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Zeng T, Ni Y, Li J, Chen H, Lu Q, Jiang M, Xu L, Liu C, Xiao P. Comprehensive analysis of the mitochondrial genome of Rehmannia glutinosa: insights into repeat-mediated recombinations and RNA editing-induced stop codon acquisition. FRONTIERS IN PLANT SCIENCE 2024; 15:1326387. [PMID: 38807783 PMCID: PMC11130359 DOI: 10.3389/fpls.2024.1326387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024]
Abstract
Rehmannia glutinosa is an economically significant medicinal plant. Yet, the structure and sequence of its mitochondrial genome has not been published, which plays a crucial role in evolutionary analysis and regulating respiratory-related macromolecule synthesis. In this study, the R. glutinosa mitogenome was sequenced employing a combination of Illumina short reads and Nanopore long reads, with subsequent assembly using a hybrid strategy. We found that the predominant configuration of the R. glutinosa mitogenome comprises two circular chromosomes. The primary structure of the mitogenome encompasses two mitochondrial chromosomes corresponding to the two major configurations, Mac1-1 and Mac1-2. The R. glutinosa mitogenome encoded an angiosperm-typical set of 24 core genes, nine variable genes, three rRNA genes, and 15 tRNA genes. A phylogenetic analysis using the 16 shared protein-coding genes (PCG) yielded a tree consistent with the phylogeny of Lamiales species and two outgroup taxa. Mapping RNA-seq data to the coding sequences (CDS) of the PCGs revealed 507 C-to-U RNA editing sites across 31 PCGs of the R. glutinosa mitogenome. Furthermore, one start codon (nad4L) and two stop codons (rpl10 and atp6) were identified as products of RNA editing events in the R. glutinosa mitogenome.
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Affiliation(s)
- Tiexin Zeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingling Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qianqi Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lijia Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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2
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Philips JG, Martin-Avila E, Robold AV. Horizontal gene transfer from genetically modified plants - Regulatory considerations. Front Bioeng Biotechnol 2022; 10:971402. [PMID: 36118580 PMCID: PMC9471246 DOI: 10.3389/fbioe.2022.971402] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.
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3
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Xu S, Zhang T, Yan R, Wang R, Yi Q, Shi W, Gao Y, Zhang Y. Environmental filtering dominated the antibiotic resistome assembly in river networks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155293. [PMID: 35447183 DOI: 10.1016/j.scitotenv.2022.155293] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
River networks play important roles in dissemination of antibiotic resistance genes (ARGs). The occurrence, diversity, and abundance of ARGs in river networks have been widely investigated. However, the assembly processes that shaped ARGs profiles across space and time are largely unknown. Here, the dynamics of ARGs profiles in river networks (Taihu Basin) were revealed by high-throughput quantitative PCR followed by multiple statistical analyses to assess the underlying ecological processes. The results revealed clear variations for ARGs profiles across wet, normal, and dry seasons. Meanwhile, a significant negative correlation (p < 0.01) was observed between the similarity of ARGs profiles and geographic distance, indicating ARGs profiles exhibited distance-decay patterns. Null model analysis showed that ARGs profiles were mainly assembled via deterministic processes. Redundancy analysis followed by hierarchical partitioning revealed that environmental attributes (mainly pH and temperature) were the major factors affecting the dynamics of ARGs profiles. Together, these results indicated that environmental filtering was the dominant ecological process that shaped ARGs profiles. This study enhances our understanding how the antibiotic resistome is assembled in river networks and will be beneficial for the development of management strategies to control ARGs dissemination.
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Affiliation(s)
- Sai Xu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Tao Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China.
| | - Ruomeng Yan
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China; School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Ruyue Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Qitao Yi
- School of Civil Engineering, Yantai University, Yantai 264005, China
| | - Wenqing Shi
- School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Yuexiang Gao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Yimin Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
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4
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Zhou GF, Chen CX, Cai QC, Yan X, Peng NN, Li XC, Cui JH, Han YF, Zhang Q, Meng JH, Tang HM, Cai CH, Long J, Luo KJ. Bracovirus Sneaks Into Apoptotic Bodies Transmitting Immunosuppressive Signaling Driven by Integration-Mediated eIF5A Hypusination. Front Immunol 2022; 13:901593. [PMID: 35664011 PMCID: PMC9156803 DOI: 10.3389/fimmu.2022.901593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022] Open
Abstract
A typical characteristics of polydnavirus (PDV) infection is a persistent immunosuppression, governed by the viral integration and expression of virulence genes. Recently, activation of caspase-3 by Microplitis bicoloratus bracovirus (MbBV) to cleave Innexins, gap junction proteins, has been highlighted, further promoting apoptotic cell disassembly and apoptotic body (AB) formation. However, whether ABs play a role in immune suppression remains to be determined. Herein, we show that ABs transmitted immunosuppressive signaling, causing recipient cells to undergo apoptosis and dismigration. Furthermore, the insertion of viral–host integrated motif sites damaged the host genome, stimulating eIF5A nucleocytoplasmic transport and activating the eIF5A-hypusination translation pathway. This pathway specifically translates apoptosis-related host proteins, such as P53, CypA, CypD, and CypJ, to drive cellular apoptosis owing to broken dsDNA. Furthermore, translated viral proteins, such Vank86, 92, and 101, known to complex with transcription factor Dip3, positively regulated DHYS and DOHH transcription maintaining the activation of the eIF5A-hypusination. Mechanistically, MbBV-mediated extracellular vesicles contained inserted viral fragments that re-integrated into recipients, potentially via the homologous recombinant repair system. Meanwhile, this stimulation regulated activated caspase-3 levels via PI3K/AKT 308 and 473 dephosphorylation to promote apoptosis of granulocyte-like recipients Sf9 cell; maintaining PI3K/AKT 473 phosphorylation and 308 dephosphorylation inhibited caspase-3 activation leading to dismigration of plasmatocyte-like recipient High Five cells. Together, our results suggest that integration-mediated eIF5A hypusination drives extracellular vesicles for continuous immunosuppression.
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Affiliation(s)
- Gui-Fang Zhou
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Chang-Xu Chen
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Qiu-Chen Cai
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Xiang Yan
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Nan-Nan Peng
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Xing-Cheng Li
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Ji-Hui Cui
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Yun-Feng Han
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Qi Zhang
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Jiang-Hui Meng
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Hong-Mei Tang
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Chen-Hui Cai
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Jin Long
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
| | - Kai-Jun Luo
- School of Life Sciences, Yunnan University, Kunming, China.,Key Laboratory of the University in Yunnan Province for International Cooperation in Intercellular Communications and Regulations, Yunnan University, Kunming, China
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5
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Meng M, Li Y, Yao H. Plasmid-Mediated Transfer of Antibiotic Resistance Genes in Soil. Antibiotics (Basel) 2022; 11:antibiotics11040525. [PMID: 35453275 PMCID: PMC9024699 DOI: 10.3390/antibiotics11040525] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 12/18/2022] Open
Abstract
Due to selective pressure from the widespread use of antibiotics, antibiotic resistance genes (ARGs) are found in human hosts, plants, and animals and virtually all natural environments. Their migration and transmission in different environmental media are often more harmful than antibiotics themselves. ARGs mainly move between different microorganisms through a variety of mobile genetic elements (MGEs), such as plasmids and phages. The soil environment is regarded as the most microbially active biosphere on the Earth’s surface and is closely related to human activities. With the increase in human activity, soils are becoming increasingly contaminated with antibiotics and ARGs. Soil plasmids play an important role in this process. This paper reviews the current scenario of plasmid-mediated migration and transmission of ARGs in natural environments and under different antibiotic selection pressures, summarizes the current methods of plasmid extraction and analysis, and briefly introduces the mechanism of plasmid splice transfer using the F factor as an example. However, as the global spread of drug-resistant bacteria has increased and the knowledge of MGEs improves, the contribution of soil plasmids to resistance gene transmission needs to be further investigated. The prevalence of multidrug-resistant bacteria has also made the effective prevention of the transmission of resistance genes through the plasmid-bacteria pathway a major research priority.
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Affiliation(s)
- Miaoling Meng
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China;
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Huaiying Yao
- Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, China;
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China;
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- Correspondence: ; Tel.: +86-0574-8678-4812
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6
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Li H, Song R, Wang Y, Zhong R, Wang T, Jia H, Zhu L. Environmental free radicals efficiently inhibit the conjugative transfer of antibiotic resistance by altering cellular metabolism and plasmid transfer. WATER RESEARCH 2022; 209:117946. [PMID: 34923439 DOI: 10.1016/j.watres.2021.117946] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/07/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Spread of antibiotic-resistant genes (ARGs) is a global public safety issue and inhibition their transfer is imperative. In this study, a novel strategy using environmental free radical exposure was developed to inhibit conjugative transfer of ARGs (RP4 plasmid) in aqueous solutions. Long-time free radical (·OH, 1O2, and O2·-) exposure significantly suppressed the conjugative transfer frequency of ARGs between Escherichia coli (E. coli) strains, and ·OH was more likely to attack ARG, thereby inhibiting the conjugate transfer frequency, compared to 1O2 and O2·-. Compared with the control, the conjugative transfer frequency significantly decreased from 4.08 × 10-5 to 1.2 × 10-8 after 10 min free radical exposure, confirming that the transfer and proliferation of ARGs were well inhibited. Correspondingly, the number of transconjugant significantly decreased by 61.7% after 10 min free radical exposure. Significant reductions in reactive oxygen species levels (ROS content and enzyme levels) and DNA damage-induced responses in the donor strains were observed after 10 min free radical exposure. Concurrently, intercellular contact was also weakened via inhibiting the synthesis of polysaccharides in extracellular polymeric substances. Moreover, the expressions of plasmid transfer genes were down-regulated after 10 min exposure due to the shortage of adenosine-triphosphate supply. This study firstly disclosed the underneath mechanisms for depressing ARGs transfer and dissemination via environmental free radical exposure.
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Affiliation(s)
- Hu Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Ruiying Song
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Yangyang Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Rongwei Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China
| | - Lingyan Zhu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi 712100, China.
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7
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Braz VS, Melchior K, Moreira CG. Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium. Front Cell Infect Microbiol 2020; 10:548492. [PMID: 33409157 PMCID: PMC7779793 DOI: 10.3389/fcimb.2020.548492] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic plasticity promotes evolution and a vast diversity in Escherichia coli varying from avirulent to highly pathogenic strains, including the emergence of virulent hybrid microorganism. This ability also contributes to the emergence of antimicrobial resistance. These hybrid pathogenic E. coli (HyPEC) are emergent threats, such as O104:H4 from the European outbreak in 2011, aggregative adherent bacteria with the potent Shiga-toxin. Here, we briefly revisited the details of these E. coli classic and hybrid pathogens, the increase in antimicrobial resistance in the context of a genetically empowered multifaceted and versatile bug and the growing need to advance alternative therapies to fight these infections.
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Affiliation(s)
- Vânia Santos Braz
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Karine Melchior
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Cristiano Gallina Moreira
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
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8
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Serrano E, Ramos C, Alonso JC, Ayora S. Recombination proteins differently control the acquisition of homeologous DNA during Bacillus subtilis natural chromosomal transformation. Environ Microbiol 2020; 23:512-524. [PMID: 33264457 DOI: 10.1111/1462-2920.15342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/30/2020] [Indexed: 12/23/2022]
Abstract
Natural chromosomal transformation (CT) plays a major role in prokaryote evolution, yet factors that govern the integration of DNA from related species remain poorly understood. We show that in naturally competent Bacillus subtilis cells the acquisition of homeologous sequences is governed by sequence divergence (SD). Integration initiates in a minimal efficient processing segment via homology-directed CT, and its frequency decreases log-linearly with increased SD up to 15%. Beyond this and up to 23% SD the interspecies boundaries prevail, the CT frequency marginally decreases, and short (<10-nucleotides) segments are integrated via homology-facilitated micro-homologous integration. Both mechanisms are RecA dependent. We identify the other recombination proteins required for the acquisition of homeologous DNA. The absence of AddAB, RecF, RecO, RuvAB or RecU, crucial for repair-by-recombination, did not affect CT. However, dprA, radA, recJ, recX or recD2 inactivation strongly decreased intraspecies and interspecies CT. Interspecies CT was not detected beyond ~8% SD in ΔdprA, ~10% in ΔrecJ, ΔradA, ΔrecX and ~14% in ΔrecD2 cells. We propose that DprA, RecX, RadA/Sms, RecJ and RecD2 accessory proteins are important for the generation of genetic diversity. Together with RecA, they facilitate gene acquisition from bacteria of related species.
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Affiliation(s)
- Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
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9
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Dordet-Frisoni E, Faucher M, Sagné E, Baranowski E, Tardy F, Nouvel LX, Citti C. Mycoplasma Chromosomal Transfer: A Distributive, Conjugative Process Creating an Infinite Variety of Mosaic Genomes. Front Microbiol 2019; 10:2441. [PMID: 31708906 PMCID: PMC6819513 DOI: 10.3389/fmicb.2019.02441] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
The capacity of Mycoplasmas to engage in horizontal gene transfers has recently been highlighted. Despite their small genome, some of these wall-less bacteria are able to exchange multiple, large portions of their chromosome via a conjugative mechanism that does not conform to canonical Hfr/oriT models. To understand the exact features underlying mycoplasma chromosomal transfer (MCT), extensive genomic analyses were performed at the nucleotide level, using individual mating progenies derived from our model organism, Mycoplasma agalactiae. Genome reconstruction showed that MCT resulted in the distributive transfer of multiple chromosomal DNA fragments and generated progenies composed of a variety of mosaic genomes, each being unique. Analyses of macro- and micro-events resulting from MCT revealed that the vast majority of the acquired fragments were unrelated and co-transferred independently from the selection marker, these resulted in up to 17% of the genome being exchanged. Housekeeping and accessory genes were equally affected by MCT, with up to 35 CDSs being gained or lost. This efficient HGT process also created a number of chimeric genes and genetic micro-variations that may impact gene regulation and/or expression. Our study unraveled the tremendous plasticity of M. agalactiae genome and point toward MCT as a major player in diversification and adaptation to changing environments, offering a significant advantage to this minimal pathogen.
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Affiliation(s)
| | - Marion Faucher
- IHAP, INRA, ENVT, Université de Toulouse, Toulouse, France
| | - Eveline Sagné
- IHAP, INRA, ENVT, Université de Toulouse, Toulouse, France
| | | | - Florence Tardy
- UMR Mycoplasmoses des Ruminants, VetAgro Sup, Laboratoire de Lyon, ANSES, Université de Lyon, Marcy-l'Étoile, France
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10
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Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications. Mar Drugs 2019; 17:md17070408. [PMID: 31323998 PMCID: PMC6669457 DOI: 10.3390/md17070408] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022] Open
Abstract
Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.
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11
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Carrasco B, Serrano E, Martín-González A, Moreno-Herrero F, Alonso JC. Bacillus subtilis MutS Modulates RecA-Mediated DNA Strand Exchange Between Divergent DNA Sequences. Front Microbiol 2019; 10:237. [PMID: 30814990 PMCID: PMC6382021 DOI: 10.3389/fmicb.2019.00237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/28/2019] [Indexed: 12/16/2022] Open
Abstract
The efficiency of horizontal gene transfer, which contributes to acquisition and spread of antibiotic resistance and pathogenicity traits, depends on nucleotide sequence and different mismatch-repair (MMR) proteins participate in this process. To study how MutL and MutS MMR proteins regulate recombination across species boundaries, we have studied natural chromosomal transformation with DNA up to ∼23% sequence divergence. We show that Bacillus subtilis natural chromosomal transformation decreased logarithmically with increased sequence divergence up to 15% in wild type (wt) cells or in cells lacking MutS2 or mismatch repair proteins (MutL, MutS or both). Beyond 15% sequence divergence, the chromosomal transformation efficiency is ∼100-fold higher in ΔmutS and ΔmutSL than in ΔmutS2 or wt cells. In the first phase of the biphasic curve (up to 15% sequence divergence), RecA-catalyzed DNA strand exchange contributes to the delineation of species, and in the second phase, homology-facilitated illegitimate recombination might aid in the restoration of inactivated genes. To understand how MutS modulates the integration process, we monitored DNA strand exchange reactions using a circular single-stranded DNA and a linear double-stranded DNA substrate with an internal 77-bp region with ∼16% or ∼54% sequence divergence in an otherwise homologous substrate. The former substrate delayed, whereas the latter halted RecA-mediated strand exchange. Interestingly, MutS addition overcame the heterologous barrier. We propose that MutS assists DNA strand exchange by facilitating RecA disassembly, and indirectly re-engagement with the homologous 5′-end of the linear duplex. Our data supports the idea that MutS modulates bidirectional RecA-mediated integration of divergent sequences and this is important for speciation.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alejandro Martín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Karimi Z, Ahmadi A, Najafi A, Ranjbar R. Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies. Open Microbiol J 2018; 12:59-70. [PMID: 29755603 PMCID: PMC5925864 DOI: 10.2174/1874285801812010059] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/08/2018] [Accepted: 04/09/2018] [Indexed: 02/08/2023] Open
Abstract
Introduction CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements. This property can be used as a tool for RNA editing in bioengineering studies. Conclusion The aim of this review was to survey some details about the history, nature, and potential applications of CRISPR arrays in both genetic engineering and bacterial genotyping studies.
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Affiliation(s)
- Zahra Karimi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Domröse A, Weihmann R, Thies S, Jaeger KE, Drepper T, Loeschcke A. Rapid generation of recombinant Pseudomonas putida secondary metabolite producers using yTREX. Synth Syst Biotechnol 2017; 2:310-319. [PMID: 29552656 PMCID: PMC5851919 DOI: 10.1016/j.synbio.2017.11.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/03/2017] [Accepted: 11/03/2017] [Indexed: 11/18/2022] Open
Abstract
Microbial secondary metabolites represent a rich source of valuable compounds with a variety of applications in medicine or agriculture. Effective exploitation of this wealth of chemicals requires the functional expression of the respective biosynthetic genes in amenable heterologous hosts. We have previously established the TREX system which facilitates the transfer, integration and expression of biosynthetic gene clusters in various bacterial hosts. Here, we describe the yTREX system, a new tool adapted for one-step yeast recombinational cloning of gene clusters. We show that with yTREX, Pseudomonas putida secondary metabolite production strains can rapidly be constructed by random targeting of chromosomal promoters by Tn5 transposition. Feasibility of this approach was corroborated by prodigiosin production after yTREX cloning, transfer and expression of the respective biosynthesis genes from Serratia marcescens. Furthermore, the applicability of the system for effective pathway rerouting by gene cluster adaptation was demonstrated using the violacein biosynthesis gene cluster from Chromobacterium violaceum, producing pathway metabolites violacein, deoxyviolacein, prodeoxyviolacein, and deoxychromoviridans. Clones producing both prodigiosin and violaceins could be readily identified among clones obtained after random chromosomal integration by their strong color-phenotype. Finally, the addition of a promoter-less reporter gene enabled facile detection also of phenazine-producing clones after transfer of the respective phenazine-1-carboxylic acid biosynthesis genes from Pseudomonas aeruginosa. All compounds accumulated to substantial titers in the mg range. We thus corroborate here the suitability of P. putida for the biosynthesis of diverse natural products, and demonstrate that the yTREX system effectively enables the rapid generation of secondary metabolite producing bacteria by activation of heterologous gene clusters, applicable for natural compound discovery and combinatorial biosynthesis.
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Affiliation(s)
- Andreas Domröse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
| | - Robin Weihmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-1), Forschungszentrum Jülich, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
- Corresponding author. Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.Institute of Molecular Enzyme TechnologyHeinrich Heine University DüsseldorfForschungszentrum JülichJülichGermany
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14
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Gennaro A, Gomes A, Herman L, Nogue F, Papadopoulou N, Tebbe C. Explanatory note on DNA sequence similarity searches in the context of the assessment of horizontal gene transfer from plants to microorganisms. ACTA ACUST UNITED AC 2017. [DOI: 10.2903/sp.efsa.2017.en-1273] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Inoue M, Fukui K, Fujii Y, Nakagawa N, Yano T, Kuramitsu S, Masui R. The Lon protease-like domain in the bacterial RecA paralog RadA is required for DNA binding and repair. J Biol Chem 2017; 292:9801-9814. [PMID: 28432121 DOI: 10.1074/jbc.m116.770180] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/16/2017] [Indexed: 11/06/2022] Open
Abstract
Homologous recombination (HR) plays an essential role in the maintenance of genome integrity. RecA/Rad51 paralogs have been recognized as an important factor of HR. Among them, only one bacterial RecA/Rad51 paralog, RadA, is involved in HR as an accessory factor of RecA recombinase. RadA has a unique Lon protease-like domain (LonC) at its C terminus, in addition to a RecA-like ATPase domain. Unlike Lon protease, RadA's LonC domain does not show protease activity but is still essential for RadA-mediated DNA repair. Reconciling these two facts has been difficult because RadA's tertiary structure and molecular function are unknown. Here, we describe the hexameric ring structure of RadA's LonC domain, as determined by X-ray crystallography. The structure revealed the two positively charged regions unique to the LonC domain of RadA are located at the intersubunit cleft and the central hole of a hexameric ring. Surprisingly, a functional domain analysis demonstrated the LonC domain of RadA binds DNA, with site-directed mutagenesis showing that the two positively charged regions are critical for this DNA-binding activity. Interestingly, only the intersubunit cleft was required for the DNA-dependent stimulation of ATPase activity of RadA, and at least the central hole was essential for DNA repair function. Our data provide the structural and functional features of the LonC domain and their function in RadA-mediated DNA repair.
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Affiliation(s)
- Masao Inoue
- From the Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043
| | - Kenji Fukui
- the Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686
| | - Yuki Fujii
- the Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, and
| | - Noriko Nakagawa
- From the Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043
| | - Takato Yano
- the Department of Biochemistry, Osaka Medical College, 2-7 Daigakumachi, Takatsuki, Osaka 569-8686
| | - Seiki Kuramitsu
- From the Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043
| | - Ryoji Masui
- the Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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16
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Torres L, Krüger A, Csibra E, Gianni E, Pinheiro VB. Synthetic biology approaches to biological containment: pre-emptively tackling potential risks. Essays Biochem 2016; 60:393-410. [PMID: 27903826 PMCID: PMC5264511 DOI: 10.1042/ebc20160013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/29/2022]
Abstract
Biocontainment comprises any strategy applied to ensure that harmful organisms are confined to controlled laboratory conditions and not allowed to escape into the environment. Genetically engineered microorganisms (GEMs), regardless of the nature of the modification and how it was established, have potential human or ecological impact if accidentally leaked or voluntarily released into a natural setting. Although all evidence to date is that GEMs are unable to compete in the environment, the power of synthetic biology to rewrite life requires a pre-emptive strategy to tackle possible unknown risks. Physical containment barriers have proven effective but a number of strategies have been developed to further strengthen biocontainment. Research on complex genetic circuits, lethal genes, alternative nucleic acids, genome recoding and synthetic auxotrophies aim to design more effective routes towards biocontainment. Here, we describe recent advances in synthetic biology that contribute to the ongoing efforts to develop new and improved genetic, semantic, metabolic and mechanistic plans for the containment of GEMs.
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Affiliation(s)
- Leticia Torres
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
| | - Antje Krüger
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Eszter Csibra
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Edoardo Gianni
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Vitor B Pinheiro
- Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, U.K.
- Birkbeck, Department of Biological Sciences, University of London, Malet Street, WC1E 7HX, U.K
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17
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Xu Q, Guerrero FD, Palavesam A, Pérez de León AA. Use of electroporation as an option to transform the horn fly, Haematobia irritans: a species recalcitrant to microinjection. INSECT SCIENCE 2016; 23:621-629. [PMID: 25645001 DOI: 10.1111/1744-7917.12207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/13/2015] [Indexed: 06/04/2023]
Abstract
The horn fly, Haematobia irritans, is a serious pest of cattle in North America. The control of horn flies has primarily relied on insecticides. However, the heavy use of insecticides has led to the development of insecticide resistance in horn flies. Novel methods to control horn flies are greatly needed. Transgenic technology is an effective tool to genetically modify insects and may lead to novel methods of pest control based on genomic approaches. Here we report a piggyBac-mediated transformation of the horn fly via electroporation. Transformation with a DsRed fluorescent marker protein coding region was verified by PCR analysis of individual fly bodies and pupal cases and sequencing of PCR products. However, Southern blot analysis failed to indicate the DsRed gene was integrated into the horn fly genome. Thus, the electroporation protocol may have caused the DsRed gene to be integrated into bacterial symbionts of the horn fly.
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Affiliation(s)
- Qiang Xu
- Department of Biology, Abilene Christian University, Abilene, TX, 79699, USA
| | - Felix D Guerrero
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory, 2700 Fredericksburg Rd., Kerrville, TX, 78028, USA
- USDA-ARS Veterinary Pest Genomics Center, Kerrville, TX, 78028, USA
| | - Azhahianambi Palavesam
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory, 2700 Fredericksburg Rd., Kerrville, TX, 78028, USA
| | - Adalberto A Pérez de León
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory, 2700 Fredericksburg Rd., Kerrville, TX, 78028, USA
- USDA-ARS Veterinary Pest Genomics Center, Kerrville, TX, 78028, USA
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18
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Genomic characterization of Italian Clostridium botulinum group I strains. INFECTION GENETICS AND EVOLUTION 2015; 36:62-71. [DOI: 10.1016/j.meegid.2015.08.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 02/07/2023]
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19
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Ying J, Wu S, Zhang K, Wang Z, Zhu W, Zhu M, Zhang Y, Cheng C, Wang H, Tou H, Zhu C, Li P, Ying J, Xu T, Yi H, Li J, Ni L, Xu Z, Bao Q, Lu J. Comparative genomics analysis of pKF3-94 in Klebsiella pneumoniae reveals plasmid compatibility and horizontal gene transfer. Front Microbiol 2015; 6:831. [PMID: 26347723 PMCID: PMC4539522 DOI: 10.3389/fmicb.2015.00831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 07/28/2015] [Indexed: 11/18/2022] Open
Abstract
In order to get insights into plasmid evolution and the dissemination of multidrug resistance, we performed extensive comparative genomics analyses of the Klebsiella pneumoniae plasmid pKF3-94 and some of its related plasmids. pKF3-94 is one of three plasmids isolated from the K. pneumoniae strain KF3. Of the 144 putative genes it harbors, 69 can be functionally assigned to be involved in transfer conjugation, transfer leading, antimicrobial resistance, transposon function, and plasmid replication. Comparison of plasmid replicon sequence types revealed that pKF3-94 carries two replicons that are distinct from those carried on the two sibling K. pneumonia plasmids pKF3-70 and pKF3-140, thereby allowing pKF3-94 to coexist with these latter plasmids in the same host cell. Comparative genomics analyses further showed that pKF3-94 is more similar to plasmids pK1HV and pC15-k, which were isolated from different K. pneumonia strains, than to pKF3-70 and pKF3-140. Interestingly, pK1HV contains a unique 49 kb region rich in mobile genetic elements and drug resistance genes, while pKF3-94 and pC15-k share a 15 kb homology region partitioned into a region rich in drug resistance genes and one containing a replicon. It is conceivable, therefore, that pK1HV and pC15-k have both arisen from a common pKF3-94-like plasmid. The comparisons lend further support for the role horizontal gene transfer plays in genome evolution and in the dissemination of genetic elements including drug resistance genes.
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Affiliation(s)
- Jianchao Ying
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Songquan Wu
- School of Medicine, Lishui College Lishui, China
| | - Kaibo Zhang
- School of Medicine, Lishui College Lishui, China
| | - Ziqiang Wang
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Wen Zhu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Mei Zhu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Ying Zhang
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Cong Cheng
- School of Medicine, Lishui College Lishui, China
| | - Huifeng Wang
- National Institute of Biological Sciences Beijing, China
| | - Huifen Tou
- Wenzhou Center for Disease Control and Prevention Wenzhou, China
| | - Chuanxin Zhu
- Wenzhou Center for Disease Control and Prevention Wenzhou, China
| | - Peizhen Li
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Jun Ying
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Teng Xu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Huiguang Yi
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Jinsong Li
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Liyan Ni
- The Second Affiliated Hospital, Wenzhou Medical University Wenzhou, China
| | - Zuyuan Xu
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Qiyu Bao
- Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University Wenzhou, China
| | - Junwan Lu
- School of Medicine, Lishui College Lishui, China
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20
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Scientific Opinion on application (EFSA‐GMO‐DE‐2011‐95) for the placing on the market of genetically modified maize 5307 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Syngenta Crop Protection AG. EFSA J 2015. [DOI: 10.2903/j.efsa.2015.4083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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21
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Brown-Jaque M, Calero-Cáceres W, Muniesa M. Transfer of antibiotic-resistance genes via phage-related mobile elements. Plasmid 2015; 79:1-7. [PMID: 25597519 DOI: 10.1016/j.plasmid.2015.01.001] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 11/29/2022]
Abstract
Antibiotic resistance is a major concern for society because it threatens the effective prevention of infectious diseases. While some bacterial strains display intrinsic resistance, others achieve antibiotic resistance by mutation, by the recombination of foreign DNA into the chromosome or by horizontal gene acquisition. In many cases, these three mechanisms operate together. Several mobile genetic elements (MGEs) have been reported to mobilize different types of resistance genes and despite sharing common features, they are often considered and studied separately. Bacteriophages and phage-related particles have recently been highlighted as MGEs that transfer antibiotic resistance. This review focuses on phages, phage-related elements and on composite MGEs (phages-MGEs) involved in antibiotic resistance mobility. We review common features of these elements, rather than differences, and provide a broad overview of the antibiotic resistance transfer mechanisms observed in nature, which is a necessary first step to controlling them.
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Affiliation(s)
- Maryury Brown-Jaque
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - William Calero-Cáceres
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Maite Muniesa
- Department of Microbiology, Faculty of Biology, University of Barcelona, Barcelona, Spain.
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Ying J, Wang H, Bao B, Zhang Y, Zhang J, Zhang C, Li A, Lu J, Li P, Ying J, Liu Q, Xu T, Yi H, Li J, Zhou L, Zhou T, Xu Z, Ni L, Bao Q. Molecular variation and horizontal gene transfer of the homocysteine methyltransferase gene mmuM and its distribution in clinical pathogens. Int J Biol Sci 2015; 11:11-21. [PMID: 25552925 PMCID: PMC4278250 DOI: 10.7150/ijbs.10320] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/28/2014] [Indexed: 12/24/2022] Open
Abstract
The homocysteine methyltransferase encoded by mmuM is widely distributed among microbial organisms. It is the key enzyme that catalyzes the last step in methionine biosynthesis and plays an important role in the metabolism process. It also enables the microbial organisms to tolerate high concentrations of selenium in the environment. In this research, 533 mmuM gene sequences covering 70 genera of the bacteria were selected from GenBank database. The distribution frequency of mmuM is different in the investigated genera of bacteria. The mapping results of 160 mmuM reference sequences showed that the mmuM genes were found in 7 species of pathogen genomes sequenced in this work. The polymerase chain reaction products of one mmuM genotype (NC_013951 as the reference) were sequenced and the sequencing results confirmed the mapping results. Furthermore, 144 representative sequences were chosen for phylogenetic analysis and some mmuM genes from totally different genera (such as the genes between Escherichia and Klebsiella and between Enterobacter and Kosakonia) shared closer phylogenetic relationship than those from the same genus. Comparative genomic analysis of the mmuM encoding regions on plasmids and bacterial chromosomes showed that pKF3-140 and pIP1206 plasmids shared a 21 kb homology region and a 4.9 kb fragment in this region was in fact originated from the Escherichia coli chromosome. These results further suggested that mmuM gene did go through the gene horizontal transfer among different species or genera of bacteria. High-throughput sequencing combined with comparative genomics analysis would explore distribution and dissemination of the mmuM gene among bacteria and its evolution at a molecular level.
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Affiliation(s)
- Jianchao Ying
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Huifeng Wang
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China ; 2. National Institute of Biological Sciences, Beijing 102206, China
| | - Bokan Bao
- 3. College of Life Science and Agriculture, Cornell University, Ithaca 14850, NY, USA
| | - Ying Zhang
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Jinfang Zhang
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Cheng Zhang
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Aifang Li
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Junwan Lu
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China ; 4. School of Medicine, Lishui College, Lishui 323000, China
| | - Peizhen Li
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Jun Ying
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Qi Liu
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China ; 5. Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Teng Xu
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Huiguang Yi
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Jinsong Li
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Li Zhou
- 6. The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Tieli Zhou
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China ; 6. The First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Zuyuan Xu
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
| | - Liyan Ni
- 7. The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou 325000, China
| | - Qiyu Bao
- 1. Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical University, Wenzhou 325035, China
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Rossi F, Rizzotti L, Felis GE, Torriani S. Horizontal gene transfer among microorganisms in food: Current knowledge and future perspectives. Food Microbiol 2014; 42:232-43. [DOI: 10.1016/j.fm.2014.04.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 04/10/2014] [Indexed: 01/01/2023]
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24
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Scientific Opinion on applications (EFSA-GMO-UK-2008-57 and EFSA-GMO-RX-MON15985) for the placing on the market of insect-resistant genetically modified cotton MON 15985 for food and feed uses, import and processing, and for the renewal of authorisation o. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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Ceuppens S, Li D, Uyttendaele M, Renault P, Ross P, Ranst MV, Cocolin L, Donaghy J. Molecular Methods in Food Safety Microbiology: Interpretation and Implications of Nucleic Acid Detection. Compr Rev Food Sci Food Saf 2014; 13:551-577. [DOI: 10.1111/1541-4337.12072] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/09/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Siele Ceuppens
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Dan Li
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Mieke Uyttendaele
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Pierre Renault
- Inst. Scientifique de Recherche Agronomique (INRA); France
| | - Paul Ross
- Moorepark Biotechnology Centre; Teagasc; Moorepark; Fermoy Co. Cork Ireland
| | | | - Luca Cocolin
- Dept. of Agricultural; Forest and Food Sciences; Univ. of Torino; Grugliasco Torino Italy
| | - John Donaghy
- Food Safety Microbiology Group; Nestle Research Center; Lausanne Switzerland
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26
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Abstract
Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.
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Horizontal gene transfer can rescue prokaryotes from Muller's ratchet: benefit of DNA from dead cells and population subdivision. G3-GENES GENOMES GENETICS 2014; 4:325-39. [PMID: 24347631 PMCID: PMC3931566 DOI: 10.1534/g3.113.009845] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Horizontal gene transfer (HGT) is a major factor in the evolution of prokaryotes. An intriguing question is whether HGT is maintained during evolution of prokaryotes owing to its adaptive value or is a byproduct of selection driven by other factors such as consumption of extracellular DNA (eDNA) as a nutrient. One hypothesis posits that HGT can restore genes inactivated by mutations and thereby prevent stochastic, irreversible deterioration of genomes in finite populations known as Muller’s ratchet. To examine this hypothesis, we developed a population genetic model of prokaryotes undergoing HGT via homologous recombination. Analysis of this model indicates that HGT can prevent the operation of Muller’s ratchet even when the source of transferred genes is eDNA that comes from dead cells and on average carries more deleterious mutations than the DNA of recipient live cells. Moreover, if HGT is sufficiently frequent and eDNA diffusion sufficiently rapid, a subdivided population is shown to be more resistant to Muller’s ratchet than an undivided population of an equal overall size. Thus, to maintain genomic information in the face of Muller’s ratchet, it is more advantageous to partition individuals into multiple subpopulations and let them “cross-reference” each other’s genetic information through HGT than to collect all individuals in one population and thereby maximize the efficacy of natural selection. Taken together, the results suggest that HGT could be an important condition for the long-term maintenance of genomic information in prokaryotes through the prevention of Muller’s ratchet.
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28
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Bao Z, Stodghill PV, Myers CR, Lam H, Wei HL, Chakravarthy S, Kvitko BH, Collmer A, Cartinhour SW, Schweitzer P, Swingle B. Genomic plasticity enables phenotypic variation of Pseudomonas syringae pv. tomato DC3000. PLoS One 2014; 9:e86628. [PMID: 24516535 PMCID: PMC3916326 DOI: 10.1371/journal.pone.0086628] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 12/16/2013] [Indexed: 11/18/2022] Open
Abstract
Whole genome sequencing revealed the presence of a genomic anomaly in the region of 4.7 to 4.9 Mb of the Pseudomonas syringae pv. tomato (Pst) DC3000 genome. The average read depth coverage of Pst DC3000 whole genome sequencing results suggested that a 165 kb segment of the chromosome had doubled in copy number. Further analysis confirmed the 165 kb duplication and that the two copies were arranged as a direct tandem repeat. Examination of the corresponding locus in Pst NCPPB1106, the parent strain of Pst DC3000, suggested that the 165 kb duplication most likely formed after the two strains diverged via transposition of an ISPsy5 insertion sequence (IS) followed by unequal crossing over between ISPsy5 elements at each end of the duplicated region. Deletion of one copy of the 165 kb region demonstrated that the duplication facilitated enhanced growth in some culture conditions, but did not affect pathogenic growth in host tomato plants. These types of chromosomal structures are predicted to be unstable and we have observed resolution of the 165 kb duplication to single copy and its subsequent re-duplication. These data demonstrate the role of IS elements in recombination events that facilitate genomic reorganization in P. syringae.
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Affiliation(s)
- Zhongmeng Bao
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Paul V. Stodghill
- United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
| | - Christopher R. Myers
- Department of Physics, Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, New York, United States of America
| | - Hanh Lam
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Hai-Lei Wei
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Suma Chakravarthy
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Brian H. Kvitko
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Alan Collmer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Samuel W. Cartinhour
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
| | - Peter Schweitzer
- Biotechnology Resource Center, Cornell University, Ithaca, New York, United States of America
| | - Bryan Swingle
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
- * E-mail:
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Nielsen KM, Bøhn T, Townsend JP. Detecting rare gene transfer events in bacterial populations. Front Microbiol 2014; 4:415. [PMID: 24432015 PMCID: PMC3882822 DOI: 10.3389/fmicb.2013.00415] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/16/2013] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.
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Affiliation(s)
- Kaare M Nielsen
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø Tromsø, Norway ; GenØk-Centre for Biosafety, The Science Park Tromsø, Norway
| | - Thomas Bøhn
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø Tromsø, Norway ; GenØk-Centre for Biosafety, The Science Park Tromsø, Norway
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University New Haven, CT, USA ; Program in Computational Biology and Bioinformatics, Yale University New Haven, CT, USA ; Program in Microbiology, Yale University New Haven, CT, USA
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Scientific Opinion on an application from Pioneer Hi‐Bred International and Dow AgroSciences LLC (EFSA‐GMO‐NL‐2005‐23) for placing on the market of genetically modified maize 59122 for food and feed uses, import, processing and cultivation under Regulation (EC) No 1829/2003. EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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31
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Moe-Behrens GHG, Davis R, Haynes KA. Preparing synthetic biology for the world. Front Microbiol 2013; 4:5. [PMID: 23355834 PMCID: PMC3554958 DOI: 10.3389/fmicb.2013.00005] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/04/2013] [Indexed: 11/21/2022] Open
Abstract
Synthetic Biology promises low-cost, exponentially scalable products and global health solutions in the form of self-replicating organisms, or “living devices.” As these promises are realized, proof-of-concept systems will gradually migrate from tightly regulated laboratory or industrial environments into private spaces as, for instance, probiotic health products, food, and even do-it-yourself bioengineered systems. What additional steps, if any, should be taken before releasing engineered self-replicating organisms into a broader user space? In this review, we explain how studies of genetically modified organisms lay groundwork for the future landscape of biosafety. Early in the design process, biological engineers are anticipating potential hazards and developing innovative tools to mitigate risk. Here, we survey lessons learned, ongoing efforts to engineer intrinsic biocontainment, and how different stakeholders in synthetic biology can act to accomplish best practices for biosafety.
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Loeschcke A, Markert A, Wilhelm S, Wirtz A, Rosenau F, Jaeger KE, Drepper T. TREX: a universal tool for the transfer and expression of biosynthetic pathways in bacteria. ACS Synth Biol 2013; 2:22-33. [PMID: 23656323 DOI: 10.1021/sb3000657] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Secondary metabolites represent a virtually inexhaustible source of natural molecules exhibiting a high potential as pharmaceuticals or chemical building blocks. To gain broad access to these compounds, sophisticated expression systems are needed that facilitate the transfer and expression of large chromosomal regions, whose genes encode complex metabolic pathways. Here, we report on the development of the novel system for the transfer and expression of biosynthetic pathways (TREX), which comprises all functional elements necessary for the delivery and concerted expression of clustered pathway genes in different bacteria. TREX employs (i) conjugation for DNA transfer, (ii) randomized transposition for its chromosomal insertion, and (iii) T7 RNA polymerase for unimpeded bidirectional gene expression. The applicability of the TREX system was demonstrated by establishing the biosynthetic pathways of two pigmented secondary metabolites, zeaxanthin and prodigiosin, in bacteria with different metabolic capacities. Thus, TREX represents a valuable tool for accessing natural products by allowing comparative expression studies with clustered genes.
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Affiliation(s)
- Anita Loeschcke
- Institute of Molecular Enzyme
Technology, Heinrich-Heine-University Düsseldorf, Research Center Jülich, Jülich, Germany
| | - Annette Markert
- Institute of Molecular Enzyme
Technology, Heinrich-Heine-University Düsseldorf, Research Center Jülich, Jülich, Germany
| | - Susanne Wilhelm
- Institute of Molecular Enzyme
Technology, Heinrich-Heine-University Düsseldorf, Research Center Jülich, Jülich, Germany
| | - Astrid Wirtz
- Institute of Molecular Enzyme
Technology, Heinrich-Heine-University Düsseldorf, Research Center Jülich, Jülich, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical
Biotechnology, Ulm University, Ulm, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme
Technology, Heinrich-Heine-University Düsseldorf, Research Center Jülich, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme
Technology, Heinrich-Heine-University Düsseldorf, Research Center Jülich, Jülich, Germany
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33
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Genetically modified foods: safety, risks and public concerns-a review. Journal of Food Science and Technology 2012; 50:1035-46. [PMID: 24426015 DOI: 10.1007/s13197-012-0899-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/16/2012] [Accepted: 11/19/2012] [Indexed: 01/17/2023]
Abstract
Genetic modification is a special set of gene technology that alters the genetic machinery of such living organisms as animals, plants or microorganisms. Combining genes from different organisms is known as recombinant DNA technology and the resulting organism is said to be 'Genetically modified (GM)', 'Genetically engineered' or 'Transgenic'. The principal transgenic crops grown commercially in field are herbicide and insecticide resistant soybeans, corn, cotton and canola. Other crops grown commercially and/or field-tested are sweet potato resistant to a virus that could destroy most of the African harvest, rice with increased iron and vitamins that may alleviate chronic malnutrition in Asian countries and a variety of plants that are able to survive weather extremes. There are bananas that produce human vaccines against infectious diseases such as hepatitis B, fish that mature more quickly, fruit and nut trees that yield years earlier and plants that produce new plastics with unique properties. Technologies for genetically modifying foods offer dramatic promise for meeting some areas of greatest challenge for the 21st century. Like all new technologies, they also pose some risks, both known and unknown. Controversies and public concern surrounding GM foods and crops commonly focus on human and environmental safety, labelling and consumer choice, intellectual property rights, ethics, food security, poverty reduction and environmental conservation. With this new technology on gene manipulation what are the risks of "tampering with Mother Nature"?, what effects will this have on the environment?, what are the health concerns that consumers should be aware of? and is recombinant technology really beneficial? This review will also address some major concerns about the safety, environmental and ecological risks and health hazards involved with GM foods and recombinant technology.
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Scientific Opinion on an application (EFSA-GMO-NL-2009-70) for the placing on the market of genetically modified drought tolerant maize MON 87460 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2936] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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35
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Scientific Opinion on application (EFSA‐GMO‐NL‐2010‐78) for the placing on the market of herbicide‐tolerant, increased oleic acid genetically modified soybean MON 87705 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2909] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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36
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Physical methods for genetic plant transformation. Phys Life Rev 2012; 9:308-45. [DOI: 10.1016/j.plrev.2012.06.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 06/04/2012] [Indexed: 01/27/2023]
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37
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The ecology of bacterial genes and the survival of the new. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:394026. [PMID: 22900231 PMCID: PMC3415099 DOI: 10.1155/2012/394026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
Abstract
Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.
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38
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Scientific Opinion on an application (EFSA‐GMO‐NL‐2005‐24) for the placing on the market of the herbicide tolerant genetically modified soybean 40‐3‐2 for cultivation under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2753] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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39
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Nordgård L, Brusetti L, Raddadi N, Traavik T, Averhoff B, Nielsen KM. An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats. BMC Res Notes 2012; 5:170. [PMID: 22463741 PMCID: PMC3364145 DOI: 10.1186/1756-0500-5-170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 04/01/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes. RESULTS Plasmid DNA with two resistance genes (nptI and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, were constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. No transformants were identified among 441 tested isolates. CONCLUSIONS The analyses showed that extensive ingestion of DNA (100 μg plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit < 1 transformant per 1,1 × 10(8) cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed. This study is consistent with other studies suggesting natural transformation is not detectable in the GIT of mammals.
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Affiliation(s)
- Lise Nordgård
- GenØk, Centre for Biosafety, Science Park, 9294 Tromsø, Norway
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40
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Scientific Opinion on applications EFSA‐GMO‐UK‐2005‐09 and EFSA‐GMO‐RX‐MON531×MON1445 for the placing on the market of food and feed produced from or containing ingredients produced from insect‐resistant and herbicide‐tolerant genetically modified cotton MON 531 × MON 1445, and for the renewal of authorisation of existing products produced from cotton MON 531 × MON 1445, both under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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41
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Townsend JP, Bøhn T, Nielsen KM. Assessing the probability of detection of horizontal gene transfer events in bacterial populations. Front Microbiol 2012; 3:27. [PMID: 22363321 PMCID: PMC3282476 DOI: 10.3389/fmicb.2012.00027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 01/16/2012] [Indexed: 11/23/2022] Open
Abstract
Experimental approaches to identify horizontal gene transfer (HGT) events of non-mobile DNA in bacteria have typically relied on detection of the initial transformants or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to be detected in a short time frame. Population genetic modeling of the growth dynamics of bacterial genotypes is therefore necessary to account for natural selection and genetic drift during the time lag and to predict realistic time frames for detection with a given sampling design. Here we draw on statistical approaches to population genetic theory to construct a cohesive probabilistic framework for investigation of HGT of exogenous DNA into bacteria. In particular, the stochastic timing of rare HGT events is accounted for. Integrating over all possible event timings, we provide an equation for the probability of detection, given that HGT actually occurred. Furthermore, we identify the key variables determining the probability of detecting HGT events in four different case scenarios that are representative of bacterial populations in various environments. Our theoretical analysis provides insight into the temporal aspects of dissemination of genetic material, such as antibiotic resistance genes or transgenes present in genetically modified organisms. Due to the long time scales involved and the exponential growth of bacteria with differing fitness, quantitative analyses incorporating bacterial generation time, and levels of selection, such as the one presented here, will be a necessary component of any future experimental design and analysis of HGT as it occurs in natural settings.
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Affiliation(s)
- Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA
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42
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Scientific opinion on application (EFSA-GMO-NL-2009-73) for the placing on the market of insect-resistant and herbicide-tolerant genetically modified soybean MON 87701 × MON 89788 for food and feed uses, import and processing under Regulation (EC) No 1829. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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43
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Scientific Opinion on application (EFSA-GMO-UK-2008-60) for placing on the market of genetically modified herbicide tolerant maize GA21 for food and feed uses, import, processing and cultivation under Regulation (EC) No 1829/2003 from Syngenta Seeds. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2480] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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44
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Scientific Opinion on application EFSA-GMO-RX-MON1445 for renewal of the authorisation for continued marketing of cottonseed oil, food additives, feed materials and feed additives produced from cotton MON 1445 that were notified as existing products under. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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45
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Scientific Opinion on application (EFSA-GMO-CZ-2008-54) for placing on the market of genetically modified insect resistant and herbicide tolerant maize MON 88017 for cultivation under Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2428] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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46
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Non-indigenous microorganisms in the Antarctic: assessing the risks. Trends Microbiol 2011; 19:540-8. [DOI: 10.1016/j.tim.2011.07.008] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 07/15/2011] [Accepted: 07/28/2011] [Indexed: 11/20/2022]
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47
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Demanèche S, Monier JM, Dugat-Bony E, Simonet P. Exploration of horizontal gene transfer between transplastomic tobacco and plant-associated bacteria. FEMS Microbiol Ecol 2011; 78:129-36. [PMID: 21564143 DOI: 10.1111/j.1574-6941.2011.01126.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The likelihood of gene transfer from transgenic plants to bacteria is dependent on the transgene copy number and on the presence of homologous sequences for recombination. The large number of chloroplast genomes in a plant cell as well as the prokaryotic origin of the transgene may thus significantly increase the likelihood of gene transfer from transplastomic plants to bacteria. In order to assess the probability of such a transfer, bacterial isolates, screened for their ability to colonize decaying tobacco plant tissue and possessing DNA sequence similarity to the chloroplastic genes accD and rbcL flanking the transgene (aadA), were tested for their ability to take up extracellular DNA (broad host-range pBBR1MCS-3-derived plasmid, transplastomic plant DNA and PCR products containing the genes accD-aadA-rbcL) by natural or electrotransformation. The results showed that among the 16 bacterial isolates tested, six were able to accept foreign DNA and acquire the spectinomycin resistance conferred by the aadA gene on plasmid, but none of them managed to integrate transgenic DNA in their chromosome. Our results provide no indication that the theoretical gene transfer-enhancing properties of transplastomic plants cause horizontal gene transfer at rates above those found in other studies with nuclear transgenes.
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Affiliation(s)
- Sandrine Demanèche
- Environmental Microbial Genomics Group, Laboratoire AMPERE, UMR CNRS 5005, Ecole Centrale de Lyon, Université de Lyon, Ecully, France.
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48
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Scientific Opinion on application EFSA‐GMO‐RX‐MON531 for renewal of the authorisation for continued marketing of existing cottonseed oil, food additives, feed materials and feed additives produced from MON 531 cotton that were notified under Articles 8(1)(a), 8(1)(b) and 20(1)(b) of Regulation (EC) No 1829/2003 from Monsanto. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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49
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Aminov RI. Horizontal gene exchange in environmental microbiota. Front Microbiol 2011; 2:158. [PMID: 21845185 PMCID: PMC3145257 DOI: 10.3389/fmicb.2011.00158] [Citation(s) in RCA: 354] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 07/11/2011] [Indexed: 01/21/2023] Open
Abstract
Horizontal gene transfer (HGT) plays an important role in the evolution of life on the Earth. This view is supported by numerous occasions of HGT that are recorded in the genomes of all three domains of living organisms. HGT-mediated rapid evolution is especially noticeable among the Bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. At the heart of the HGT-driven bacterial evolution and adaptation are highly sophisticated natural genetic engineering tools in the form of a variety of mobile genetic elements (MGEs). The main aim of this review is to give a brief account of the occurrence and diversity of MGEs in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.
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Affiliation(s)
- Rustam I Aminov
- Rowett Institute of Nutrition and Health, University of Aberdeen Aberdeen, UK
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Al-Attar S, Westra ER, van der Oost J, Brouns SJ. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes. Biol Chem 2011; 392:277-89. [DOI: 10.1515/bc.2011.042] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
AbstractMany prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences (repeats), interspaced by highly variable sequences referred to as spacers. The spacers originate from either phages or plasmids and comprise the prokaryotes' ‘immunological memory’. CRISPR-associated (cas) genes encode conserved proteins that together with CRISPRs make-up the CRISPR/Cas system, responsible for defending the prokaryotic cell against invaders. CRISPR-mediated resistance has been proposed to involve three stages: (i) CRISPR-Adaptation, the invader DNA is encountered by the CRISPR/Cas machinery and an invader-derived short DNA fragment is incorporated in the CRISPR array. (ii) CRISPR-Expression, the CRISPR array is transcribed and the transcript is processed by Cas proteins. (iii) CRISPR-Interference, the invaders' nucleic acid is recognized by complementarity to the crRNA and neutralized. An application of the CRISPR/Cas system is the immunization of industry-relevant prokaryotes (or eukaryotes) against mobile-genetic invasion. In addition, the high variability of the CRISPR spacer content can be exploited for phylogenetic and evolutionary studies. Despite impressive progress during the last couple of years, the elucidation of several fundamental details will be a major challenge in future research.
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