1
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Chiba M, Miri S, Yousuf B, Esmail GA, Leao L, Li Y, Hincke M, Minic Z, Mottawea W, Hammami R. Dual bacteriocin and extracellular vesicle-mediated inhibition of Campylobacter jejuni by the potential probiotic candidate Ligilactobacillus salivarius UO.C249. Appl Environ Microbiol 2024; 90:e0084524. [PMID: 39078127 PMCID: PMC11337818 DOI: 10.1128/aem.00845-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Campylobacter jejuni (C. jejuni) is one of the most common causes of foodborne infections worldwide and a major contributor to diarrheal diseases. This study aimed to explore the ability of commensal gut bacteria to control C. jejuni infection. Bacterial strains from the intestinal mucosa of broilers were screened in vitro against C. jejuni ATCC BAA1153. The cell-free supernatant (CFS) of Ligilactobacillus salivarius UO.C249 showed potent dose-dependent antimicrobial activity against the pathogen, likely due to the presence of bacteriocin-like moieties, as confirmed by protease treatment. Genome and exoproteome analyses revealed the presence of known bacteriocins, including Abp118. The genome of Lg. salivarius UO.C249 harbors a 1.8-Mb chromosome and a 203-kb megaplasmid. The strain was susceptible to several antibiotics and had a high survival rate in the simulated chicken gastrointestinal tract (GIT). Post-protease treatment revealed residual inhibitory activity, suggesting alternative antimicrobial mechanisms. Short-chain fatty acid (SCFA) quantification confirmed non-inhibitory levels of acetic (24.4 ± 1.2 mM), isovaleric (34 ± 1.0 µM), and butyric (32 ± 2.5 µM) acids. Interestingly, extracellular vesicles (EVs) isolated from the CFS of Lg. salivarius UO.C249 were found to inhibit C. jejuni ATCC BAA-1153. Proteome profiling of these EVs revealed the presence of unique proteins distinct from bacteriocins identified in CFS. The majority of the identified proteins in EVs are located in the membrane and play roles in transmembrane transport and peptidoglycan degradation, peptidase, proteolysis, and hydrolysis. These findings suggest that although bacteriocins are a primary antimicrobial mechanism, EV production also contributes to the inhibitory activity of Lg. salivarius UO.C249 against C. jejuni. IMPORTANCE Campylobacter jejuni (C. jejuni) is a major cause of gastroenteritis and a global public health concern. The increasing antibiotic resistance and lack of effective alternatives in livestock production pose serious challenges for controlling C. jejuni infections. Therefore, alternative strategies are needed to control this pathogen, especially in the poultry industry where it is prevalent and can be transmitted to humans through contaminated food products. In this study, Ligilactobacillus salivarius UO.C249 isolated from broiler intestinal mucosa inhibited C. jejuni and exhibited important probiotic features. Beyond bacteriocins, Lg. salivarius UO.C249 secretes antimicrobial extracellular vesicles (EVs) with a unique protein set distinct from bacteriocins that are involved in transmembrane transport and peptidoglycan degradation. Our findings suggest that beyond bacteriocins, EV production is also a distinct inhibitory signaling mechanism used by Lg. salivarius UO.C249 to control C. jejuni. These findings hold promise for the application of probiotic EVs for pathogen control.
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Affiliation(s)
- Mariem Chiba
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Saba Miri
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Basit Yousuf
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Galal Ali Esmail
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Luana Leao
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Yingxi Li
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Maxwell Hincke
- Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Walid Mottawea
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Riadh Hammami
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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2
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Kozlova S, Morozova N, Ispolatov Y, Severinov K. Dependence of post-segregational killing mediated by Type II restriction-modification systems on the lifetime of restriction endonuclease effective activity. mBio 2024; 15:e0140824. [PMID: 38980007 PMCID: PMC11324026 DOI: 10.1128/mbio.01408-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
Plasmid-borne Type II restriction-modification (RM) systems mediate post-segregational killing (PSK). PSK is thought to be caused by the dilution of restriction and modification enzymes during cell division, resulting in accumulation of unmethylated DNA recognition sites and their cleavage by restriction endonucleases. PSK is the likely reason for stabilization of plasmids carrying RM systems in the absence of selection for plasmid maintenance. In this study, we developed a CRISPR interference-based method to eliminate RM-carrying plasmids and study PSK-related phenomena with minimal perturbation to the Escherichia coli host. Plasmids carrying the EcoRV, Eco29kI, and EcoRI RM systems were highly stable, and their loss resulted in SOS response and PSK. In contrast, plasmids carrying the Esp1396I system were poorly stabilized; their loss led to a temporary cessation of growth, followed by full recovery. We demonstrate that this unusual behavior is due to a limited lifetime of the Esp1396I restriction endonuclease activity, which, upon Esp1396I plasmid loss, disappears approximately after two cycles of cell division, i.e., before unmethylated sites appear in significant numbers. Our results indicate that whenever PSK induced by a loss of RM systems, and, possibly, other toxin-antitoxin systems, is considered, the lifetimes of individual system components and the growth rate of host cells shall be taken in account. Mathematical modeling shows, that unlike the situation with classical toxin-antitoxin systems, RM system-mediated PSK is possible when the lifetimes of restriction endonuclease and methyltransferase activities are similar, as long as the toxic restriction endonuclease activity persists for more than two chromosome replication cycles.IMPORTANCEIt is widely accepted that many Type II restriction-modification (RM) systems mediate post-segregational killing (PSK) if plasmids that encode them are lost. In this study, we harnessed an inducible CRISPR-Cas system to remove RM plasmids from Escherichia coli cells to study PSK while minimally perturbing cell physiology. We demonstrate that PSK depends on restriction endonuclease activity lifetime and is not observed when it is less than two replication cycles. We present a mathematical model that explains experimental data and shows that unlike the case of toxin-antitoxin-mediated PSK, the loss of an RM system induced PSK even when the RM enzymes have identical lifetimes.
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Affiliation(s)
- Svetlana Kozlova
- Skolkovo Institute of
Science and Technology, Center for Molecular and Cellular
Biology, Moscow,
Russia
| | - Natalia Morozova
- Peter the Great St.
Petersburg Polytechnic University,
St. Petersburg, Russia
| | - Yaroslav Ispolatov
- Physics Department,
University of Santiago of Chile, Center for Interdisciplinary Research
in Astrophysics and Space Science,
Santiago, Chile
| | - Konstantin Severinov
- Waksman Institute for
Microbiology and Department of Molecular Biology and Biochemistry,
Rutgers, State University of New
Jersey, Piscataway, New
Jersey, USA
- Institute of Gene
Biology, Moscow,
Russia
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3
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Diao M, Chen X, Li J, Shi Y, Yu B, Ma Z, Li J, Xie N. Metabolic Engineering of Escherichia coli for High-Level Production of ( R)-Acetoin from Low-Cost Raw Materials. Microorganisms 2023; 11:microorganisms11010203. [PMID: 36677495 PMCID: PMC9867144 DOI: 10.3390/microorganisms11010203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Acetoin is an important four-carbon platform chemical with versatile applications. Optically pure (R)-acetoin is more valuable than the racemate as it can be applied in the asymmetric synthesis of optically active α-hydroxy ketone derivatives, pharmaceuticals, and liquid crystal composites. As a cytotoxic solvent, acetoin at high concentrations severely limits culture performance and impedes the acetoin yield of cell factories. In this study, putative genes that may improve the resistance to acetoin for Escherichia coli were screened. To obtain a high-producing strain, the identified acetoin-resistance gene was overexpressed, and the synthetic pathway of (R)-acetoin was strengthened by optimizing the copy number of the key genes. The engineered E. coli strain GXASR-49RSF produced 81.62 g/L (R)-acetoin with an enantiomeric purity of 96.5% in the fed-batch fermentation using non-food raw materials in a 3-L fermenter. Combining the systematic approach developed in this study with the use of low-cost feedstock showed great potential for (R)-acetoin production via this cost-effective biotechnological process.
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Affiliation(s)
- Mengxue Diao
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
- Correspondence: (M.D.); (N.X.)
| | - Xianrui Chen
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Life Science and Technology College, Guangxi University, Nanning 530004, China
| | - Ya’nan Shi
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhilin Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Life Science and Technology College, Guangxi University, Nanning 530004, China
| | - Jianxiu Li
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Nengzhong Xie
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
- Correspondence: (M.D.); (N.X.)
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4
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Balbuena-Alonso MG, Cortés-Cortés G, Kim JW, Lozano-Zarain P, Camps M, Del Carmen Rocha-Gracia R. Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes. Plasmid 2022; 123-124:102650. [PMID: 36130651 PMCID: PMC10896638 DOI: 10.1016/j.plasmid.2022.102650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.
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Affiliation(s)
- María G Balbuena-Alonso
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Gerardo Cortés-Cortés
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico; Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico.
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5
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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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6
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Lu AE, Maloney AJ, Dalvie NC, Brady JR, Love KR, Love JC, Braatz RD. Modeling of copy number variability in Pichia pastoris. Biotechnol Bioeng 2021; 118:1832-1839. [PMID: 33527350 DOI: 10.1002/bit.27698] [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: 07/19/2020] [Revised: 12/02/2020] [Accepted: 01/21/2021] [Indexed: 11/09/2022]
Abstract
Development of continuous biopharmaceutical manufacturing processes is an area of active research. This study considers the long-term transgene copy number stability of Pichia pastoris in continuous bioreactors. We propose a model of copy number loss that quantifies population heterogeneity. An analytical solution is derived and compared with existing experimental data. The model is then used to provide guidance for stable operating timescales. The model is extended to consider copy number dependent growth such as in the case of Zeocin supplementation. The model is also extended to analyze a continuous seeding strategy. This study is a critical step towards understanding the impact of continuous processing on the stability of Pichia pastoris and the resultant products.
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Affiliation(s)
- Amos E Lu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew J Maloney
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Neil C Dalvie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Joseph R Brady
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kerry R Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - J Christopher Love
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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7
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Evolutionary model for the unequal segregation of high copy plasmids. PLoS Comput Biol 2019; 15:e1006724. [PMID: 30835726 PMCID: PMC6420036 DOI: 10.1371/journal.pcbi.1006724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/15/2019] [Accepted: 12/18/2018] [Indexed: 01/04/2023] Open
Abstract
Plasmids are extrachromosomal DNA elements of microorganisms encoding beneficial genetic information. They were thought to be equally distributed to daughter cells during cell division. Here we use mathematical modeling to investigate the evolutionary stability of plasmid segregation for high-copy plasmids—plasmids that are present in up to several hundred copies per cell—carrying antibiotic resistance genes. Evolutionary stable strategies (ESS) are determined by numerical analysis of a plasmid-load structured population model. The theory predicts that the evolutionary stable segregation strategy of a cell depends on the plasmid copy number: For low and medium plasmid load, both daughters receive in average an equal share of plasmids, while in case of high plasmid load, one daughter obtains distinctively and systematically more plasmids. These findings are in good agreement with recent experimental results. We discuss the interpretation and practical consequences. In the last years, it becomes more and more clear that heterogeneity in isogenic bacterial populations is rather the rule than the exception. This observation is interesting as it reveals the complex social life of bacteria, and also because of tremendous practical implications in medicine, biotechnology, and ecology. The central questions in this field are the identification of the underlying proximate causes (molecular mechanisms) on the one hand and on the other hand the identification of ultimate causes (evolutionary forces) that shape the social life of bacteria. We focus on plasmid dynamics, in particular on plasmid segregation. Recent experiments showed that plasmid segregation depends on the plasmid load. We identify possible evolutionary factors that shaped this process. It turns out that the ambivalence in the effect of plasmids—advantageous if present in low copy numbers, a metabolic burden if present in high copy numbers—is able to explain the experimental observations. The experimental findings can be interpreted as a variant of the principle of division of labor, as it is well known from e.g. persister cells or sporulation. Our model extends the theory of unequal segregation of damage to the ambivalent role of plasmids. Similarly, it is known that certain gene regulatory proteins are acting in a dose-dependent manner. Due to differences in their cellular concentrations and in their affinities to various target promoters, differential gene expression patterns are achieved. Consequently, tight concentration control is observed [1]. Another example is the strict copy-dependent utilization of autolysins during cell division. These enzymes carefully open the bacterial cell wall to allow for its extension [2]. Overproduction of these enzymes leads to cell lysis [3]. These molecules are in principle also candidates for a segregation characteristic similar to that of high copy plasmids described here.
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8
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Tran PT, Fang M, Widyasari K, Kim KH. A plant intron enhances the performance of an infectious clone in planta. J Virol Methods 2019; 265:26-34. [PMID: 30578897 DOI: 10.1016/j.jviromet.2018.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 01/13/2023]
Abstract
Although infectious clones are fundamental tools in virology and plant pathology, their efficacy is often reduced by the instability of viral sequences in Escherichia coli. In this study, we constructed an infectious clone of PepMoV (pPepMoV) in a bacterial binary vector (pSNU1); the clone induces symptoms of PepMoV in agroinfiltrated plants. During its modification and maintenance in E. coli, however, the pPepMoV infectious clone was instable in the bacteria. Manipulation of this unstable clone in the bacterial strain DH10B led to the spontaneous formation of a recombined clone with high stability in the bacteria but with reduced infectivity due to an unwanted insertion of an E. coli sequence in the NIa-protease coding region. Replacement of this sequence with a plant intron restored infectivity and maintained plasmid stability. In addition to restoring plasmid growth in both E. coli and Agrobacterium, the presence of the intron in the PepMoV sequence enhanced the accumulation of PepMoV in agroinfiltrated leaves and resulted in symptom induction in upper systemic leaves that was nearly as strong as with PepMoV sap-inoculation. Plant introns have been previously used to stabilize plasmids in E. coli without any effect or with an unexpected lag in symptom development. In contrast, the current results demonstrated the in vivo enhancement of an infectious clone by a plant intron.
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Affiliation(s)
- Phu-Tri Tran
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Miao Fang
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Kristin Widyasari
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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9
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Standley MS, Million-Weaver S, Alexander DL, Hu S, Camps M. Genetic control of ColE1 plasmid stability that is independent of plasmid copy number regulation. Curr Genet 2018; 65:179-192. [PMID: 29909438 DOI: 10.1007/s00294-018-0858-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 02/07/2023]
Abstract
ColE1-like plasmid vectors are widely used for expression of recombinant genes in E. coli. For these vectors, segregation of individual plasmids into daughter cells during cell division appears to be random, making them susceptible to loss over time when no mechanisms ensuring their maintenance are present. Here we use the plasmid pGFPuv in a recA relA strain as a sensitized model to study factors affecting plasmid stability in the context of recombinant gene expression. We find that in this model, plasmid stability can be restored by two types of genetic modifications to the plasmid origin of replication (ori) sequence: point mutations and a novel 269 nt duplication at the 5' end of the plasmid ori, which we named DAS (duplicated anti-sense) ori. Combinations of these modifications produce a range of copy numbers and of levels of recombinant expression. In direct contradiction with the classic random distribution model, we find no correlation between increased plasmid copy number and increased plasmid stability. Increased stability cannot be explained by reduced levels of recombinant gene expression either. Our observations would be more compatible with a hybrid clustered and free-distribution model, which has been recently proposed based on detection of individual plasmids in vivo using super-resolution fluorescence microscopy. This work suggests a role for the plasmid ori in the control of segregation of ColE1 plasmids that is distinct from replication initiation, opening the door for the genetic regulation of plasmid stability as a strategy aimed at enhancing large-scale recombinant gene expression or bioremediation.
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Affiliation(s)
- Melissa S Standley
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Samuel Million-Weaver
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- College of Engineering, University of Wisconsin-Madison, Madison, 53706, USA
| | - David L Alexander
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Biomolecular Engineering, UCSC, Santa Cruz, USA
| | - Shuai Hu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA.
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10
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Wons E, Mruk I, Kaczorowski T. Isospecific adenine DNA methyltransferases show distinct preferences towards DNA substrates. Sci Rep 2018; 8:8243. [PMID: 29844340 PMCID: PMC5974420 DOI: 10.1038/s41598-018-26434-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/09/2018] [Indexed: 11/09/2022] Open
Abstract
Here, we report results on systematic analysis of DNA substrate preferences of three N6-adenine β-class DNA methyltransferases that are part of the type II restriction-modification systems. The studied enzymes were: M.EcoVIII, M.HindIII and M.LlaCI, which although found in phylogenetically distant bacteria (γ-proteobacteria and low-GC Gram-positive bacteria), recognize the same palindromic specific sequence 5′-AAGCTT-3′ and catalyze formation of N6-methyladenine at the first A-residue. As expected overall the enzymes share the most analyzed features, but they show also some distinct differences in substrate recognition. Therefore DNA methylation reactions were carried out not only under standard, but also under relaxed conditions using DMSO or glycerol. We found that all of these enzymes preferred DNA containing a hemimethylated target site, but differ in modification of ssDNA, especially more pronounced for M.EcoVIII under relaxed conditions. In these conditions they also have shown varied preferences toward secondary sites, which differ by one nucleotide from specific sequence. They preferred sequences with substitutions at the 1st (A1 → G/C) and at the 2nd position (A2 → C), while sites with substitutions at the 3rd position (G3 → A/C) were modified less efficiently. Kinetic parameters of the methylation reaction carried out by M.EcoVIII were determined. Methylation efficiency (kcat/Km) of secondary sites was 4.5–10 times lower when compared to the unmethylated specific sequences, whilst efficiency observed for the hemimethylated substrate was almost 4.5 times greater. We also observed a distinct effect of analyzed enzymes on unspecific interaction with DNA phosphate backbone. We concluded that for all three enzymes the most critical is the phosphodiester bond between G3-C4 nucleotides at the center of the target site.
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Affiliation(s)
- Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland. .,Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, Gdansk, 80-308, Poland.
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