Analysis of core genes supports the reclassification of strains Agrobacterium radiobacter K84 and Agrobacterium tumefaciens AKE10 into the species Rhizobium rhizogenes

Velázquez, Encarna; Palomo, José Luis Rodríguez-Arias; Rivas, Raúl; Guerra, Hilario; Peix, Álvaro; Trujillo, Martha E.; García-Benavides, Pablo; Mateos, Pedro F.; Wabiko, Hiroetsu; Martínez‐Molina, Eustoquio

doi:10.1016/j.syapm.2010.04.004

Cited by 51 publications

(35 citation statements)

References 22 publications

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“…The availability of the complete genomic sequences of A. tumefaciens strain C58 (18), Rhizobium rhizogenes strain K84 (35) (formerly A. radiobacter, formerly A. rhizogenes [41]), and A. vitis strain S4 (35) allowed the use of multilocus basedmethods to study the genetic diversity in Agrobacterium species populations. The aim of the present study was to analyze a large collection of clinical and environmental Agrobacterium strains using multilocus genetics and phenotypic traits in order to determine whether clinical isolates displayed specific characteristics.…”

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confidence: 99%

Multilocus Sequence-Based Analysis Delineates a Clonal Population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of Human Origin

et al. 2011

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The genus Agrobacterium includes plant-associated bacteria and opportunistic human pathogens. Taxonomy and nomenclature within the genus remain controversial. In particular, isolates of human origin were all affiliated with the species Agrobacterium (Rhizobium) radiobacter, while phytopathogenic strains were designated under the synonym denomination Agrobacterium tumefaciens. In order to study the relative distribution of Agrobacterium strains according to their origins, we performed a multilocus sequence-based analysis (MLSA) on a large collection of 89 clinical and environmental strains from various origins. We proposed an MLSA scheme based on the partial sequence of 7 housekeeping genes (atpD, zwf, trpE, groEL, dnaK, glnA, and rpoB) present on the circular chromosome of A. tumefaciens C58. Multilocus phylogeny revealed that 88% of the clinical strains belong to genovar A7, which formed a homogeneous population with linkage disequilibrium, suggesting a low rate of recombination. Comparison of genomic fingerprints obtained by pulsed-field gel electrophoresis (PFGE) showed that the strains of genovar A7 were epidemiologically unrelated. We present genetic evidence that genovar A7 may constitute a human-associated population distinct from the environmental population. Also, phenotypic characteristics, such as culture at 42°C, agree with this statement. This human-associated population might represent a potential novel species in the genus Agrobacterium.

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confidence: 99%

Multilocus Sequence-Based Analysis Delineates a Clonal Population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of Human Origin

et al. 2011

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“…We have recently shown that the biocontrol agent R. rhizogenes (formerly A. radiobacter [56]) strain K84 is able to form biofilms not only on abiotic surfaces but also on plant root surfaces, where biofilms become complex and structured, with cells adhering to the surface and to each other (1). Based on these observations, we…”

Section: Discussionmentioning

confidence: 89%

“…During the bacterium-plant cell interactions in wounded tissues, tumorigenic strains have the ability to transfer a particular DNA segment from the Ti plasmid of the bacterium to the plant genome, and its expression in the transformed plant cell leads to the development of a crown gall tumor (reviewed in references 61 and 62). It is well known that crown gall disease can be controlled by treatment of the root plant system with the biocontrol agent Rhizobium rhizogenes (formerly Agrobacterium radiobacter [56]) strain K84 (reviewed in reference 45). Strain K84 also attaches to root tips ex planta and efficiently colonizes the plant root system (29,43,53,57).…”

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Role for Rhizobium rhizogenes K84 Cell Envelope Polysaccharides in Surface Interactions

Abarca-Grau

Burbank

Paz

et al. 2012

Appl Environ Microbiol

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dRhizobium rhizogenes strain K84 is a commercial biocontrol agent used worldwide to control crown gall disease. The organism binds tightly to polypropylene substrate and efficiently colonizes root surfaces as complex, multilayered biofilms. A genetic screen identified two mutants in which these surface interactions were affected. One of these mutants failed to attach and form biofilms on the abiotic surface although, interestingly, it exhibited normal biofilm formation on the biological root tip surface. This mutant is disrupted in a wcbD ortholog gene, which is part of a large locus predicted to encode functions for the biosynthesis and export of a group II capsular polysaccharide (CPS). Expression of a functional copy of wcbD in the mutant background restored the ability of the bacteria to attach and form normal biofilms on the abiotic surface. The second identified mutant attached and formed visibly denser biofilms on both abiotic and root tip surfaces. This mutant is disrupted in the rkpK gene, which is predicted to encode a UDP-glucose 6-dehydrogenase required for O-antigen lipopolysaccharide (LPS) and K-antigen capsular polysaccharide (KPS) biosynthesis in rhizobia. The rkpK mutant from strain K84 was deficient in O-antigen synthesis and exclusively produced rough LPS. We also show that strain K84 does not synthesize the KPS typical of some other rhizobia strains. In addition, we identified a putative type II CPS, distinct from KPS, that mediates cell-surface interactions, and we show that O antigen of strain K84 is necessary for normal cell-cell interactions in the biofilms.

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“…strain AP16 is closely related to Rhizobium rhizogenes K84. Rhizobium rhizogenes K84 (formerly Agrobacterium radiobacter K84 [38]) has been commercially used as a biocontrol agent against crown gall disease for decades (39). As visualized in the phylogenetic tree shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Production of Proteasome Inhibitor Syringolin A by the Endophyte Rhizobium sp. Strain AP16

Dudnik

Bigler

Dudler

2014

Appl Environ Microbiol

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bSyringolin A, the product of a mixed nonribosomal peptide synthetase/polyketide synthase encoded by the syl gene cluster, is a virulence factor secreted by certain Pseudomonas syringae strains. Together with the glidobactins produced by a number of betaand gammaproteobacterial human and animal pathogens, it belongs to the syrbactins, a structurally novel class of proteasome inhibitors. In plants, proteasome inhibition by syringolin A-producing P. syringae strains leads to the suppression of host defense pathways requiring proteasome activity, such as the ones mediated by salicylic acid and jasmonic acid. Here we report the discovery of a syl-like gene cluster with some unusual features in the alphaproteobacterial endophyte Rhizobium sp. strain AP16 that encodes a putative syringolin A-like synthetase whose components share 55% to 65% sequence identity (72% to 79% similarity) at the amino acid level. As revealed by average nucleotide identity (ANI) calculations, this strain likely belongs to the same species as biocontrol strain R. rhizogenes K84 (formely known as Agrobacterium radiobacter K84), which, however, carries a nonfunctional deletion remnant of the syl-like gene cluster. Here we present a functional analysis of the syl-like gene cluster of Rhizobium sp. strain AP16 and demonstrate that this endophyte synthesizes syringolin A and some related minor variants, suggesting that proteasome inhibition by syrbactin production can be important not only for pathogens but also for endophytic bacteria in the interaction with their hosts. Syringolin A was originally isolated from culture supernatants of the phytopathogenic gammaproteobacterium Pseudomonas syringae pv. syringae B301D-R based on its ability to elicit defense responses and pathogen resistance in rice plants (1, 2). It is a tripeptide derivative consisting an N-terminal valine and the two nonproteinogenic amino acids, 3,4-dehydrolysine and 5-methyl-4-amino-2-hexenoic acid; the first is N-acylated with an unusual ureido-valine moiety, and the latter two form a 12-member macrolactam ring (Fig. 1A). Syringolin A is the major variant of a family of related compounds in which one or both valine residues can be replaced by isoleucine and/or 3,4-dehydrolysine can be replaced by lysine (3). Syringolin A was shown to be a virulence factor in the interaction of P. syringae strain B728a with its host plant Phaseolus vulgaris (bean) where loss of syringolin A production resulted in a significantly diminished lesion number (4). The elucidation of the mode of action of syringolin A revealed that it irreversibly inhibited all three proteolytic activities (i.e., the caspase-, trypsin-, and chymotrypsin-like activities) of the eukaryotic proteasome by covalent ether bond formation with the active-site N-terminal threonine residues of the catalytic ␤1, ␤2, and ␤5 subunits of the 20S core proteasome (4). Proteasome inhibition suppresses the action of many plant hormones, including defense reactions mediated by the important defense hormones jasmonic acid (JA) and salicyl...

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Analysis of core genes supports the reclassification of strains Agrobacterium radiobacter K84 and Agrobacterium tumefaciens AKE10 into the species Rhizobium rhizogenes

Cited by 51 publications

References 22 publications

Multilocus Sequence-Based Analysis Delineates a Clonal Population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of Human Origin

Multilocus Sequence-Based Analysis Delineates a Clonal Population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of Human Origin

Role for Rhizobium rhizogenes K84 Cell Envelope Polysaccharides in Surface Interactions

Production of Proteasome Inhibitor Syringolin A by the Endophyte Rhizobium sp. Strain AP16

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