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Weisberg AJ, Wu Y, Chang JH, Lai EM, Kuo CH. Virulence and Ecology of Agrobacteria in the Context of Evolutionary Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:1-23. [PMID: 37164023 DOI: 10.1146/annurev-phyto-021622-125009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Among plant-associated bacteria, agrobacteria occupy a special place. These bacteria are feared in the field as agricultural pathogens. They cause abnormal growth deformations and significant economic damage to a broad range of plant species. However, these bacteria are revered in the laboratory as models and tools. They are studied to discover and understand basic biological phenomena and used in fundamental plant research and biotechnology. Agrobacterial pathogenicity and capability for transformation are one and the same and rely on functions encoded largely on their oncogenic plasmids. Here, we synthesize a substantial body of elegant work that elucidated agrobacterial virulence mechanisms and described their ecology. We review findings in the context of the natural diversity that has been recently unveiled for agrobacteria and emphasize their genomics and plasmids. We also identify areas of research that can capitalize on recent findings to further transform our understanding of agrobacterial virulence and ecology.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Yu Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan;
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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2
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Kuzmanović N, diCenzo GC, Bunk B, Spröer C, Frühling A, Neumann‐Schaal M, Overmann J, Smalla K. Genomics of the "tumorigenes" clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov. Microbiologyopen 2023; 12:e1352. [PMID: 37186225 PMCID: PMC10064268 DOI: 10.1002/mbo3.1352] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 04/03/2023] Open
Abstract
Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct "tumorigenes" clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high-quality, closed genomes of representatives of the "tumorigenes" clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, the phenotypic characteristics of representatives of the "tumorigenes" clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in the United States, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the "tumorigenes" clade were identified, and their biological functions and roles in the ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.
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Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated PlantsInstitute for Plant Protection in Horticulture and Urban GreenBraunschweigGermany
| | | | - Boyke Bunk
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Cathrin Spröer
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Anja Frühling
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Meina Neumann‐Schaal
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - Jörg Overmann
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
- MicrobiologyTechnical University of BraunschweigBraunschweigGermany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated PlantsInstitute for Epidemiology and Pathogen DiagnosticsBraunschweigGermany
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3
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Weisberg AJ, Miller M, Ream W, Grünwald NJ, Chang JH. Diversification of plasmids in a genus of pathogenic and nitrogen-fixing bacteria. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200466. [PMID: 34839700 PMCID: PMC8628075 DOI: 10.1098/rstb.2020.0466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Members of the agrobacteria-rhizobia complex (ARC) have multiple and diverse plasmids. The extent to which these plasmids are shared and the consequences of their interactions are not well understood. We extracted over 4000 plasmid sequences from 1251 genome sequences and constructed a network to reveal interactions that have shaped the evolutionary histories of oncogenic virulence plasmids. One newly discovered type of oncogenic plasmid is a mosaic with three incomplete, but complementary and partially redundant virulence loci. Some types of oncogenic plasmids recombined with accessory plasmids or acquired large regions not known to be associated with pathogenicity. We also identified two classes of partial virulence plasmids. One class is potentially capable of transforming plants, but not inciting disease symptoms. Another class is inferred to be incomplete and non-functional but can be found as coresidents of the same strain and together are predicted to confer pathogenicity. The modularity and capacity for some plasmids to be transmitted broadly allow them to diversify, convergently evolve adaptive plasmids and shape the evolution of genomes across much of the ARC. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marilyn Miller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Walt Ream
- Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, United States Department of Agriculture and Agricultural Research Service, Corvallis, OR 97330, USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Hooykaas MJG, Hooykaas PJJ. Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid. BMC Microbiol 2021; 21:295. [PMID: 34711172 PMCID: PMC8554961 DOI: 10.1186/s12866-021-02358-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/06/2021] [Indexed: 01/18/2023] Open
Abstract
Background The Agrobacterium strain AB2/73 has a unique host range for the induction of crown gall tumors, and contains an exceptionally large, over 500 kbp mega Ti plasmid. We used whole genome sequencing to fully characterize and comparatively analyze the complex genome of strain AB2/73, including its Ti plasmid and virulence factors. Results We obtained a high-quality, full genomic sequence of AB2/73 by a combination of short-read Illumina sequencing and long-read Nanopore sequencing. The AB2/73 genome has a total size of 7,266,754 bp with 59.5% GC for which 7012 genes (6948 protein coding sequences) are predicted. Phylogenetic and comparative genomics analysis revealed that strain AB2/73 does not belong to the genus Agrobacterium, but to a new species in the genus Rhizobium, which is most related to Rhizobium tropici. In addition to the chromosome, the genome consists of 6 plasmids of which the largest two, of more than 1 Mbp, have chromid-like properties. The mega Ti plasmid is 605 kbp in size and contains two, one of which is incomplete, repABC replication units and thus appears to be a cointegrate consisting of about 175 kbp derived from an unknown Ti plasmid linked to 430 kbp from another large plasmid. In pTiAB2/73 we identified a complete set of virulence genes and two T-DNAs. Besides the previously described T-DNA we found a larger, second T-DNA containing a 6b-like onc gene and the acs gene for agrocinopine synthase. Also we identified two clusters of genes responsible for opine catabolism, including an acc-operon for agrocinopine degradation, and genes putatively involved in ridéopine catabolism. The plasmid also harbours tzs, iaaM and iaaH genes for the biosynthesis of the plant growth regulators cytokinin and auxin. Conclusions The comparative genomics analysis of the high quality genome of strain AB2/73 provided insight into the unusual phylogeny and genetic composition of the limited host range Agrobacterium strain AB2/73. The description of its unique genomic composition and of all the virulence determinants in pTiAB2/73 will be an invaluable tool for further studies into the special host range properties of this bacterium. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02358-0.
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Otten L. T-DNA regions from 350 Agrobacterium genomes: maps and phylogeny. PLANT MOLECULAR BIOLOGY 2021; 106:239-258. [PMID: 33826062 DOI: 10.1007/s11103-021-01140-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/12/2021] [Indexed: 05/27/2023]
Abstract
Analysis of 350 Agrobacterium wgs sequences reveals complex evolutionary history of T-DNA regions Virulent Agrobacterium strains transfer one or more plasmid DNA fragments to plant cells during a well-characterized transformation process. The transferred DNA sequences (T-DNA regions) are delimited by 25 nucleotide long conserved border sequences. Until recently, relatively few T-DNA regions were known. However, due to increased whole genome sequencing efforts, about 400 Agrobacterium sequences have now become available, 350 of which contain T-DNA regions. Detailed analysis identified 92 different T-DNA regions and several new T-DNA genes. T-DNA regions can be divided into three groups. I. Typical Agrobacterium rhizogenes T-DNA regions with rol genes. II. A large group of T-DNA regions with iaa and ipt genes, which can be further subdivided into seven subgroups. III. A small group of unusual T-DNA regions. The evolutionary relation between the T-DNA regions could not be completely elucidated, because of the lack of evolutionary intermediates. Several clusters of highly related structures suggest that evolution of T-DNA regions proceeds by slow, progressive evolution of gene sequences, accompanied by rapid changes in overall structure, due to recombination between T-DNA regions of different origins, and insertion of bacterial insertion sequences (IS). Divergence values for T-DNA genes suggest that they were recruited at different times in evolution. An attempt was made to link T-DNA region evolution to plasmid evolution. The present study provides a solid basis for further studies on T-DNA region diversity and evolution.
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Affiliation(s)
- Léon Otten
- Institut de Biologie Moléculaire des Plantes, 12 Rue du Général Zimmer, 67084, Strasbourg, France.
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6
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Barton IS, Fuqua C, Platt TG. Ecological and evolutionary dynamics of a model facultative pathogen: Agrobacterium and crown gall disease of plants. Environ Microbiol 2018; 20:16-29. [PMID: 29105274 PMCID: PMC5764771 DOI: 10.1111/1462-2920.13976] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 01/09/2023]
Abstract
Many important pathogens maintain significant populations in highly disparate disease and non-disease environments. The consequences of this environmental heterogeneity in shaping the ecological and evolutionary dynamics of these facultative pathogens are incompletely understood. Agrobacterium tumefaciens, the causative agent for crown gall disease of plants has proven a productive model for many aspects of interactions between pathogens and their hosts and with other microbes. In this review, we highlight how this past work provides valuable context for the use of this system to examine how heterogeneity and transitions between disease and non-disease environments influence the ecology and evolution of facultative pathogens. We focus on several features common among facultative pathogens, such as the physiological remodelling required to colonize hosts from environmental reservoirs and the consequences of competition with host and non-host associated microbiota. In addition, we discuss how the life history of facultative pathogens likely often results in ecological tradeoffs associated with performance in disease and non-disease environments. These pathogens may therefore have different competitive dynamics in disease and non-disease environments and are subject to shifting selective pressures that can result in pathoadaptation or the within-host spread of avirulent phenotypes.
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Affiliation(s)
- Ian S. Barton
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Thomas G. Platt
- Division of Biology, Kansas State University, Manhattan, KS, USA
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7
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Llop P, Barbé S, López MM. Functions and origin of plasmids in Erwinia species that are pathogenic to or epiphytically associated with pome fruit trees. TREES (BERLIN, GERMANY : WEST) 2011; 26:31-46. [PMID: 25983394 PMCID: PMC4425259 DOI: 10.1007/s00468-011-0630-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 09/17/2011] [Accepted: 09/21/2011] [Indexed: 05/29/2023]
Abstract
The genus Erwinia includes plant-associated pathogenic and non-pathogenic species. Among them, all species pathogenic to pome fruit trees (E. amylovora, E. pyrifoliae, E. piriflorinigrans, Erwinia sp. from Japan) cause similar symptoms, but differ in their degrees of aggressiveness, i.e. in symptoms, host range or both. The presence of plasmids of similar size, in the range of 30 kb, is a common characteristic that they possess. Besides, they share some genetic content with high homology in several genes associated with exopolysaccharide production and hence, with virulence, as well as in some other genes. Knowledge of the content of these plasmids and comparative genetic analyses may provide interesting new clues to understanding the origin and evolution of these pathogens and the level of symptoms they produce. Furthermore, genetic similarities observed among some of the plasmids (and genomes) from the above indicated pathogenic species and E. tasmaniensis or E. billingiae, which are epiphytic on the same hosts, may reveal associations that could expose the mechanisms of origin of pathogens. A summary of the current information on their plasmids and the relationships among them is presented here.
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Affiliation(s)
- Pablo Llop
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km 4.5, 46113 Moncada, Valencia Spain
| | - Silvia Barbé
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km 4.5, 46113 Moncada, Valencia Spain
| | - María M. López
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km 4.5, 46113 Moncada, Valencia Spain
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8
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The BlcC (AttM) lactonase of Agrobacterium tumefaciens does not quench the quorum-sensing system that regulates Ti plasmid conjugative transfer. J Bacteriol 2008; 191:1320-9. [PMID: 19011037 DOI: 10.1128/jb.01304-08] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conjugative transfer of Agrobacterium plasmids is controlled by a quorum-sensing system consisting of TraR and its acyl-homoserine lactone (HSL) ligand. The acyl-HSL is essential for the TraR-mediated activation of the Ti plasmid Tra genes. Strains A6 and C58 of Agrobacterium tumefaciens produce a lactonase, BlcC (AttM), that can degrade the quormone, leading some to conclude that the enzyme quenches the quorum-sensing system. We tested this hypothesis by examining the effects of the mutation, induction, or mutational derepression of blcC on the accumulation of acyl-HSL and on the conjugative competence of strain C58. The induction of blc resulted in an 8- to 10-fold decrease in levels of extracellular acyl-HSL but in only a twofold decrease in intracellular quormone levels, a measure of the amount of active intracellular TraR. The induction or mutational derepression of blc as well as a null mutation in blcC had no significant effect on the induction of or continued transfer of pTiC58 from donors in any stage of growth, including stationary phase. In matings performed in developing tumors, wild-type C58 transferred the Ti plasmid to recipients, yielding transconjugants by 14 to 21 days following infection. blcC-null donors yielded transconjugants 1 week earlier, but by the following week, transconjugants were recovered at numbers indistinguishable from those of the wild type. Donors mutationally derepressed for blcC yielded transconjugants in planta at numbers 10-fold lower than those for the wild type at weeks 2 and 3, but by week 4, the two donors showed no difference in recoverable transconjugants. We conclude that BlcC has no biologically significant effect on Ti plasmid transfer or its regulatory system.
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9
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Baek CH, Farrand SK, Park DK, Lee KE, Hwang W, Kim KS. Genes for utilization of deoxyfructosyl glutamine (DFG), an amadori compound, are widely dispersed in the family Rhizobiaceae. FEMS Microbiol Ecol 2005; 53:221-33. [PMID: 16329942 DOI: 10.1016/j.femsec.2004.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2004] [Revised: 10/18/2004] [Accepted: 12/12/2004] [Indexed: 11/28/2022] Open
Abstract
Amadori compounds form spontaneously in decomposing plant material and can be found in the rhizosphere. As such, these compounds could influence microbial populations by serving as sources of carbon, nitrogen and energy to microorganisms expressing suitable catabolic pathways. Two distinct sets of genes for utilization of deoxyfructosyl glutamine (DFG), an Amadori compound, have been identified in isolates of Agrobacterium spp. One, the soc gene set, is encoded by pAtC58, a 543 kb plasmid in A. tumefaciens strain C58. The second, mocD dissimilates DFG formed in the pathway for catabolism of mannopine (MOP) a non-Amadori, imine-type member of the mannityl opine family characteristic of certain Ti and Ri plasmids. To assess the level of dispersal of these two Amadori-utilizing systems, isolates of Agrobacterium spp. and related bacteria in the family Rhizobiaceae were examined by Southern analysis for homologs of socD and mocD. Homologs of mocD were associated only with Ti plasmid-encoded pathways for catabolism of MOP. Homologs of socD were more widely distributed, being detectable in many but not all of the isolates of Agrobacterium, Sinorhizobium, and Rhizobium spp. tested. However, this gene was never associated with the virulence elements, such as the Ti and Ri plasmids, in these strains. Regardless of genus most of the isolates containing socD homologs could utilize DFG as sole source of carbon, nitrogen and energy. Correlation studies suggested that mocD has evolved uniquely as part of the mannityl opine catabolic pathway while socD has evolved for the general utilization of Amadori compounds. Certain isolates of Agrobacterium and Rhizobium that lacked detectable homologs of socD and mocD also could utilize DFG suggesting the existence of additional, unrelated pathways for the catabolism of this Amadori compound. These results suggest that Amadori compounds constitute a source of nutrition that is important to microflora in the rhizosphere.
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Affiliation(s)
- Chang-Ho Baek
- Department of Life Science, Sogang University, Mapo-Gu, Seoul, Republic of Korea
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10
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Gelvin SB. Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiol Mol Biol Rev 2003; 67:16-37, table of contents. [PMID: 12626681 PMCID: PMC150518 DOI: 10.1128/mmbr.67.1.16-37.2003] [Citation(s) in RCA: 620] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agrobacterium tumefaciens and related Agrobacterium species have been known as plant pathogens since the beginning of the 20th century. However, only in the past two decades has the ability of Agrobacterium to transfer DNA to plant cells been harnessed for the purposes of plant genetic engineering. Since the initial reports in the early 1980s using Agrobacterium to generate transgenic plants, scientists have attempted to improve this "natural genetic engineer" for biotechnology purposes. Some of these modifications have resulted in extending the host range of the bacterium to economically important crop species. However, in most instances, major improvements involved alterations in plant tissue culture transformation and regeneration conditions rather than manipulation of bacterial or host genes. Agrobacterium-mediated plant transformation is a highly complex and evolved process involving genetic determinants of both the bacterium and the host plant cell. In this article, I review some of the basic biology concerned with Agrobacterium-mediated genetic transformation. Knowledge of fundamental biological principles embracing both the host and the pathogen have been and will continue to be key to extending the utility of Agrobacterium for genetic engineering purposes.
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Affiliation(s)
- Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.
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11
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Peripheral Blood CD14+ Cells From Healthy Subjects Carry a Circular Conformation of Latent Cytomegalovirus Genome. Blood 1999. [DOI: 10.1182/blood.v93.1.394.401k44_394_398] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The majority of the human population harbors latent cytomegalovirus. Although CD14+ peripheral blood mononuclear cells have been implicated as sites of latency, the conformation of the latent viral genome in these cells is unknown. In this study, the conformation of viral genomic DNA was assessed in CD14+ cells from healthy virus seropositive carriers using an electrophoretic separation on native agarose gels in combination with polymerase chain reaction detection. Here we show that the viral genome migrates as a circular plasmid with a mobility equivalent to a circular 230-kb Shigella flexneri megaplasmid marker. Neither linear nor complex or integrated forms of the viral genome were detected. This report provides further evidence that the CD14+ cell population is an important site of viral latency in the naturally infected human host. Detection of the viral genome as a circular plasmid during latency suggests that this virus maintains its genome in a manner analogous to other herpesviruses where latent viral genome conformation has been studied.
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12
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Peripheral Blood CD14+ Cells From Healthy Subjects Carry a Circular Conformation of Latent Cytomegalovirus Genome. Blood 1999. [DOI: 10.1182/blood.v93.1.394] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The majority of the human population harbors latent cytomegalovirus. Although CD14+ peripheral blood mononuclear cells have been implicated as sites of latency, the conformation of the latent viral genome in these cells is unknown. In this study, the conformation of viral genomic DNA was assessed in CD14+ cells from healthy virus seropositive carriers using an electrophoretic separation on native agarose gels in combination with polymerase chain reaction detection. Here we show that the viral genome migrates as a circular plasmid with a mobility equivalent to a circular 230-kb Shigella flexneri megaplasmid marker. Neither linear nor complex or integrated forms of the viral genome were detected. This report provides further evidence that the CD14+ cell population is an important site of viral latency in the naturally infected human host. Detection of the viral genome as a circular plasmid during latency suggests that this virus maintains its genome in a manner analogous to other herpesviruses where latent viral genome conformation has been studied.
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13
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Otten L, Schmidt J. A T-DNA from the Agrobacterium tumefaciens limited-host-range strain AB2/73 contains a single oncogene. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1998; 11:335-342. [PMID: 9574502 DOI: 10.1094/mpmi.1998.11.5.335] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Agrobacterium tumefaciens strain AB2/73 isolated from Lippia canescens has been described as a limited-host-range strain. Its tumor-inducing (Ti) plasmid has been found to lack DNA homology to known T-DNAs (L. Unger, S. F. Ziegler, G. A. Huffman, V. C. Knauf, R. Peet, L. W. Moore, M. P. Gordon, and E. W. Nester. J. Bacteriol. 164:723-730, 1985). We have isolated a T-DNA from AB2/73 by using a heterologous border sequence as a probe. The AB2/73 T-DNA sequence (3,504 bp) is flanked by canonical border sequences, has no detectable DNA homology with other T-DNAs, and contains only two genes: lsn (Lippia strain nopaline synthaselike gene) and lso (Lippia strain oncogene). The lso gene induces nondifferentiating tumors on a limited number of hosts when transferred by a Ti plasmid from a wide-host-range strain. Part of the predicted Lso protein is weakly homologous to other Agrobacterium oncoproteins encoded by rolB, rolB, orf13, gene e, gene 5, and gene 3'. A 28-kb fragment corresponding to the virA to virE region was cloned by using a heterologous vir fragment as probe. The AB2/73 vir region is homologous to most of the C58 virulence region; however, the virA gene is most related to the virA gene of the Agrobacterium vitis limited-host-range strain Ag162.
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Affiliation(s)
- L Otten
- Department of Cell Biology, Plant Molecular Biology Institute of the C.N.R.S., Strasbourg, France.
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14
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Albiach MR, Lopez MM. Plasmid Heterogeneity in Spanish Isolates of
Agrobacterium tumefaciens
from Thirteen Different Hosts. Appl Environ Microbiol 1992; 58:2683-7. [PMID: 16348756 PMCID: PMC195841 DOI: 10.1128/aem.58.8.2683-2687.1992] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmid DNA was isolated from 80 Spanish isolates of
Agrobacterium tumefaciens
from 13 hosts of several geographical and temporal origins. One to five plasmids occurred in all of the isolates studied. Plasmid sizes varied between 5 and greater than 1,000 MDa. Generally, there was no correlation between plasmid number or size and geographical origin, host, biovar, sensitivity to agrocin 84, or opine-catabolizing ability of the different isolates.
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Affiliation(s)
- M R Albiach
- Instituto Valenciano de Investigaciones Agrarias, Apartado Oficial, 46113 Moncada, Valencia, Spain
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15
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Lowe BA, Krul WR. Physical, Chemical, Developmental, and Genetic Factors that Modulate the Agrobacterium-Vitis Interaction. PLANT PHYSIOLOGY 1991; 96:121-9. [PMID: 16668140 PMCID: PMC1080722 DOI: 10.1104/pp.96.1.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Tumor formation in Vitis species and hybrids, incited by Agrobacterium tumefaciens, was altered by chemical, physical, developmental, and genetic variables. Knowledge of the effect of these variables was used to develop a stringent in vitro assay system to select parents for a study of genetic factors that modulate tumor formation. Tumor formation was reduced by short day preconditioning of assay plants and by inoculation of the morphological apex of isolated stem segments. Pretreatment of plants with auxin or cytokinin altered specificity in various combinations of strains and host genotypes. All Vitis species and hybrids formed tumors in response to strains designated as limited host range, but some displayed a necrotic reaction (cell death at and below site of inoculation) or a null response (same as the response to inoculation with an avirulent strain) to strains designated as wide host range (VC Knauf, CG Panagopoulos, EW Nester [1982] Phytopathology 72: 1545-1549). Screens of F(1) progeny, derived from crosses of null, necrotic, and tumor-producing phenotypes, demonstrated that the null and the necrotic phenotypes were modulated by dominant and recessive host genes. The extent of cellular necrosis in the necrotic phenotype was modified by the morphological location of the inoculation site, by the presence of buds on the host stem, and by deletion of the tryptophane monooxygenase locus gene of the Ti-plasmid.
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Affiliation(s)
- B A Lowe
- United States Department of Agriculture, Agricultural Research Service, Plant Gene Expression Center, Albany, California 94710
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Charles TC, Finan TM. Analysis of a 1600-kilobase Rhizobium meliloti megaplasmid using defined deletions generated in vivo. Genetics 1991; 127:5-20. [PMID: 1849856 PMCID: PMC1204311 DOI: 10.1093/genetics/127.1.5] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A series of 120-600 kilobase deletions with defined endpoints were made in the 1600-kilobase Rhizobium meliloti megaplasmid pRmeSU47b, by homologous recombination between the IS50 elements of transposon insertions. Utilizing IS 50-mediated homologous recombination we also made defined reductions in deletion size and combined adjacent deletions. Deletion structure was confirmed by phage transduction and Southern hybridization analysis. Collectively these deletions span 1400 kilobases of pRmeSU47b, indicating that the majority of the plasmid is not essential for cell viability. This was further confirmed by the construction of a strain SU47 derivative which carries only 450 kilobases of the pRmeSU47b megaplasmid. Examination of the deletion mutants for phenotype revealed novel loci required for dulcitol, melibiose, raffinose, beta-hydroxybutyrate, acetoacetate, protocatechuate and quinate utilization. Previously unidentified loci required for effective root nodule development and exopolysaccharide synthesis were also found. Various deletion mutants were deficient in dicarboxylate transport, lactose utilization, and thiamine and exopolysaccharide biosynthesis, as predicted from earlier studies of this megaplasmid.
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Affiliation(s)
- T C Charles
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Abstract
The structure of several T-DNAs of Agrobacterium tumefaciens was determined by molecular cloning and Southern hybridization. The T-DNAs cloned in Escherichia coli vectors from four different nopaline type strains (PyTE1, PO31, PO22, and AKE10) showed various sizes of restriction enzyme fragments. Comparative analysis of the restriction maps revealed that the T-DNAs were composed of three distinct structural domains: (1) the region proximal to the right border (Domain I) containing the portion essential for tumorigenicity, (2) the proximity to the left border (Domain II), and (3) the region between the two domains (Domain III) to both of which no functional assignments have yet been made. The restriction map indicated that the Domains I and II were conserved in the most clones, including the well-characterized T37 T-DNA. The only exception was AKK1 (obtained from AKE10) which differed in Domain I. In the Domain III, insertions of 1.5- or 1.6-kb DNA were found in four clones, whereas an additional 2.5-kb insertion was found in one clone (PO22P1). The individual T-DNAs including Domain III with insertions was demonstrated in petunia and poplar tumors induced by the referred A. tumefaciens strains. However, resulting tumors differed in morphology and growth. These results suggest that the length polymorphism of the nopaline type T-DNA can be accounted by DNA insertions, and that diverse T-DNAs reflect their different roles in tumorigenicity.
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Affiliation(s)
- H Wabiko
- Laboratory of Molecular Genetics, Biotechnology Institute, Akita Prefectural College of Agriculture, Japan
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Nautiyal CS, Dion P. Characterization of the Opine-Utilizing Microflora Associated with Samples of Soil and Plants. Appl Environ Microbiol 1990; 56:2576-2579. [PMID: 16348265 PMCID: PMC184770 DOI: 10.1128/aem.56.8.2576-2579.1990] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms utilizing an opine as the sole carbon source were recovered from crown gall tumors, soil, and surface-disinfected potato tubers. The effect of the opines octopine, nopaline, succinamopine, and mannopine as selective substrates was compared with that of the auxin indoleacetic acid. Selection on octopine and indoleacetic acid favored the fluorescent pseudomonads, whereas mannopine allowed the frequent recovery of agrobacteria. Coryneforms which utilized succinamopine or mannopine were detected in soil, but not in tumors. Fungi growing on succinamopine or mannopine and a mannopine-utilizing Pseudomonas putida were isolated from tumor and soil, respectively.
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Affiliation(s)
- C S Nautiyal
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec, Canada G1K 7P4
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Abstract
A circular linkage map of the Rhizobium meliloti megaplasmid pRmeSU47b was constructed. The map consists of transposon insertions carrying alternating antibiotic resistance markers linked by phi M12 transduction. Data from conjugation experiments utilizing donor strains carrying Tn5-oriT insertions in the megaplasmid supported the proposed genetic map. In addition, the positions of previously identified Fix, exopolysaccharide synthetic, thiamine synthetic, and C4-dicarboxylate transport loci on the megaplasmid map were determined. By converting cotransduction frequencies to physical distance, we calculated the replicon to be 1,600 kilobases in size, which compares favorably with previous physical estimates.
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Affiliation(s)
- T C Charles
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Bonnard G, Vincent F, Otten L. Sequence and distribution of IS866, a novel T region-associated insertion sequence from Agrobacterium tumefaciens. Plasmid 1989; 22:70-81. [PMID: 2550985 DOI: 10.1016/0147-619x(89)90037-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have identified a new insertion sequence, IS866, located in the auxin synthesis gene TA iaaH of Tm4, a wide host range biotype III octopine/cucumopine type Agrobacterium tumefaciens strain with two T regions on its tumor-inducing (Ti) plasmid, TA, and TB. IS866 is 2716 bp long, has inverted repeats of 27 bp with three mismatches, and generates 8-bp direct repeats upon integration. In addition to IS866, pTiTm4 carries two copies of a related element, IS867, associated with TA and TB, respectively. A systematic study of 92 virulent Agrobacterium strains has shown that among the three biotypes all octopine/cucumopine and vitopine biotype III isolates contain IS866-like elements. The various octopine/cucumopine Ti plasmids always carry IS866 and IS867 at the same position as in pTiTm4. The chromosomes of the bacteria which contain these Ti plasmids also carry IS866 and IS867 copies but in varying numbers and locations.
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Affiliation(s)
- G Bonnard
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
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Wabiko H, Kagaya M, Kodama I, Masuda K, Kodama Y, Yamamoto H, Shibano Y, Sano H. Isolation and characterization of diverse nopaline type Ti plasmids of Agrobacterium tumefaciens from Japan. Arch Microbiol 1989. [DOI: 10.1007/bf00456088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hawes MC, Robbs SL, Pueppke SG. Use of a Root Tumorigenesis Assay to Detect Genotypic Variation in Susceptibility of Thirty-four Cultivars of Pisum sativum to Crown Gall. PLANT PHYSIOLOGY 1989; 90:180-4. [PMID: 16666732 PMCID: PMC1061695 DOI: 10.1104/pp.90.1.180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We developed a quantitative assay to measure tumorigenesis on roots and root crowns, the natural sites of Agrobacterium tumefaciens infection. Efficiency of tumor formation and tumor weight on seedlings of Pisum sativum ;Little Marvel' were directly proportional to the logarithm of inoculum concentration. Depth of wounding prior to inoculation also significantly influenced tumor weight but not efficiency. Mean weight of tumors that developed in response to inoculation with strain B6 varied significantly among 34 different commercial cultivars. Tumors on the most susceptible cultivar, Target, were more than tenfold heavier than those formed on the least susceptible cultivar, Sweet Snap. Efficiency of tumorigenesis on ;Sweet Snap' was also relatively low: only 64% of inoculated seedlings developed tumors compared with 89 to 100% efficiencies for all other cultivars.
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Affiliation(s)
- M C Hawes
- Department of Plant Pathology, University of Arizona, Tucson, Arizona 85721
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Abstract
The production of cytokinins by plant-associated bacteria was examined by radioimmunoassay. Strains producing trans-zeatin were identified in the genera Agrobacterium and Pseudomonas. Agrobacterium tumefaciens strains containing nopaline tumor-inducing plasmids, A. tumefaciens Lippia isolates, and Agrobacterium rhizogenes strains produced trans-zeatin in culture at 0.5 to 44 micrograms/liter. Pseudomonas solanacearum and Pseudomonas syringae pv. savastanoi produced trans-zeatin at levels of up to 1 mg/liter. In vitro cytokinin biosynthetic activity was measured for representative strains and was found to correlate with trans-zeatin production. The genetic locus for trans-zeatin secretion (tzs) was cloned from four strains: A. tumefaciens T37, A. rhizogenes A4, P. solanacearum K60, and P. syringae pv. savastanoi 1006. Southern blot analysis showed substantial homology of the Agrobacterium tzs genes to each other but not to the two Pseudomonas genes.
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Smarrelli J, Watters MT, Diba LH. Response of various cucurbits to infection by plasmid-harboring strains of agrobacterium. PLANT PHYSIOLOGY 1986; 82:622-4. [PMID: 16665082 PMCID: PMC1056173 DOI: 10.1104/pp.82.2.622] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Tumor formation in cucurbit cultivars resulting from infection by various strains of Agrobacterium tumefaciens and Agrobacterium rhizogenes is environmentally affected. In all instances, tumors could be induced on excised cotyledons while inoculating attached cotyledons or stems resulted in no tumor formation. In addition, buttercup squash (Cucurbita maxima Duch. buttercup) was most susceptible to tumor formation, while butterbush squash (Cucurbita maxima Duch. butterbush) failed to form tumors when inoculated with any of the strains of Agrobacterium. Other tested cucurbit cultivars showed intermediate susceptibility to tumor induction by the various Agrobacterium strains.
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Affiliation(s)
- J Smarrelli
- Department of Biology, Loyola University of Chicago, Chicago, Illinois 60626
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