Science Institute, Columbia University, New York, NY 10027, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK; Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
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4
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Ao X, Yao Y, Li T, Yang TT, Dong X, Zheng ZT, Chen GQ, Wu Q, Guo Y. A Multiplex Genome Editing Method for Escherichia coli Based on CRISPR-Cas12a. Front Microbiol 2018; 9:2307. [PMID: 30356638 PMCID: PMC6189296 DOI: 10.3389/fmicb.2018.02307] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/10/2018] [Indexed: 12/26/2022] Open
Abstract
Various methods for editing specific sites in the Escherichia coli chromosome are available, and gene-size (∼1 kb) integration into a single site or to introduce deletions, short insertions or point mutations into multiple sites can be conducted in a short period of time. However, a method for rapidly integrating multiple gene-size sequences into different sites has not been developed yet. Here, we describe a method and plasmid system that makes it possible to simultaneously insert genes into multiple specific loci of the E. coli genome without the need for chromosomal markers. The method uses a CRISPR-Cas12a system to eliminate unmodified cells by double-stranded DNA cleavage in conjunction with the phage-derived λ-Red recombinases to facilitate recombination between the chromosome and the donor DNA. We achieved the insertion of up to 3 heterologous genes in one round of recombination and selection. To demonstrate the practical application of this gene-insertion method, we constructed a recombinant E. coli producing an industrially useful chemical, 5-aminolevulinic acid (ALA), with high-yield. Moreover, a similar two-plasmid system was built to edit the genome of the extremophile Halomonas bluephagenesis.
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Affiliation(s)
- Xiang Ao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Yi Yao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Tian Li
- China National Center for Biotechnology Development, Beijing, China
| | - Ting-Ting Yang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Dong
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Ze-Tong Zheng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Guo-Qiang Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Qiong Wu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Yingying Guo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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5
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Englaender JA, Jones JA, Cress BF, Kuhlman TE, Linhardt RJ, Koffas MAG. Effect of Genomic Integration Location on Heterologous Protein Expression and Metabolic Engineering in E. coli. ACS Synth Biol 2017; 6:710-720. [PMID: 28055177 DOI: 10.1021/acssynbio.6b00350] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chromosomal integration offers a selection-free alternative to DNA plasmids for expression of foreign proteins and metabolic pathways. Episomal plasmid DNA is convenient but has drawbacks including increased metabolic burden and the requirement for selection in the form of antibiotics. E. coli has long been used for the expression of foreign proteins and for the production of valuable metabolites by expression of complete metabolic pathways. The gene encoding the fluorescent reporter protein mCherry was integrated into four genomic loci on the E. coli chromosome to measure protein expression at each site. Expression levels ranged from 25% to 500% compared to the gene expressed on a high-copy plasmid. Modular expression of DNA is one of the most commonly used methods for optimizing metabolite production by metabolic engineering. By combining a recently developed method for integration of large synthetic DNA constructs into the genome, we were able to integrate two foreign pathways into the same four genomic loci. We have demonstrated that only one of the genomic loci resulted in the production of violacein, and that all four loci produced trans-cinnamic acid from the TAL pathway.
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Affiliation(s)
- Jacob A Englaender
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - J Andrew Jones
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemistry, Hamilton College , Clinton, New York 13323, United States
| | - Brady F Cress
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Thomas E Kuhlman
- Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Carl. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Robert J Linhardt
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Mattheos A G Koffas
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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6
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McDaniel MM, Krishna N, Handagama WG, Eda S, Ganusov VV. Quantifying Limits on Replication, Death, and Quiescence of Mycobacterium tuberculosis in Mice. Front Microbiol 2016; 7:862. [PMID: 27379030 PMCID: PMC4906525 DOI: 10.3389/fmicb.2016.00862] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/23/2016] [Indexed: 02/02/2023] Open
Abstract
When an individual is exposed to Mycobacterium tuberculosis (Mtb) three outcomes are possible: bacterial clearance, active disease, or latent infection. It is generally believed that most individuals exposed to Mtb become latently infected and carry the mycobacteria for life. How Mtb is maintained during this latent infection remains largely unknown. During an Mtb infection in mice, there is a phase of rapid increase in bacterial numbers in the murine lungs within the first 3 weeks, and then bacterial numbers either stabilize or increase slowly over the period of many months. It has been debated whether the relatively constant numbers of bacteria in the chronic infection result from latent (dormant, quiescent), non-replicating bacteria, or whether the observed Mtb cell numbers are due to balance between rapid replication and death. A recent study of mice, infected with a Mtb strain carrying an unstable plasmid, showed that during the chronic phase, Mtb was replicating at significant rates. Using experimental data from this study and mathematical modeling we investigated the limits of the rates of bacterial replication, death, and quiescence during Mtb infection of mice. First, we found that to explain the data the rates of bacterial replication and death could not be constant and had to decrease with time since infection unless there were large changes in plasmid segregation probability over time. While a decrease in the rate of Mtb replication with time since infection was expected due to depletion of host's resources, a decrease in the Mtb death rate was counterintuitive since Mtb-specific immune response, appearing in the lungs 3–4 weeks after infection, should increase removal of bacteria. Interestingly, we found no significant correlation between estimated rates of Mtb replication and death suggesting the decline in these rates was driven by independent mechanisms. Second, we found that the data could not be explained by assuming that bacteria do not die, suggesting that some removal of bacteria from lungs of these mice had to occur even though the total bacterial counts in these mice always increased over time. Third and finally, we showed that to explain the data the majority of bacterial cells (at least ~60%) must be replicating in the chronic phase of infection further challenging widespread belief of nonreplicating Mtb in latency. Our predictions were robust to some changes in the structure of the model, for example, when the loss of plasmid-bearing cells was mainly due to high fitness cost of the plasmid. Further studies should determine if more mechanistic models for Mtb dynamics are also able to accurately explain these data.
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Affiliation(s)
- Margaret M McDaniel
- National Institute for Mathematical and Biological SynthesisKnoxville, TN, USA; Department of Biochemistry, Cellular and Molecular Biology, University of TennesseeKnoxville, TN, USA; Department of Mathematics, University of TennesseeKnoxville, TN, USA
| | - Nitin Krishna
- National Institute for Mathematical and Biological SynthesisKnoxville, TN, USA; The College at the University of ChicagoChicago, IL, USA
| | - Winode G Handagama
- National Institute for Mathematical and Biological SynthesisKnoxville, TN, USA; Departments of Chemistry and Mathematics, Maryville CollegeMaryville, TN, USA
| | - Shigetoshi Eda
- National Institute for Mathematical and Biological SynthesisKnoxville, TN, USA; Department of Forestry, Wildlife and Fisheries, University of TennesseeKnoxville, TN, USA
| | - Vitaly V Ganusov
- National Institute for Mathematical and Biological SynthesisKnoxville, TN, USA; Department of Mathematics, University of TennesseeKnoxville, TN, USA; Department of Microbiology, University of TennesseeKnoxville, TN, USA
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7
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Ongley SE, Bian X, Neilan BA, Müller R. Recent advances in the heterologous expression of microbial natural product biosynthetic pathways. Nat Prod Rep 2013; 30:1121-38. [PMID: 23832108 DOI: 10.1039/c3np70034h] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The heterologous expression of microbial natural product biosynthetic pathways coupled with advanced DNA engineering enables optimisation of product yields, functional elucidation of cryptic gene clusters, and generation of novel derivatives. This review summarises the recent advances in cloning and maintenance of natural product biosynthetic gene clusters for heterologous expression and the efforts fundamental for discovering novel natural products in the post-genomics era, with a focus on polyketide synthases (PKSs) and non-ribosomal polypeptide synthetases (NRPS).
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Affiliation(s)
- Sarah E Ongley
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
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8
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Mozzetti V, Grattepanche F, Moine D, Berger B, Rezzonico E, Arigoni F, Lacroix C. Transcriptome analysis and physiology of Bifidobacterium longum NCC2705 cells under continuous culture conditions. Benef Microbes 2013; 3:261-72. [PMID: 23234728 DOI: 10.3920/bm2012.0025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A central issue in the use of probiotics in food and food supplements is their sensitivity to many environmental stress factors. The resistance of probiotic cells to lethal stress can be improved by application of homologous or heterologous sub-lethal stress during culture. This screening procedure is generally performed using batch cultures. Continuous cultures could be a suitable and more efficient method to test different stress factors on one culture instead of repeating several batch cultures. However, before testing stresses using continuous cultures, the physiological stability of continuously produced cells over a considered time period must be first evaluated. A continuous culture of Bifidobacterium longum NCC2705 was maintained for 211 h at a dilution rate of 0.1 per h, mimicking a deceleration growth phase culture. Stable viable cell counts were measured over the culture period, decreasing only moderately from 8.8 to 8.6 log10 cfu/ml. A slight shift in metabolite production, characterized by increased lactate and decreased acetate, formate and ethanol concentrations was observed. Susceptibilities to antibiotics and stress conditions were stable (cefotaxim, ampicillin, ceftazidime) or moderately affected (simulated gastric juices, heat, bile salts, tetracycline, chloramphenicol, penicillin, vancomycin and neomycin) over culturing time. Comparison of gene transcription profiles between samples collected after 31 h of continuous culture and samples collected after 134 and 211 h revealed only limited changes in expression of 1.0 and 3.8% of total genes, respectively. Based on these results, we propose that continuous culture can be used to produce bacterial cells with stable physiological properties suitable for fast and efficient screening of sub-lethal stress conditions.
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Affiliation(s)
- V Mozzetti
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Zürich, Switzerland
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9
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Sunya S, Bideaux C, Molina-Jouve C, Gorret N. Short-term dynamic behavior of Escherichia coli in response to successive glucose pulses on glucose-limited chemostat cultures. J Biotechnol 2013; 164:531-42. [DOI: 10.1016/j.jbiotec.2013.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/22/2012] [Accepted: 01/14/2013] [Indexed: 01/20/2023]
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10
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Chong CL, Chen ML, Wu YC, Tsai KN, Huang CC, Hu CP, Jeng KS, Chou YC, Chang C. Dynamics of HBV cccDNA expression and transcription in different cell growth phase. J Biomed Sci 2011; 18:96. [PMID: 22208719 PMCID: PMC3262020 DOI: 10.1186/1423-0127-18-96] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/30/2011] [Indexed: 01/04/2023] Open
Abstract
Background The covalently closed-circular DNA (cccDNA) of hepatitis B virus (HBV) is associated with viral persistence in HBV-infected hepatocytes. However, the regulation of cccDNA and its transcription in the host cells at different growth stages is not well understood. Methods We took advantages of a stably HBV-producing cell line, 1.3ES2, and examine the dynamic changes of HBV cccDNA, viral transcripts, and viral replication intermediates in different cellular growth stages. Results In this study, we showed that cccDNA increased suddenly in the initial proliferation phase of cell growth, probably attributable to its nuclear replenishment by intracellular nucleocapsids. The amount of cccDNA then decreased dramatically in the cells during their exponential proliferation similar to the loss of extrachromosomal plasmid DNA during cell division, after which it accumulated gradually while the host cells grew to confluency. We found that cccDNA was reduced in dividing cells and could be removed when proliferating cells were subjected to long term of lamivudine (3TC) treatment. The amounts of viral replicative intermediates were rapidly reduced in these proliferating cells and were significantly increased after cells reaching confluency. The expression levels of viral transcripts were increased in parallel with the elevated expression of hepatic transcription factors (HNF4α, CEBPα, PPARα, etc.) during cell growth confluency. The HBV transcripts were transcribed from both integrated viral genome and cccDNA, however the transcriptional abilities of cccDNA was less efficient then that from integrated viral genome in all cell growth stages. We also noted increases in the accumulation of intracellular viral particles and the secretion of mature virions as the cells reached confluency and ceased to grow. Conclusions Based on the dynamics of HBV replication, we propose that HBV replication is modulated differently in the different stages of cell growth, and can be divided into three phases (initial proliferation phase, exponential proliferation phase and growth confluency phase) according to the cell growth curve. The regulation of cccDNA in different cell growth phase and its importance regarding HBV replication are discussed.
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Affiliation(s)
- Chin-Liew Chong
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
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11
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Baranauskaite L, Sereikaite J, Gedminiene G, Bumeliene Z, Bumelis VA. Refolding of porcine growth hormone from inclusion bodies ofEscherichia coli. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420500175820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Carneiro S, Amaral AL, Veloso ACA, Dias T, Peres AM, Ferreira EC, Rocha I. Assessment of physiological conditions inE. colifermentations by epifluorescent microscopy and image analysis. Biotechnol Prog 2009; 25:882-91. [DOI: 10.1002/btpr.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Blais BW, Martinez-Perez A, Gauthier M, Allain R, Pagotto F, Tyler K. Development of unique bacterial strains for use as positive controls in the food microbiology testing laboratory. J Food Prot 2008; 71:2301-6. [PMID: 19044277 DOI: 10.4315/0362-028x-71.11.2301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nalidixic acid-resistant (NalR) mutants of Salmonella enterica serovar Berta and Escherichia coli O157:H7 were derived from wild-type laboratory cultures to serve as distinguishable control strains for routine use in food microbiology testing programs. The prevalence of the NalR phenotype among different bacteria was verified using panels of related and unrelated strains with the ability to grow vigorously on plating media containing nalidixic acid, being restricted to the NalR mutants. The NalR phenotype was stable in both mutant strains over several generations in the absence of selective pressure and enabled their differentiation from wild-type bacteria on the basis of their ability to grow on plating media containing nalidixic acid. A similar approach for the development of a distinguishable Listeria monocytogenes control strain was not possible due to the inherent resistance of this organism to nalidixic acid. Instead, an L. monocytogenes isolate with rare genotypic and serologic features was identified as a possible candidate to serve as a unique and distinguishable positive control strain.
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Affiliation(s)
- Burton W Blais
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Building 22, C.E.F., Ottawa, Ontario, Canada.
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14
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Shuvaev AN, Brilkov AV. A model of bacterial cell cycle duration based on DnaA dynamics and estimation of the population cost of bacterial plasmids. DOKL BIOCHEM BIOPHYS 2007; 416:233-6. [PMID: 18064819 DOI: 10.1134/s1607672907050018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- A N Shuvaev
- Institute of Biophysics, Siberian Branch, Russian Academy of Sciences, Krasnovarsk, 660036 Russia
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15
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Miki T, Ueki M, Kawabata Z, Yamamura N. Long-term dynamics of catabolic plasmids introduced to a microbial community in a polluted environment: a mathematical model. FEMS Microbiol Ecol 2007; 62:211-21. [PMID: 17627781 DOI: 10.1111/j.1574-6941.2007.00357.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The long-term dynamics of mobile plasmids in natural environments are unclear. This is the first study of the long-term dynamics of introduced plasmids with xenobiotic degradation abilities using a mathematical model that describes the horizontal gene transfer (HGT) of plasmids into indigenous bacteria via conjugation. We focussed on negative feedback between the spread of plasmids and their selective advantage, i.e. the severe competition between plasmid-bearing and plasmid-free bacteria resulting from a decrease in xenobiotic concentration caused by the gene expression of plasmids, favoring plasmid-free bacteria. Two types of HGT enhanced the persistence of plasmids and the degradation of the xenobiotic in different conditions: a relatively low rate of 'intergeneric HGT' from introduced to indigenous bacteria and a high rate of 'intraindigenous HGT' from indigenous to indigenous bacteria. In addition, when the indigenous resource supply rate was high and when the cost of bearing plasmids was low, both types of HGT made large contributions to xenobiotic degradation compared to the contribution of vertical transfer via plasmid replication within the introduced host population. Initial conditions were also important; a higher initial density of introduced plasmid-bearing bacteria led to a lower degradation rate over a long time scale.
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Affiliation(s)
- Takeshi Miki
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
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16
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Ponciano JM, De Gelder L, Top EM, Joyce P. The population biology of bacterial plasmids: a hidden Markov model approach. Genetics 2006; 176:957-68. [PMID: 17151258 PMCID: PMC1894622 DOI: 10.1534/genetics.106.061937] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal plasmid transfer plays a key role in bacterial adaptation. In harsh environments, bacterial populations adapt by sampling genetic material from a horizontal gene pool through self-transmissible plasmids, and that allows persistence of these mobile genetic elements. In the absence of selection for plasmid-encoded traits it is not well understood if and how plasmids persist in bacterial communities. Here we present three models of the dynamics of plasmid persistence in the absence of selection. The models consider plasmid loss (segregation), plasmid cost, conjugative plasmid transfer, and observation error. Also, we present a stochastic model in which the relative fitness of the plasmid-free cells was modeled as a random variable affected by an environmental process using a hidden Markov model (HMM). Extensive simulations showed that the estimates from the proposed model are nearly unbiased. Likelihood-ratio tests showed that the dynamics of plasmid persistence are strongly dependent on the host type. Accounting for stochasticity was necessary to explain four of seven time-series data sets, thus confirming that plasmid persistence needs to be understood as a stochastic process. This work can be viewed as a conceptual starting point under which new plasmid persistence hypotheses can be tested.
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Affiliation(s)
- José M. Ponciano
- Department of Mathematics and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 and Department of Ecology, Montana State University, Bozeman, Montana 59717-3460
| | - Leen De Gelder
- Department of Mathematics and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 and Department of Ecology, Montana State University, Bozeman, Montana 59717-3460
| | - Eva M. Top
- Department of Mathematics and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 and Department of Ecology, Montana State University, Bozeman, Montana 59717-3460
| | - Paul Joyce
- Department of Mathematics and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 and Department of Ecology, Montana State University, Bozeman, Montana 59717-3460
- Corresponding author: Department of Mathematics, 413 Brink Hall, University of Idaho, Moscow, ID 83844-3051. E-mail:
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Abstract
Plasmid pB15 was previously shown to evolve increased horizontal (infectious) transfer at the expense of reduced vertical (intergenerational) transfer and vice versa, a key trade-off assumed in theories of parasite virulence. Whereas the models predict that susceptible host abundance should determine which mode of transfer is selectively favored, host density failed to mediate the trade-off in pB15. One possibility is that the plasmid's transfer deviates from the assumption that horizontal spread (conjugation) occurs in direct proportion to cell density. I tested this hypothesis using Escherichia coli/pB15 associations in laboratory serial culture. Contrary to most models of plasmid transfer kinetics, my data show that pB15 invades static (nonshaking) bacterial cultures only at intermediate densities. The results can be explained by phenotypic plasticity in traits governing plasmid transfer. As cells become more numerous, the plasmid's conjugative transfer unexpectedly declines, while the trade-off between transmission routes causes vertical transfer to increase. Thus, at intermediate densities the plasmid's horizontal transfer can offset selection against plasmid-bearing cells, but at high densities pB15 conjugates so poorly that it cannot invade. I discuss adaptive vs. nonadaptive causes for the phenotypic plasticity, as well as potential mechanisms that may lead to complex transfer dynamics of plasmids in liquid environments.
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Affiliation(s)
- Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.
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18
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Sprincova A, Javorsky P, Pristas P. pSRD191, a new member of RepL replicating plasmid family from Selenomonas ruminantium. Plasmid 2005; 54:39-47. [PMID: 15907537 DOI: 10.1016/j.plasmid.2004.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Revised: 11/12/2004] [Accepted: 11/15/2004] [Indexed: 11/16/2022]
Abstract
A numerous plasmid population was detected in strain 19 of Selenomonas ruminantium. The population was found to consist of six plasmids in size ranging from 1.4 to more than 20kb. The smallest 1.4kb cryptic plasmid pSRD191 was further characterized. Sequence analysis identified a single ORF encoding the 177-residue putative replication protein (Rep191) which shared significant homology with RepL family of replication protein from Firmicutes (staphylococci and bacilli). PCR analysis and Southern hybridisation showed that pSRD191 related plasmids are frequently encountered in rumen selenomonads.
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Affiliation(s)
- Adriana Sprincova
- Institute of Animal Physiology, Slovak Academy of Sciences, Soltesovej 4-6, 040 01 Kosice, Slovakia
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