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Evaluation of Scopoletin from Penicillium janthinellum Snef1650 for the Control of Heterodera glycines in Soybean. Life (Basel) 2021; 11:life11111143. [PMID: 34833019 PMCID: PMC8625814 DOI: 10.3390/life11111143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is responsible for causing a major soybean disease globally. The fungal strain Penicillium janthinellum Snef1650 was evaluated against H. glycines. However, the effective determinants of the P. janthinellum strain are unknown. By performing pot experiments, a functioning compound was isolated from P. janthinellum Snef1650 through organic solvent extraction, semi-preparative HPLC, Sephadex LH-20 column chromatography, and silica gel column chromatography, and the isolated compound was identified to be scopoletin through 1H NMR, 13C NMR, and HPLC–MS. The pot experiments indicated that the treatment of soybean seeds with scopoletin drastically reduced the SCN population. The field experiments performed in 2017 and 2018 revealed that scopoletin decreased over 43.7% juveniles in the roots and over 61.55% cysts in the soil. Scopoletin treatment also promoted soybean growth and improved its yield, with an increase in plot yield by >5.33%. Scopoletin obtained from P. janthinellum Snef1650 could be used as an anti-H. glycines biocontrol agent.
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2
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Remus-Emsermann MNP, Aicher D, Pelludat C, Gisler P, Drissner D. Conjugation Dynamics of Self-Transmissible and Mobilisable Plasmids into E. coli O157:H7 on Arabidopsis thaliana Rosettes. Antibiotics (Basel) 2021; 10:antibiotics10080928. [PMID: 34438978 PMCID: PMC8388966 DOI: 10.3390/antibiotics10080928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 01/01/2023] Open
Abstract
Many antibiotic resistance genes present in human pathogenic bacteria are believed to originate from environmental bacteria. Conjugation of antibiotic resistance conferring plasmids is considered to be one of the major reasons for the increasing prevalence of antibiotic resistances. A hotspot for plasmid-based horizontal gene transfer is the phyllosphere, i.e., the surfaces of aboveground plant parts. Bacteria in the phyllosphere might serve as intermediate hosts with transfer capability to human pathogenic bacteria. In this study, the exchange of mobilisable and self-transmissible plasmids via conjugation was evaluated. The conjugation from the laboratory strain Escherichia coli S17-1, the model phyllosphere coloniser Pantoea eucalypti 299R, and the model pathogen E. coli O157:H7 to the recipient strain E. coli O157:H7::MRE103 (EcO157:H7red) in the phyllosphere of Arabidopsis thaliana was determined. The results suggest that short-term occurrence of a competent donor is sufficient to fix plasmids in a recipient population of E. coli O157:H7red. The spread of self-transmissible plasmids was limited after initial steep increases of transconjugants that contributed up to 10% of the total recipient population. The here-presented data of plasmid transfer will be important for future modelling approaches to estimate environmental spread of antibiotic resistance in agricultural production environments.
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Affiliation(s)
- Mitja N. P. Remus-Emsermann
- Microbiology of Plant Foods, Agroscope, 8820 Waedenswil, Switzerland;
- School of Biological Sciences, University of Canterbury, Christchurch 8053, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8053, New Zealand
- Institute of Biology-Microbiology, Freie Universität Berlin, 14195 Berlin, Germany
- Correspondence: (M.N.P.R.-E.); (D.D.); Tel.: +49-3083-85-8031 (M.N.P.R.-E.); +49-7571-732-8278 (D.D.)
| | - David Aicher
- Department of Life Sciences, Albstadt-Sigmaringen University, 72488 Sigmaringen, Germany;
| | - Cosima Pelludat
- Plant Pathology and Zoology in Fruit and Vegetable Production, Agroscope, 8820 Waedenswil, Switzerland;
| | - Pascal Gisler
- Microbiology of Plant Foods, Agroscope, 8820 Waedenswil, Switzerland;
| | - David Drissner
- Microbiology of Plant Foods, Agroscope, 8820 Waedenswil, Switzerland;
- Department of Life Sciences, Albstadt-Sigmaringen University, 72488 Sigmaringen, Germany;
- Correspondence: (M.N.P.R.-E.); (D.D.); Tel.: +49-3083-85-8031 (M.N.P.R.-E.); +49-7571-732-8278 (D.D.)
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3
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Samantarrai D, Yakkala H, Siddavattam D. Analysis of indigenous plasmid sequences of A. baumannii DS002 reveals the existence of lateral mobility and extensive genetic recombination among Acinetobacter plasmids. J Genet 2020. [DOI: 10.1007/s12041-020-01232-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Shan F, Diwu Y, Yang X, Tu X. Expression and Interactions of Kinetoplastid Kinetochore Proteins (KKTs) from Trypanosoma brucei. Protein Pept Lett 2019; 26:860-868. [PMID: 31621553 DOI: 10.2174/0929866526666190723152359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023]
Abstract
Background:
Kinetochores are the macromolecular protein complex that drives
chromosome segregation by interacting with centromeric DNA and spindle microtubules in
eukaryotes. Kinetochores in well studied eukaryotes bind DNA through widely conserved
components like Centromere Protein (CENP)-A and bind microtubules through the Ndc80
complex. However, unconventional type of kinetochore proteins (KKT1-20) were identified in
evolutionarily divergent kinetoplastid species such as Trypanosoma brucei (T. brucei), indicating
that chromosome segregation is driven by a distinct set of proteins. KKT proteins are comprised of
sequential α-helixes that tend to form coiled-coil structures, which will further lead to
polymerization and misfolding of proteins, resulting in the formation of inclusion bodies.
Results and Conclusion:
We expressed and purified the stable KKT proteins with Maltose Binding
Protein (MBP) fusion tag in E. coli or Protein A tag in Human Embryonic Kidney (HEK) 293T
cells. Furthermore, we identified interactions among KKT proteins using yeast two-hybrid system.
The study provides an important basis for further better understanding of the structure and function
of KKT proteins.
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Affiliation(s)
- Fangzhen Shan
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Yating Diwu
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiao Yang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaoming Tu
- Hefei National Laboratory for Physical Science at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui, China
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5
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Stal LJ, Bolhuis H, Cretoiu MS. Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities. Environ Microbiol 2018; 21:1529-1551. [PMID: 30507057 DOI: 10.1111/1462-2920.14494] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 01/02/2023]
Abstract
Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.
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Affiliation(s)
- Lucas J Stal
- IBED Department of Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, The Netherlands.,Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Mariana S Cretoiu
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
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6
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de Santis B, Stockhofe N, Wal JM, Weesendorp E, Lallès JP, van Dijk J, Kok E, De Giacomo M, Einspanier R, Onori R, Brera C, Bikker P, van der Meulen J, Kleter G. Case studies on genetically modified organisms (GMOs): Potential risk scenarios and associated health indicators. Food Chem Toxicol 2018; 117:36-65. [DOI: 10.1016/j.fct.2017.08.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/03/2017] [Accepted: 08/22/2017] [Indexed: 01/07/2023]
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7
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Machado AMD, Sommer MOA. Human intestinal cells modulate conjugational transfer of multidrug resistance plasmids between clinical Escherichia coli isolates. PLoS One 2014; 9:e100739. [PMID: 24955767 PMCID: PMC4067368 DOI: 10.1371/journal.pone.0100739] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/30/2014] [Indexed: 12/29/2022] Open
Abstract
Bacterial conjugation in the human gut microbiota is believed to play a major role in the dissemination of antibiotic resistance genes and virulence plasmids. However, the modulation of bacterial conjugation by the human host remains poorly understood and there is a need for controlled systems to study this process. We established an in vitro co-culture system to study the interaction between human intestinal cells and bacteria. We show that the conjugation efficiency of a plasmid encoding an extended spectrum beta-lactamase is reduced when clinical isolates of Escherichia coli are co-cultured with human intestinal cells. We show that filtered media from co-cultures contain a factor that reduces conjugation efficiency. Protease treatment of the filtered media eliminates this inhibition of conjugation. This data suggests that a peptide or protein based factor is secreted on the apical side of the intestinal cells exposed to bacteria leading to a two-fold reduction in conjugation efficiency. These results show that human gut epithelial cells can modulate bacterial conjugation and may have relevance to gene exchange in the gut.
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Affiliation(s)
| | - Morten O. A. Sommer
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- * E-mail:
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8
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de Meeûs T, Michalakis Y, Renaud F. Santa rosalia revisited: or why are there so many kinds of parasites in ;the garden of earthly delights'? ACTA ACUST UNITED AC 2013; 14:10-3. [PMID: 17040683 DOI: 10.1016/s0169-4758(97)01163-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
As is the case for free-living species, a very large number of parasitic species are not described adequately by the biological species concept. Furthermore, Thierry de Meeûs, Yannis Michalakis and François Renaud argue that because hosts represent a highly heterogeneous and changing environment as well as a breeding site, favouring the association of host-adaptation and host-choice genes, sympatric speciation may occur frequently in parasitic organisms. Therefore, parasites appear to be ideal biological models for the study of ecological specialization and speciation. Beyond the relevance of such considerations in fundamental science, the study of the origin and evolution of parasite diversity has important implications for more applied fields such as epidemiology and diagnosis.
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Affiliation(s)
- T de Meeûs
- Laboratoire de Parasitologie Comparée, UMR 5555 CNRS, Université Montpellier II, Place E. Bataillon, 34095 Montpellier, Cedex 05 France
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9
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Antonova ES, Hammer BK. Quorum-sensing autoinducer molecules produced by members of a multispecies biofilm promote horizontal gene transfer to Vibrio cholerae. FEMS Microbiol Lett 2011; 322:68-76. [PMID: 21658103 DOI: 10.1111/j.1574-6968.2011.02328.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Vibrio cholerae, the causative agent of cholera and a natural inhabitant of aquatic environments, regulates numerous behaviors using a quorum-sensing (QS) system conserved among many members of the marine genus Vibrio. The Vibrio QS response is mediated by two extracellular autoinducer (AI) molecules: CAI-I, which is produced only by Vibrios, and AI-2, which is produced by many bacteria. In marine biofilms on chitinous surfaces, QS-proficient V. cholerae become naturally competent to take up extracellular DNA. Because the direct role of AIs in this environmental behavior had not been determined, we sought to define the contribution of CAI-1 and AI-2 in controlling transcription of the competence gene, comEA, and in DNA uptake. In this study we demonstrated that comEA transcription and the horizontal acquisition of DNA by V. cholerae are induced in response to purified CAI-1 and AI-2, and also by autoinducers derived from other Vibrios co-cultured with V. cholerae within a mixed-species biofilm. These results suggest that autoinducer communication within a consortium may promote DNA exchange among Vibrios, perhaps contributing to the evolution of these bacterial pathogens.
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Affiliation(s)
- Elena S Antonova
- School of Biology, Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
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10
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Abstract
Plasmids are key vectors of horizontal gene transfer and essential genetic engineering tools. They code for genes involved in many aspects of microbial biology, including detoxication, virulence, ecological interactions, and antibiotic resistance. While many studies have decorticated the mechanisms of mobility in model plasmids, the identification and characterization of plasmid mobility from genome data are unexplored. By reviewing the available data and literature, we established a computational protocol to identify and classify conjugation and mobilization genetic modules in 1,730 plasmids. This allowed the accurate classification of proteobacterial conjugative or mobilizable systems in a combination of four mating pair formation and six relaxase families. The available evidence suggests that half of the plasmids are nonmobilizable and that half of the remaining plasmids are conjugative. Some conjugative systems are much more abundant than others and preferably associated with some clades or plasmid sizes. Most very large plasmids are nonmobilizable, with evidence of ongoing domestication into secondary chromosomes. The evolution of conjugation elements shows ancient divergence between mobility systems, with relaxases and type IV coupling proteins (T4CPs) often following separate paths from type IV secretion systems. Phylogenetic patterns of mobility proteins are consistent with the phylogeny of the host prokaryotes, suggesting that plasmid mobility is in general circumscribed within large clades. Our survey suggests the existence of unsuspected new relaxases in archaea and new conjugation systems in cyanobacteria and actinobacteria. Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts.
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11
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Heinemann JA, Rosén H, Savill M, Burgos-Caraballo S, Toranzos GA. Environment arrays: a possible approach for predicting changes in waterborne bacterial disease potential. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2006; 40:7150-6. [PMID: 17180961 DOI: 10.1021/es060331x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Current molecular techniques for identifying bacteria in water have proven useful, but they are not reliably predictive of impending disease outbreaks. Genomics-based approaches will help to detect the presence of pathogens quickly and well before they grow into a population that poses a risk to public health. We suggest that genomics is only one component of the toolbox that will be needed to identify emerging waterborne threats. We propose a methodology beyond genomics, based on activity in the mobile genome. This approach makes use of a new device called an environment array. The array will depend upon the same research necessary for genomics-based detection, but will not require an a priori knowledge of virulence genes. Environment arrays are assembled from molecular profiles of the infectious elements that transfer between bacteria. The advantage of the array is that it monitors the activity of the mobile genome, rather than the presence of particular DNA sequences. Environmental arrays should thus be many times more sensitive than traditional hybridization or PCR-based techniques that target already-known DNA sequences. Mobile elements are known to respond to new environmental conditions that may correlate with a chemical contamination or the bloom of bacterial pathogens, potentially allowing for a much broader application in detecting unknown or unanticipated biological and chemical contaminants.
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Affiliation(s)
- Jack A Heinemann
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
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12
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Willms AR, Roughan PD, Heinemann JA. Static recipient cells as reservoirs of antibiotic resistance during antibiotic therapy. Theor Popul Biol 2006; 70:436-51. [PMID: 16723146 DOI: 10.1016/j.tpb.2006.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Revised: 03/28/2006] [Accepted: 04/11/2006] [Indexed: 11/25/2022]
Abstract
How does taking the full course of antibiotics prevent antibiotic resistant bacteria establishing in patients? We address this question by testing the possibility that horizontal/lateral gene transfer (HGT) is critical for the accumulation of the antibiotic-resistance phenotype while bacteria are under antibiotic stress. Most antibiotics prevent bacterial reproduction, some by preventing de novo gene expression. Nevertheless, in some cases and at some concentrations, the effects of most antibiotics on gene expression may not be irreversible. If the stress is removed before the bacteria are cleared from the patients by normal turnover, gene expression restarts, converting the residual population to phenotypic resistance. Using mathematical models we investigate how static recipients of resistance genes carried by plasmids accumulate resistance genes, and how specifically an environment cycling between presence and absence of the antibiotic uniquely favors the evolution of horizontally mobile resistance genes. We found that the presence of static recipients can substantially increase the persistence of the plasmid and that this effect is most pronounced when the cost of carriage of the plasmid decreases the cell's growth rate by as much as a half or more. In addition, plasmid persistence can be enhanced even when conjugation rates are as low as half the rate required for the plasmid to persist as a parasite on its own.
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Affiliation(s)
- Allan R Willms
- Department of Mathematics and Statistics, University of Guelph, Guelph, ON, Canada.
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13
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Cooper† T, Heinemann J. Selection for plasmid post-segregational killing depends on multiple infection: evidence for the selection of more virulent parasites through parasite-level competition. Proc Biol Sci 2005; 272:403-10. [PMID: 15734695 PMCID: PMC1634991 DOI: 10.1098/rspb.2004.2921] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Accepted: 09/06/2004] [Indexed: 11/12/2022] Open
Abstract
Is the virulence of parasites an outcome of optimized infection? Virulence has often been considered an inevitable consequence of parasite reproduction when the cost incurred by the parasite in reducing the fitness of its current host is offset by increased infection of new hosts. More recent models have focused on how competition occurring between parasites during co-infection might effect selection of virulence. For example, if co-infection was common, parasites with higher intrinsic growth rates might be selected, even at the expense of being optimally adapted to infect new hosts. If growth rate is positively correlated with virulence, then competition would select increased virulence. We tested these models using a plasmid-encoded virulence determinant. The virulence determinant did not contribute to the plasmid's reproduction within or between hosts. Despite this, virulent plasmids were more successful than avirulent derivatives during selection in an environment allowing within-host competition. To explain these findings we propose and test a model in which virulent parasites are selected by reducing the reproduction of competitors.
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Affiliation(s)
| | - J.A. Heinemann
- School of Biological Sciences and New Zealand Institute of Gene Ecology, University of CanterburyPrivate Bag 4800, ChristchurchNew Zealand
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14
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Heinemann JA, Traavik T. Problems in monitoring horizontal gene transfer in field trials of transgenic plants. Nat Biotechnol 2005; 22:1105-9. [PMID: 15340480 DOI: 10.1038/nbt1009] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant bacteria and of the sensitivity of current techniques for monitoring HGT from transgenic plants to soil microorganisms has two major implications for field trial assessments of transgenic crops: first, HGT from transgenic plants to microbes could still have an environmental impact at a frequency approximately a trillion times lower than the current risk assessment literature estimates the frequency to be; and second, current methods of environmental sampling to capture genes or traits in a recombinant are too insensitive for monitoring evolution by HGT. A model for HGT involving iterative short-patch events explains how HGT can occur at high frequencies but be detected at extremely low frequencies.
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Affiliation(s)
- Jack A Heinemann
- New Zealand Institute of Gene Ecology, University of Canterbury, 8020, Private Bag 4800, Christchurch, New Zealand.
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15
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van den Eede G, Aarts H, Buhk HJ, Corthier G, Flint HJ, Hammes W, Jacobsen B, Midtvedt T, van der Vossen J, von Wright A, Wackernagel W, Wilcks A. The relevance of gene transfer to the safety of food and feed derived from genetically modified (GM) plants. Food Chem Toxicol 2004; 42:1127-56. [PMID: 15123384 DOI: 10.1016/j.fct.2004.02.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2003] [Accepted: 02/04/2004] [Indexed: 12/31/2022]
Abstract
In 2000, the thematic network ENTRANSFOOD was launched to assess four different topics that are all related to the testing or assessment of food containing or produced from genetically modified organisms (GMOs). Each of the topics was linked to a European Commission (EC)-funded large shared cost action (see http://www.entransfood.com). Since the exchange of genetic information through horizontal (lateral) gene transfer (HGT) might play a more important role, in quantity and quality, than hitherto imagined, a working group dealing with HGT in the context of food and feed safety was established. This working group was linked to the GMOBILITY project (GMOBILITY, 2003) and the results of the deliberations are laid down in this review paper. HGT is reviewed in relation to the potential risks of consuming food or feed derived from transgenic crops. First, the mechanisms for obtaining transgenic crops are described. Next, HGT mechanisms and its possible evolutionary role are described. The use of marker genes is presented in detail as a special case for genes that may pose a risk. Furthermore, the exposure to GMOs and in particular to genetically modified (GM) deoxyribonucleic acid (DNA) is discussed as part of the total risk assessment. The review finishes off with a number of conclusions related to GM food and feed safety. The aim of this paper is to provide a comprehensive overview to assist risk assessors as well as regulators and the general public in understanding the safety issues related to these mechanisms.
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Affiliation(s)
- G van den Eede
- European Commission Directorate General Joint Research Centre, Institute for Health and Consumer Protection, Biotechnology and GMOs Unit, Via E. Fermi 1-T.P. 331, I-21020 Ispra (VA), Italy.
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16
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Gomis-Rüth FX, Moncalían G, de la Cruz F, Coll M. Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein. Detailed structural features and mapping of the active site cleft. J Biol Chem 2002; 277:7556-66. [PMID: 11748238 DOI: 10.1074/jbc.m110462200] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial conjugation is an example of macromolecular trafficking between cells and responsible for the spreading of antibiotic resistance among bacteria. It involves translocation of single-stranded DNA across membranes through a type IV secretion system. A coupling protein links the DNA-processing nucleoprotein complex, the relaxosome, with the transport apparatus during cell mating. In Escherichia coli plasmid R388 such a protein is TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein. TrwB is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export. The structure of a soluble TrwB variant unveils an elongated molecule with six equivalent protein units featuring a spherical quaternary structure, leaving a central channel. The structures of the non-liganded protein and four different complexes with substrate analogues and products allow the precise description of the active site architecture. The active sites are located at the interface between protomers, each of them shaped mainly by residues of one monomer, but including two crucial arginine residues belonging to the adjacent molecule. Upon substrate binding and putative hydrolysis, conformational changes are transferred from the external surface to the interior central channel.
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Affiliation(s)
- F Xavier Gomis-Rüth
- Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, c/Jordi Girona, 18-26, 08034 Barcelona, Spain.
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17
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Bertolla F, Kay E, Simonet P. Potential dissemination of antibiotic resistance genes from transgenic plants to microorganisms. Infect Control Hosp Epidemiol 2000; 21:390-3. [PMID: 10879570 DOI: 10.1086/501779] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Evidence that genes were transferred during evolution from plants to bacteria was obtained from nucleotide and protein sequence analyses. However, the extent of such transfers among phylogenetically distant organisms is limited by various factors, including those related to complexity of the environment and those endogenous to the bacteria, designed to prevent a drift of the genome integrity. The goal of this article is to give an overview of the potentials and limits of natural interkingdom gene transfers, with a particular focus on prokaryote originating sequences fitting the nuclear genome of transgenic plants.
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Affiliation(s)
- F Bertolla
- Laboratoire d'Ecologie Microbienne du Sol, Villeurbanne, UMR CNRS 5557, Université Lyon I, France
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18
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Abstract
The evolutionary history of organisms is often assumed to be recorded in the structure of important molecules, such as DNA sequences. Whereas the structure of these molecules does sometimes affirm other evidence of ancestry, like fossil records, it sometimes does not. Horizontal gene transfer can distort perceptions of ancestry. Determining the impact of horizontal gene transfer on evolution has been limited by the crude tools available to detect it. Physical and genetic vectors are now known to conduct genes between organisms, even between biological kingdoms of organisms. The effects are being noticed in important molecules preserved in the genomes of organisms. This article will review the systematic bias in using molecular morphology, like DNA sequences, to infer ancestry and how this bias is the unavoidable result of the way that experimental genetics itself evolved. We present the novel hypothesis that genes usually called epigenes, like methylation patterns and prions, are infectiously transferred, sometimes using DNA as a vector, but not as a gene.
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Affiliation(s)
- J A Heinemann
- Department of Plant and Microbial Sciences, University of Canterbury, Christchurch, New Zealand.
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Suzuki K, Hattori Y, Uraji M, Ohta N, Iwata K, Murata K, Kato A, Yoshida K. Complete nucleotide sequence of a plant tumor-inducing Ti plasmid. Gene 2000; 242:331-6. [PMID: 10721727 DOI: 10.1016/s0378-1119(99)00502-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Crown gall tumor disease in dicot plants is caused by Agrobacterium tumefaciens harboring a giant tumor-inducing (Ti) plasmid. Here, for the first time among agrobacterial plasmids, the nucleotide sequence of a typical nopaline-type Ti plasmid (pTi-SAKURA) was determined completely. In total, 195 open reading frames (ORFs) were estimated in the 206479 bp long sequence. 20 genes for conjugation, three for replication, 22 for pathogenesis and 37 for genetic colonization of host plants were found within two-thirds of the plasmid. These genes formed seven functional gene clusters with narrow inter-cluster spaces. In the remaining one-third of the plasmid, novel genes including homologs of mutT, Rhizobium nodQ and Sphingomonas ligE genes were found, which are likely to be responsible for the broad host range. Restriction fragment length variation indicates extreme plasticity of the part required for conjugational gene transfer and the above-mentioned one-third of the plasmid, even among closely related Ti plasmids.
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Affiliation(s)
- K Suzuki
- Department of Biological Science, Faculty of Science, Hiroshima University, Higashi-Hiroshima, Japan
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20
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Aoki S, Syno K. Horizontal gene transfer and mutation: ngrol genes in the genome of Nicotiana glauca. Proc Natl Acad Sci U S A 1999; 96:13229-34. [PMID: 10557303 PMCID: PMC23930 DOI: 10.1073/pnas.96.23.13229] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/1999] [Indexed: 11/18/2022] Open
Abstract
Ngrol genes (NgrolB, NgrolC, NgORF13, and NgORF14) that are similar in sequence to genes in the left transferred DNA (TL-DNA) of Agrobacterium rhizogenes have been found in the genome of untransformed plants of Nicotiana glauca. It has been suggested that a bacterial infection resulted in transformation of Ngrol genes early in the evolution of the genus Nicotiana. Although the corresponding four rol genes in TL-DNA provoked hairy-root syndrome in plants, present-day N. glauca and plants transformed with Ngrol genes did not exhibit this phenotype. Sequenced complementation analysis revealed that the NgrolB gene did not induce adventitious roots because it contained two point mutations. Single-base site-directed mutagenesis at these two positions restored the capacity for root induction to the NgrolB gene. When the NgrolB, with these two base substitutions, was positioned under the control of the cauliflower mosaic virus 35S promoter (P35S), transgenic tobacco plants exhibited morphological abnormalities that were not observed in P35S-RirolB plants. In contrast, the activity of the NgrolC gene may have been conserved after an ancient infection by bacteria. Discussed is the effect of the horizontal gene transfer of the Ngrol genes and mutations in the NgrolB gene on the phenotype of ancient plants during the evolution of N. glauca.
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Affiliation(s)
- S Aoki
- Department of Biology, Faculty of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522 Japan.
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21
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Bertolla F, Simonet P. Horizontal gene transfers in the environment: natural transformation as a putative process for gene transfers between transgenic plants and microorganisms. Res Microbiol 1999; 150:375-84. [PMID: 10466405 DOI: 10.1016/s0923-2508(99)80072-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Horizontal gene transfers among bacteria, such as natural transformation or conjugation, may have played an important role in bacterial evolution. They are thought to have been involved in promoting genome plasticity which permitted bacteria to adapt very efficiently to any change in their environment and to colonize a wide range of ecosystems. Evidence that some genes were transferred from eukaryotes, and in particular, from plants to bacteria, was obtained from nucleotide and protein sequence analyses. However, numerous factors, including some which are endogenous to the bacterial cells, tend to limit the extent of transfer, particularly among phylogenetically distant organisms. The goal of this paper is to give an overview of the potentials and limits of natural interkingdom gene transfers, with particular focus on prokaryote-originating sequences which fit the nuclear genome of transgenic plants.
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Affiliation(s)
- F Bertolla
- Laboratoire d'Ecologie Microbienne du Sol, UMR CNRS 5557, Université Lyon I, Villeurbanne, France.
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22
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Abstract
DNA can be transferred from eubacteria to at least plants, fungi, and all other eubacteria by related, plasmid-mediated conjugation. Little is known about the biochemistry of intraspecies or interspecies DNA transfer. Even less is known about what other molecules may accompany the DNA, or the direct or inheritable effects on recipients of these escort molecules. This report describes a genetic assay for detecting protein transfer during conjugation. The assay monitored phage lambda released from lysogenic recipients as a result of the concomitant delivery of the Escherichia coli RecA protein and plasmid DNA. The heretofore unexpected transfer of a donor chromosome-encoded protein initiates a heritable change in the recipient without altering its genetic make-up. The mechanism of transfer could be independent of transferred DNA.
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Affiliation(s)
- J A Heinemann
- Department of Plant and Microbial Sciences, University of Canterbury, Christchurch, 643 364 2926, New Zealand
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23
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Chou AY, Archdeacon J, Kado CI. Agrobacterium transcriptional regulator Ros is a prokaryotic zinc finger protein that regulates the plant oncogene ipt. Proc Natl Acad Sci U S A 1998; 95:5293-8. [PMID: 9560269 PMCID: PMC20254 DOI: 10.1073/pnas.95.9.5293] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Virulence genes of Agrobacterium tumefaciens are under the control of positive and negative transcriptional regulators. We found that the transcriptional regulator Ros controls expression of the plant oncogene ipt, which encodes isopentenyl transferase, in A. tumefaciens. This enzyme is involved in biosynthesis of the plant growth hormone cytokinin in the host plant. An ipt promoter::cat reporter gene fusion showed a 10-fold increase in ipt promoter activity in A. tumefaciens ros mutant strains when compared with wild type. Also, increased levels (10- to 20-fold) of isopentenyl adenosine, the product of the reaction catalyzed by isopentenyl transferase, were detected in ros mutant strains. In vitro studies using purified Ros showed it binds directly to the ipt promoter. Analysis of the deduced Ros amino acid sequence identified a novel type of C2H2 zinc finger. In Ros the peptide loop spacing of the zinc finger is 9 amino acids as opposed to the invariant 12 amino acids in the classical C2H2 motif. Site-directed mutagenesis of Cys-82 and His-92 in this motif showed that these residues are essential for Zn2+ and DNA binding activities of Ros. The existence of such a regulator in Agrobacterium may be due to horizontal interkingdom retrotransfer of the ros gene from plant to bacteria.
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Affiliation(s)
- A Y Chou
- Davis Crown Gall Group, University of California, Davis, CA 95616, USA
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24
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25
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26
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Natural genetic engineering of plant cells: the molecular biology of crown gall and hairy root disease. World J Microbiol Biotechnol 1996; 12:327-51. [DOI: 10.1007/bf00340209] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/07/1996] [Accepted: 02/10/1996] [Indexed: 11/26/2022]
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27
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Sia EA, Kuehner DM, Figurski DH. Mechanism of retrotransfer in conjugation: prior transfer of the conjugative plasmid is required. J Bacteriol 1996; 178:1457-64. [PMID: 8631725 PMCID: PMC177822 DOI: 10.1128/jb.178.5.1457-1464.1996] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Bacterial conjugation normally involves the unidirectional transfer of DNA from donor to recipient. Occasionally, conjugation results in the transfer of DNA from recipient to donor, a phenomenon known as retrotransfer. Two distinct models have been generally considered for the mechanism of retrotransfer. In the two-way conduction model, no transfer of the conjugative plasmid is required. The establishment of a single conjugation bridge between donor and recipient is sufficient for the transfer of DNA in both directions. In the one-way conduction model, transfer of the conjugative plasmid to the recipient is required to allow the synthesis of a new conjugation bridge for the transfer of DNA from recipient to donor. We have tested these models by the construction of a mutant of the self-transmissible, IncP plasmid RK2lac that allows the establishement of the conjugation bridge but is incapable of self-transfer. Four nucleotides of the nic region of the origin of transfer (oriT) were changed directly in the 67-kb plasmid RK2lac by a simple adaptation of the vector-mediated excision (VEX) strategy for precision mutagenesis of large plasmids (E. K.Ayres, V. J. Thomson, G. Merino, D. Balderes, and D. H. Figurski, J. Mol. Biol. 230:174-185, 1993). The resulting RK2lac oriT1 mutant plasmid mobilizes IncQ or IncP oriT+ plasmids efficiently but transfers itself at a frequency which is 10(4)-fold less than that of the wild type. Whereas the wild-type RK2lac oriT+ plasmid promotes the retrotransfer of an IncQ plasmid from Escherichia coli or Pseudomonas aeruginosa recipients, the RK2lac oriT1 mutant is severely defective in retrotransfer. Therefore, retrotransfer requires prior transfer of the conjugative plasmid to the recipient. The results prove that retrotransfer occurs by two sequential DNA transfer events.
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Affiliation(s)
- E A Sia
- Department of Microbiology and Cancer Center, College of Physicians and Surgeons, Columbia University, New York 10032, USA
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28
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Piers KL, Heath JD, Liang X, Stephens KM, Nester EW. Agrobacterium tumefaciens-mediated transformation of yeast. Proc Natl Acad Sci U S A 1996; 93:1613-8. [PMID: 8643679 PMCID: PMC39990 DOI: 10.1073/pnas.93.4.1613] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Agrobacterium tumefaciens transfers a piece of its Ti plasmid DNA (transferred DNA or T-DNA) into plant cells during crown gall tumorigenesis. A. tumefaciens can transfer its T-DNA to a wide variety of hosts, including both dicotyledonous and monocotyledonous plants. We show that the host range of A. tumefaciens can be extended to include Saccharomyces cerevisiae. Additionally, we demonstrate that while T-DNA transfer into S. cerevisiae is very similar to T-DNA transfer into plants, the requirements are not entirely conserved. The Ti plasmid-encoded vir genes of A. tumefaciens that are required for T-DNA transfer into plants are also required for T-DNA transfer into S. cerevisiae, as is vir gene induction. However, mutations in the chromosomal virulence genes of A. tumefaciens involved in attachment to plant cells have no effect on the efficiency of T-DNA transfer into S. cerevisiae. We also demonstrate that transformation efficiency is improved 500-fold by the addition of yeast telomeric sequences within the T-DNA sequence.
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Affiliation(s)
- K L Piers
- Department of Microbiology, University of Washington, Seattle, 98195, USA
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29
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Abstract
Barriers to chromosomal gene transfer between bacterial species control their genetic isolation. These barriers, such as different microhabitats, the host ranges of genetic exchange vectors and restriction-modification systems, limit gene exchange, but the major limitation is genomic sequence divergence. The mismatch-repair system inhibits interspecies recombination, the inducible SOS system stimulates interspecies recombination, while natural selection determines the effective recombination frequencies.
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Affiliation(s)
- I Matic
- Laboratoire de Mutagenese, Institut Jacques Monod, Paris, France.
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30
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Meyer AD, Ichikawa T, Meins F. Horizontal gene transfer: regulated expression of a tobacco homologue of the Agrobacterium rhizogenes rolC gene. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:265-73. [PMID: 7500950 DOI: 10.1007/bf00290526] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A tobacco homologue (trolC) of the rolC gene of the Agrobacterium rhizogenes Ri-plasmid was cloned and sequenced from Nicotiana tabacum L. cv. Havana 425. The coding region of trolC is similar in sequence (69-87% for DNA and 54-89% for the deduced amino acid sequence) to rolC genes of the agropine, mannopine, and mikimopine strains of Ri-plasmids and the N. glauca rolC homologue. Southern analyses showed that trolC is encoded by a small gene family derived from the tomentosiformis ancestor of tobacco. This suggests that trolC resulted from an ancient transfer of DNA between A. rhizogenes and a progenitor of modern tobacco. Transcripts of trolC were detected in three morphologically distinct cultivars of tobacco. trolC mRNA accumulated in young leaves and shoot tips, but not in lower leaves and roots of mature plants. Accumulation of trolC mRNA in cultured leaf tissues was strongly down-regulated by auxin and induced by cytokinin. These results are of particular interest because they suggest that a gene of bacterial origin introduced during evolution can have a function in a modern plant.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Base Sequence
- Biological Evolution
- Blotting, Northern
- Blotting, Southern
- Cells, Cultured
- Cloning, Molecular
- Gene Expression Regulation, Plant
- Gene Transfer, Horizontal
- Genes, Plant
- Molecular Sequence Data
- Plant Proteins/genetics
- Plants, Toxic
- Rhizobium/genetics
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Nicotiana/cytology
- Nicotiana/genetics
- beta-Glucosidase
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Affiliation(s)
- A D Meyer
- Friedrich Miescher-Institute, Basel, Switzerland
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31
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Itaya M. Toward a bacterial genome technology: integration of the Escherichia coli prophage lambda genome into the Bacillus subtilis 168 chromosome. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:9-16. [PMID: 7651332 DOI: 10.1007/bf02456608] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A novel approach to the cloning large DNAs in the Bacillus subtilis chromosome was examined. An Escherichia coli prophage lambda DNA (48.5 kb) was assembled in the chromosome of B. subtilis. The lambda DNA was first subcloned in four segments, having partially overlapping regions. Assembly of the complete prophage was achieved by successive transformation using three discrete DNA integration modes: overlap-elongation, Campbell-type integration, and gap-filling. In the B. subtilis chromosome, DNA was elongated, using contiguous DNA segments, via overlap-elongation. Jumping from one end of a contiguous DNA stretch to another segment was achieved by Campbell-type integration. The remaining gap was sealed by gap-filling. The incorporated lambda DNA thus assembled was stably replicated as part of the 4188 kb B. subtilis chromosome under non-selective conditions. The present method can be used to accommodate larger DNAs in the B. subtilis chromosome and possible applications of this technique are discussed.
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Affiliation(s)
- M Itaya
- Mitsubishi Kasei Institute of Life Sciences, Tokyo, Japan
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32
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Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM. Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Mol Microbiol 1995; 16:955-67. [PMID: 7476192 DOI: 10.1111/j.1365-2958.1995.tb02321.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report on the analysis of 214kb of the parasitic eubacterium Mycoplasma capricolum sequenced by genomic walking techniques. The 287 putative proteins detected to date represent about half of the estimated total number of 500 predicted for this organism. A large fraction of these (75%) can be assigned a likely function as a result of similarity searches. Several important features of the functional organization of this small genome are already apparent. Among these are (i) the expected relatively large number of enzymes involved in metabolic transport and activation, for efficient use of host cell nutrients; (ii) the presence of anabolic enzymes; (iii) the unexpected diversity of enzymes involved in DNA replication and repair; and (iv) a sizeable number of orthologues (82 so far) in Escherichia coli. This survey is beginning to provide a detailed view of how M. capricolum manages to maintain essential cellular processes with a genome much smaller than that of its bacterial relatives.
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Affiliation(s)
- P Bork
- Max-Delbrück-Centre for Molecular Medicine, Berlin-Buch, Germany
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33
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Matic I, Rayssiguier C, Radman M. Interspecies gene exchange in bacteria: the role of SOS and mismatch repair systems in evolution of species. Cell 1995; 80:507-15. [PMID: 7859291 DOI: 10.1016/0092-8674(95)90501-4] [Citation(s) in RCA: 240] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Analysis of interspecies matings between S. typhimurium and E. coli indicates that the genetic barrier that separates these (and perhaps many other) related species is primarily recombinational. The structural component of this barrier is genomic sequence divergence. The mismatch repair enzymes act as potent inhibitors of interspecies recombination, whereas the SOS system acts as an inducible positive regulator. Interspecies mating triggers a RecBC-dependent SOS response in female bacteria that increases recombination mainly through overproduction of the RecA protein. Mismatch repair acts to reduce the mutation rate and recombination between similar sequences, whereas SOS acts to increase both. These opposing activities allow mismatch repair and SOS systems to determine both the rate of accumulation of sequence divergence and the extent of genetic isolation, which are the key components of the speciation process.
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Affiliation(s)
- I Matic
- Laboratoire de Mutagénèse, Institut Jacques Monod, Paris, France
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34
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Matic I. Les mécanismes du contrôle des échanges génétiques interspécifiques et de la variabilité génétique chez les bactéries. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0020-2452(96)81489-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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35
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Kawano S, Takano H, Kuroiwa T. Sexuality of mitochondria: fusion, recombination, and plasmids. INTERNATIONAL REVIEW OF CYTOLOGY 1995; 161:49-110. [PMID: 7558693 DOI: 10.1016/s0074-7696(08)62496-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mitochondrial fusion, recombination, and mobile genetic elements, which are essential for mitochondrial sexuality, are well established in various organisms. The recombination of mitochondrial DNA (mtDNA) depends upon fusion between parental mitochondria, and between their mtDNA-containing areas (mt-nuclei), to allow pairing between the parental mtDNAs. Such mitochondrial fusion followed by recombination may be called "mitochondrial sex." We have identified a novel mitochondrial plasmid named mF. This plasmid is apparently responsible for promoting mitochondrial fusion and crosses over with mtDNA in successive sexual crosses with mF- strains. Only in mF+ strains carrying the mF plasmid did small spherical mitochondria fuse which subsequently underwent fusion between the mt-nuclei that contained the mtDNA derived from individual mitochondria. Several successive mitochondrial divisions followed, accompanied by mt-nuclear divisions. The resulting mitochondria contained recombinant mtDNA with the mF plasmid. Such features remind us also of the bacterial conjugative plasmids such as F plasmid. Therefore, in the final part of this chapter, we discuss the origin of sex and its relationship to the sexuality of mitochondria.
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Affiliation(s)
- S Kawano
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
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36
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Abstract
Bacteria (prokaryotes) were the sole form of life on earth for some two billion years--roughly half its history. During this time they evolved into a giant, global superorganism and developed a remarkable mechanism for the creation and exchange of genetic material. Apart from its intrinsic interest, this has practical significance, for example in the development of multiple resistance to antibiotics of pathogenic bacteria such as those of tuberculosis. Eukaryotes, with nucleated cells, may have developed from a permanent symbiosis of three or more prokaryotes.
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Affiliation(s)
- L G Mathieu
- Department of Microbiology and Immunology, Faculty of Medicine, Université de Montréal
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37
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Paquin B, Laforest MJ, Lang BF. Interspecific transfer of mitochondrial genes in fungi and creation of a homologous hybrid gene. Proc Natl Acad Sci U S A 1994; 91:11807-10. [PMID: 7991539 PMCID: PMC45324 DOI: 10.1073/pnas.91.25.11807] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In eukaryotes, horizontal gene transfer is a rare event. Here we show that the mitochondrial genome of a lower fungus, Allomyces macrogynus, has an extra DNA segment not present in a close relative, Allomyces arbusculus. This insert consists of the C terminus of a foreign gene encoding a subunit of the ATP synthetase complex (atp6) plus an open reading frame encoding an endonuclease. The inserted atp6 portion is fused in phase to the resident gene, resulting in expression of a hybrid atp6 gene and the displacement of the original C-terminal atp6 region. We present evidence that this insertion may have been acquired by interspecific transfer and we discuss the possible role of the endonuclease in this process.
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Affiliation(s)
- B Paquin
- Département de Biochimie, Université de Montréal, PQ, Canada
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38
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Little E, Bork P, Doolittle RF. Tracing the spread of fibronectin type III domains in bacterial glycohydrolases. J Mol Evol 1994; 39:631-43. [PMID: 7528812 DOI: 10.1007/bf00160409] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The evolutionary spread of 22 fibronectin type III (Fn3) sequences among a dozen bacterial enzymes has been traced by searching databases with the non-Fn3 parts of the enzyme sequences. Numerous homologues were found that lacked the Fn3 domains. In each case the related sequences were aligned, phylogenetic trees were constructed, and the occurrences of Fn3 units on the trees were noted. Comparison with phylogenetic trees prepared from the Fn3 segments themselves allowed inferences to be made about when the Fn3 units were shuffled into their present positions.
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Affiliation(s)
- E Little
- Center for Molecular Genetics, University of California, San Diego, La Jolla 92093-0634
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39
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Schäfer A, Schwarzer A, Kalinowski J, Pühler A. Cloning and characterization of a DNA region encoding a stress-sensitive restriction system from Corynebacterium glutamicum ATCC 13032 and analysis of its role in intergeneric conjugation with Escherichia coli. J Bacteriol 1994; 176:7309-19. [PMID: 7961503 PMCID: PMC197120 DOI: 10.1128/jb.176.23.7309-7319.1994] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
RP4-mediated transfer of mobilizable plasmids in intergeneric conjugation of Escherichia coli donors with Corynebacterium glutamicum ATCC 13032 is severely affected by a restriction system in the recipient that can be inactivated by a variety of exogenous stress factors. In this study a rapid test procedure based on intergeneric conjugal plasmid transfer that permitted the distinction between restriction-negative and restriction-positive C. glutamicum clones was developed. By using this procedure, clones of the restriction-deficient mutant strain C. glutamicum RM3 harboring a plasmid library of the wild-type chromosome were checked for their restriction properties. A complemented clone with a restriction-positive phenotype was isolated and found to contain a plasmid with a 7-kb insertion originating from the wild-type chromosome. This plasmid, termed pRES806, is able to complement the restriction-deficient phenotype of different C. glutamicum mutants. Sequence analysis revealed the presence of two open reading frames (orf1 and orf2) on the complementing DNA fragment. The region comprising orf1 and orf2 displayed a strikingly low G+C content and was present exclusively in C. glutamicum strains. Gene disruption experiments with the wild type proved that orf1 is essential for complementation, but inactivation of orf2 also resulted in a small but significant increase in fertility. These results were confirmed by infection assays with the bacteriophage CL31 from Corynebacterium lilium ATCC 15990.
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Affiliation(s)
- A Schäfer
- Department of Genetics, University of Bielefeld, Germany
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40
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Lorenz MG, Wackernagel W. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 1994; 58:563-602. [PMID: 7968924 PMCID: PMC372978 DOI: 10.1128/mr.58.3.563-602.1994] [Citation(s) in RCA: 462] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Natural genetic transformation is the active uptake of free DNA by bacterial cells and the heritable incorporation of its genetic information. Since the famous discovery of transformation in Streptococcus pneumoniae by Griffith in 1928 and the demonstration of DNA as the transforming principle by Avery and coworkers in 1944, cellular processes involved in transformation have been studied extensively by in vitro experimentation with a few transformable species. Only more recently has it been considered that transformation may be a powerful mechanism of horizontal gene transfer in natural bacterial populations. In this review the current understanding of the biology of transformation is summarized to provide the platform on which aspects of bacterial transformation in water, soil, and sediments and the habitat of pathogens are discussed. Direct and indirect evidence for gene transfer routes by transformation within species and between different species will be presented, along with data suggesting that plasmids as well as chromosomal DNA are subject to genetic exchange via transformation. Experiments exploring the prerequisites for transformation in the environment, including the production and persistence of free DNA and factors important for the uptake of DNA by cells, will be compiled, as well as possible natural barriers to transformation. The efficiency of gene transfer by transformation in bacterial habitats is possibly genetically adjusted to submaximal levels. The fact that natural transformation has been detected among bacteria from all trophic and taxonomic groups including archaebacteria suggests that transformability evolved early in phylogeny. Probable functions of DNA uptake other than gene acquisition will be discussed. The body of information presently available suggests that transformation has a great impact on bacterial population dynamics as well as on bacterial evolution and speciation.
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Affiliation(s)
- M G Lorenz
- Genetik, Fachbereich Biologie, Carl-von-Ossietzky Universität Oldenburg, Germany
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41
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Inomata K, Nishikawa M, Yoshida K. The yeast Saccharomyces kluyveri as a recipient eukaryote in transkingdom conjugation: behavior of transmitted plasmids in transconjugants. J Bacteriol 1994; 176:4770-3. [PMID: 8045911 PMCID: PMC196303 DOI: 10.1128/jb.176.15.4770-4773.1994] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The prokaryote Escherichia coli successfully conjugated with the eukaryote Saccharomyces kluyveri, which is relatively distant from the species S. cerevisiae. To achieve this transkingdom conjugation, we constructed three types of conjugative plasmids, namely integrative, replicative, and centromere vectors, for S. cerevisiae. By transfer of any of the three plasmids from E. coli, an S. kluyveri Ura- mutant was converted to the Ura+ phenotype. This phenotype was easily lost under nonselective conditions. Southern analysis of the transconjugants clearly indicated the presence of the plasmids in many different structures and sizes.
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Affiliation(s)
- K Inomata
- Department of Biological Science, Faculty of Science, Hiroshima University, Japan
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Sandmeier H. Acquisition and rearrangement of sequence motifs in the evolution of bacteriophage tail fibres. Mol Microbiol 1994; 12:343-50. [PMID: 8065255 DOI: 10.1111/j.1365-2958.1994.tb01023.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular analysis reveals a surprising sharing of short gene segments among a variety of large double-stranded DNA bacteriophages of enteric bacteria. Ancestral genomes from otherwise unrelated phages, including lambda, Mu, P1, P2 and T4, must have exchanged parts of their tail-fibre genes. Individual genes appear as mosaics with parts derived from a common gene pool. Therefore, horizontal gene transfer emerges as a major factor in the evolution of a specific part of phage genomes. Current concepts of homologous recombination cannot account for the formation of such chimeric genes and the recombinational mechanisms responsible are not known. However, recombination sites for DNA invertases and recombination site-like sequences are present at the boundaries of gene segments conferring the specificity for the host receptor. This, together with the properties of the DNA inversion mechanism, suggests that these site-specific recombination enzymes could be responsible for the exchange of host-range determinants.
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Affiliation(s)
- H Sandmeier
- Department of Preventive Dentistry and Oral Microbiology, University of Basel, Switzerland
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Kado CI. Promiscuous DNA transfer system of Agrobacterium tumefaciens: role of the virB operon in sex pilus assembly and synthesis. Mol Microbiol 1994; 12:17-22. [PMID: 7914664 DOI: 10.1111/j.1365-2958.1994.tb00990.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conjugative transfer of DNA that occurs between bacteria also operates between bacteria and higher organisms. The transfer of DNA between Gram-negative bacteria requires initial contact by a sex pilus followed by DNA traversing four membranes (donor plus recipient) using a transmembrane pore. Accumulating evidence suggests that transfer of the T-DNA from Agrobacterium tumefaciens to plants may also occur via a conjugative mechanism. The virB operon of the Ti plasmid exhibits close homologies to genes that are known to encode the pilin subunits and pilin assembly proteins. The proteins encoded by the PilW operon of IncW plasmid R388 share strong similarities (average similarity = 50.8%) with VirB proteins. Similarly, the TraA, TraL and TraC proteins of IncF plasmid F have similarities to VirB2, VirB3 and VirB4 respectively (average similarity = 45.3%). VirB2 protein (12.3 kDa) contains a signal peptidase-I cleavage sequence that generates a polypeptide of 7.2 kDa. Likewise, the 12.8 kDa propilin protein TraA of plasmid F also possesses a peptidase-I cleavage site that generates the 7.2 kDa pilin structural protein. Similar amino acid sequences of the conjugative transfer genes of F, R388 as well as plasmid RP4 and the genes of the ptI operon of Bortedella pertussis suggest the existence of a superfamily of transmembrane proteins adapted to the promiscuous transfer of DNA-protein complexes.
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Affiliation(s)
- C I Kado
- Department of Plant Pathology, University of California, Davis 95616
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Schäfer A, Kalinowski J, Pühler A. Increased fertility of Corynebacterium glutamicum recipients in intergeneric matings with Escherichia coli after stress exposure. Appl Environ Microbiol 1994; 60:756-9. [PMID: 8135527 PMCID: PMC201381 DOI: 10.1128/aem.60.2.756-759.1994] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Corynebacterial recipient cells exposed to heat, organic solvents, pH shifts, or detergents show an increased fertility in subsequent interspecific matings with Escherichia coli. This effect is independent of de novo protein biosynthesis and seems to be due to a direct inactivation of a restriction system active against foreign DNA that enters the cell by IncP-mediated conjugation.
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Affiliation(s)
- A Schäfer
- Department of Genetics, University of Bielefeld, Germany
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Ochman H, Groisman EA. The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium. EXS 1994; 69:479-93. [PMID: 7994120 DOI: 10.1007/978-3-0348-7527-1_27] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Since diverging from a common ancestor some 120 million years, Escherichia coli and Salmonella typhimurium have accumulated numerous phenotypic characteristics which have traditionally been used to distinguish these enteric species. While most of the genetic differences between these species are due to the accumulation of point mutations, the majority of the observed variation in phenotypic characters is attributable to segments of the genome confined to only one of the species. We have analyzed the map positions, G+C contents, nucleotide sequences and functions of regions unique to the Salmonella chromosome in an attempt to determine the ancestry of species-specific sequences. Some of the Salmonella-specific regions had uncharacteristically low base compositions and contained open reading frames of atypical codon usage patterns suggesting that portions of the genome were acquired by horizontal transfer from distantly-related bacterial species. The role of these species-specific sequences was assayed by constructing mutant strains harboring deletions in the corresponding regions of the genome. Several functions were ascribed to these unique portions of the Salmonella chromosome, including one encoding proteins involved in virulence and invasion of host epithelial cells.
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Affiliation(s)
- H Ochman
- Department of Biology, University of Rochester, NY 14627
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Heinemann JA, Ankenbauer RG. Retrotransfer of IncP plasmid R751 from Escherichia coli maxicells: evidence for the genetic sufficiency of self-transferable plasmids for bacterial conjugation. Mol Microbiol 1993; 10:57-62. [PMID: 7968518 DOI: 10.1111/j.1365-2958.1993.tb00903.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Gene transfer between organisms is a prime contributor to evolution. Bacterial conjugation is probably the most important mechanism by which genes are spread among prokaryotes and perhaps also contributes to eukaryotic evolution. Conjugation is mediated by plasmids. The mechanism of conjugation remains ill-understood despite progress in the identification, mapping and sequencing of genes required for plasmid transmission. All conjugation-specific genes (those required only for DNA transfer and establishment) identified to date map to plasmids. We found that IncP plasmids could enter and subsequently convert maxicells, which are trapped in a metabolic state that prevents de novo expression of chromosomal genes, into conjugative donors. This suggests that IncP plasmids encode not only necessary functions but indeed all functions specific to DNA transmission. Thus, like viruses, plasmids can convert non-viable cells into gene vectors.
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Affiliation(s)
- J A Heinemann
- NIH, NIAID, LMSF, Rocky Mountain Laboratories, Hamilton, Montana 59840
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Heinemann JA, Ankenbauer RG. Retrotransfer in Escherichia coli conjugation: bidirectional exchange or de novo mating? J Bacteriol 1993; 175:583-8. [PMID: 8423133 PMCID: PMC196192 DOI: 10.1128/jb.175.3.583-588.1993] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
DNA can be transferred among eubacteria and to plants and fungi by related, plasmid-mediated processes collectively referred to as bacterial conjugation. Conjugation occurs between cells in contact with one another and results in the unidirectional delivery of DNA from a bacterial donor to a recipient. Recent experiments that have reexamined the directionality of DNA flow during conjugation have come to different conclusions, some suggesting that genetic material also flows from recipient cells into the donor and that this process, termed retrotransfer, is likewise directed by donor-encoded functions. Given that bacteria are perhaps united with all living creatures by conjugation, the possibility of gene flow into donor bacteria during conjugation raises interesting evolutionary and biocontainment issues. Here we report that plasmid transmission from bacterial recipients to donors is not a donor-mediated event. Movement of genetic material from recipients to donors was inhibited by streptomycin, which does not inhibit the conjugative donor, indicating that retrotransfer requires gene expression in recipients. Furthermore, retrotransfer was reduced in matings mediated by plasmids that encode strong entry exclusion, to a similar degree as matings between two donors. Therefore we suggest that retrotransfer is in fact newly initiated conjugation between transconjugants and donors.
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Affiliation(s)
- J A Heinemann
- Laboratory of Microbial Structure and Function, National Institute of Allergy and Infectious Diseases, Rocky Mountain Laboratories, Hamilton, Montana 59840
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Kawano S, Takano H, Imai J, Mori K, Kurioiwa T. A genetic system controlling mitochondrial fusion in the slime mould, Physarum polycephalum. Genetics 1993; 133:213-24. [PMID: 8436271 PMCID: PMC1205312 DOI: 10.1093/genetics/133.2.213] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We have identified two distinct mitochondrial phenotypes, namely, Mif+ (mitochondrial fusion) and Mif- (mitochondrial fusion-deficient), and have studied the genetic system that controls mitochondrial fusion in the slime mould, Physarum polycephalum. A mitochondrial plasmid of approximately 16 kbp was identified in all Mif+ plasmodial strains. This plasmid is apparently responsible for promoting mitochondrial fusion, and it is inserted into the mitochondrial DNA (mtDNA) in successive sexual crossing with Mif- strains. This recombinant mtDNA and the unchanged free plasmid spread through the mitochondrial population via the promotion of mitochondrial fusion. The Mif+ strains with the plasmid were further classified as being two types: high frequency and low frequency mitochondrial fusion. Restriction analysis of the mtDNA suggested that the high frequency mitochondrial fusion type was more often heteroplasmic; within each plasmodium, mtDNAs of both parental types were usually present, in addition to the presence of the plasmid. Genetic analysis with the progeny obtained from crossing myxamoebae derived from three different isolates suggested that these progeny carried different alleles at a nuclear locus that controlled the frequency of mitochondrial fusion. These alleles (mitochondrial mating-type alleles, mitA1, 2 and 3) appear to function like the mating type of the myxamoebae; mitochondrial fusion occurs at high frequency with the combination of unlike alleles, but at low frequency with the combination of like alleles.
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Affiliation(s)
- S Kawano
- Department of Biology, Faculty of Science, University of Tokyo, Japan
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