Publications by authors named "Denis Faure"

90 Publications

European Population of : Genomic Diversity, Tuber Maceration Capacity and a Detection Tool for This Rarely Occurring Potato Pathogen.

Microorganisms 2021 Apr 8;9(4). Epub 2021 Apr 8.

French Federation of Seed Potato Growers (FN3PT-inov3PT), 43-45 Rue de Naples, 75008 Paris, France.

Enterobacteria belonging to the and genera are responsible for soft rot and blackleg diseases occurring in many crops around the world. Since 2016, the number of described species has more than doubled. However, some new species, such as , are often poorly characterized, and little is known about their genomic and phenotypic variation. Here, we explored several European culture collections and identified seven strains of All were collected from potato blackleg symptoms, sometimes from a long time ago, i.e., the IFB5596 strain isolated almost 25 years ago. We showed that this species remains rare, with less than 0.24% of strains identified among pectinolytic bacteria present in the surveyed collections. The analysis of the genomic diversity revealed the non-clonal character of species. Furthermore, the strains showed aggressiveness differences. Finally, a qPCR Taqman assay was developed for rapid and specific strain characterization and for use in diagnostic programs.
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http://dx.doi.org/10.3390/microorganisms9040781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8068253PMC
April 2021

Is there a unique integration mechanism of Agrobacterium T-DNA into a plant genome?

Authors:
Denis Faure

New Phytol 2021 03;229(5):2386-2388

CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Paris-Saclay University, 91 190, Gif-sur-Yvette, France.

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http://dx.doi.org/10.1111/nph.17184DOI Listing
March 2021

: Genomics, Host Range and Disease Management.

Microorganisms 2021 Jan 5;9(1). Epub 2021 Jan 5.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, 91190 Gif-sur-Yvette, France.

(Pbr) is considered as one of the most virulent species among the Pectobacteriaceae. This species has a broad host range within horticulture crops and is well distributed elsewhere. It has been found to be pathogenic not only in the field causing blackleg and soft rot of potato, but it is also transmitted via storage causing soft rot of other vegetables. Genomic analysis and other cost-effective molecular detection methods such as a quantitative polymerase chain reaction (qPCR) are essential to investigate the ecology and pathogenesis of the Pbr. The lack of fast, field deployable point-of-care testing (POCT) methods, specific control strategies and current limited genomic knowledge make management of this species difficult. Thus far, no comprehensive review exists about Pbr, however there is an intense need to research the biology, detection, pathogenicity and management of Pbr, not only because of its fast distribution across Europe and other countries but also due to its increased survival to various climatic conditions. This review outlines the information available in peer-reviewed literature regarding host range, detection methods, genomics, geographical distribution, nomenclature and taxonomical evolution along with some of the possible management and control strategies. In summary, the conclusions and a further directions highlight the management of this species.
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http://dx.doi.org/10.3390/microorganisms9010106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824751PMC
January 2021

Pattern and causes of the establishment of the invasive bacterial potato pathogen Dickeya solani and of the maintenance of the resident pathogen D. dianthicola.

Mol Ecol 2021 01 4;30(2):608-624. Epub 2020 Dec 4.

Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Paris-Saclay University, Gif-sur-Yvette, France.

Invasive pathogens can be a threat when they affect human health, food production or ecosystem services, by displacing resident species, and we need to understand the cause of their establishment. We studied the patterns and causes of the establishment of the pathogen Dickeya solani that recently invaded potato agrosystems in Europe by assessing its invasion dynamics and its competitive ability against the closely related resident D. dianthicola species. Epidemiological records over one decade in France revealed the establishment of D. solani and the maintenance of the resident D. dianthicola in potato fields exhibiting blackleg symptoms. Using experimentations, we showed that D. dianthicola caused a higher symptom incidence on aerial parts of potato plants than D. solani, while D. solani was more aggressive on tubers (i.e. with more severe symptoms). In co-infection assays, D. dianthicola outcompeted D. solani in aerial parts, while the two species co-existed in tubers. A comparison of 76 D. solani genomes (56 of which have been sequenced here) revealed balanced frequencies of two previously uncharacterized alleles, VfmB and VfmB , at the vfmB virulence gene. Experimental inoculations showed that the VfmB population was more aggressive on tubers, while the VfmB population outcompeted the VfmB population in stem lesions, suggesting an important role of the vfmB virulence gene in the ecology of the pathogens. This study thus brings novel insights allowing a better understanding of the pattern and causes of the D.solani invasion into potato production agrosystems, and the reasons why the endemic D. dianthicola nevertheless persisted.
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http://dx.doi.org/10.1111/mec.15751DOI Listing
January 2021

Complete Genome Sequence of the Type Strain Pectobacterium punjabense SS95, Isolated from a Potato Plant with Blackleg Symptoms.

Microbiol Resour Announc 2020 Aug 6;9(32). Epub 2020 Aug 6.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS University Paris-Saclay, Gif-sur-Yvette, France

is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of SS95, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.
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http://dx.doi.org/10.1128/MRA.00420-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409842PMC
August 2020

Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.

Microorganisms 2020 Jun 13;8(6). Epub 2020 Jun 13.

Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France.

Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015-2017). Pathogens were characterized by sequence determination of both the gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to (19%), (3%), (5%), (56%) and (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of LAR.16.03.LID was obtained and compared with other genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a strain isolated in Morocco that will be suitable for further epidemiological studies.
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http://dx.doi.org/10.3390/microorganisms8060895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7356628PMC
June 2020

Species Diversity of and Causing Potato Blackleg Disease in Pakistan.

Plant Dis 2020 May 8;104(5):1492-1499. Epub 2020 Mar 8.

Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.

Potato blackleg is caused by a diverse species of pectinolytic bacteria. In Pakistan, approximately 90% of the pathogens involved belong to Survey (2014 to 2017), sampling, and isolation from different potato growing areas of Punjab, Pakistan depicted an overall disease incidence of approximately 15%. Thirty-six pectinolytic strains confirmed through biochemical and pathogenicity testing were characterized via gene to identify them at the species level. To further validate the identification, one strain from each species SS26 (), SS28 (), SS70 (), SS90 (), SS95 (), and SS96 () were selected for draft genome sequencing and multilocus sequence analysis of 13 housekeeping genes (, , , , , , , , , , , , and ). Phylogenetic analysis revealed considerable genetic diversity in the genus . DNA-DNA hybridization and average nucleotide identity values of the strains selected for genome sequencing were determined with other reference and strains. Moreover, all six representative strains were also phenotypically characterized on the basis of metabolism of different carbon sources. Overall, on the basis of genotypic and phenotypic characteristics, these 36 isolates were grouped into six species: , , , , , and .
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http://dx.doi.org/10.1094/PDIS-08-19-1743-REDOI Listing
May 2020

Elevation of subsp. to species level as sp. nov., proposal of sp. nov. and sp. nov., emended description of and description of sp. nov., isolated from streams and symptoms on diverse plants.

Int J Syst Evol Microbiol 2019 Oct;69(10):3207-3216

Sorbonne Université, INRA, Institute of Ecology and Environmental sciences-Paris, 4 place Jussieu, F-75 252 Paris, France.

The species corresponds to a complex, including two subspecies with validly published names, two proposed subspecies and two new species, and Recent studies suggested that this complex needed revision. We examined the taxonomic status of 144 strains isolated from a wide range of plant species, various geographical origins and waterways. Sequences of the , and housekeeping genes clustered 114 of these strains together within a not yet described clade. We sequenced eight strains of this clade and analysed them together with the 102 genomes available in the NCBI database. Phylogenetic analysis, average nucleotide identity calculation and DNA-DNA hybridization allowed us to differentiate seven clades. This led us to propose the elevation of subsp. to species level as sp. nov. (type strain CFBP 1878=LMG 5863=NCPPB 3839=ICMP 11533), the proposal of sp. nov. (type strain KKH3=LMG 26003 =KCTC 23131) and sp. nov. (type strain CFBP 6617= LMG 21371=NCPPB 4609), to emend the description of (type strain CFBP 2046=LMG 2404=NCPPB 312=ICMP 5702), and to propose a novel species, sp. nov (type strain CFBP6051= NCPPB 3387=ICMP 9168) which includes the strains previously described as 'Candidatus '. Phenotypic analysis performed using Biolog GENIII plates on eight strains of sp. nov. and related strains completed our analysis.
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http://dx.doi.org/10.1099/ijsem.0.003611DOI Listing
October 2019

Dickeya undicola sp. nov., a novel species for pectinolytic isolates from surface waters in Europe and Asia.

Int J Syst Evol Microbiol 2019 Aug 5;69(8):2440-2444. Epub 2019 Jun 5.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91 190 Gif-sur-Yvette, France.

Strains 2B12, FVG1-MFV-O17 and FVG10-MFV-A16 were isolated from fresh water samples collected in Asia and Europe. The nucleotide sequences of the gapA barcodes revealed that all three strains belonged to the same cluster within the genus Dickeya. Using 13 housekeeping genes (fusA, rpoD, rpoS, glyA, purA, groEL, gapA, rplB, leuS, recA, gyrB, infB and secY), multilocus sequence analysis confirmed the existence of a new clade. When the genome sequences of these three isolates and other Dickeya species were compared, the in silico DNA-DNA hybridization and average nucleotide identity values were found to be no more than 45.50 and 91.22 %, respectively. The closest relative species was Dickeya fangzhongdai. Genome comparisons also highlighted genetic traits differentiating the new strains from D. fangzhongdai strains DSM 101947 (=CFBP 8607) and B16. Phenotypical tests were performed to distinguish the three strains from D. fangzhongdai and other Dickeya species. The name Dickeya undicola sp. nov. is proposed with strain 2B12 (=CFBP 8650=LMG 30903) as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.003497DOI Listing
August 2019

Biofilm-Constructing Variants of Paraburkholderia phytofirmans PsJN Outcompete the Wild-Type Form in Free-Living and Static Conditions but Not .

Appl Environ Microbiol 2019 06 16;85(11). Epub 2019 May 16.

Unité EA 4707 Résistance Induite et Bioprotection des Plantes, SFR Condorcet FR CNRS 3417, Université de Reims Champagne-Ardenne, Reims, France

Members of the genus colonize diverse ecological niches. Among the plant-associated strains, PsJN is an endophyte with a broad host range. In a spatially structured environment (unshaken broth cultures), biofilm-constructing specialists of PsJN colonizing the air-liquid interface arose at high frequency. In addition to forming a robust biofilm and on roots, those mucoid phenotypic variants display a reduced swimming ability and modulate the expression of several microbe-associated molecular patterns (MAMPs), including exopolysaccharides (EPS), flagellin, and GroEL. Interestingly, the variants induce low and expression compared to that of the parental strain, suggesting a possible evasion of plant host immunity. We further demonstrated that switching from the planktonic to the sessile form did not involve quorum-sensing genes but arose from spontaneous mutations in two genes belonging to an iron-sulfur cluster: (encoding a cochaperone protein) and (encoding a cysteine desulfurase). A mutational approach validated the implication of these two genes in the appearance of variants. We showed for the first time that in a heterogeneous environment, strain PsJN is able to rapidly diversify and coexpress a variant that outcompete the wild-type form in free-living and static conditions but not strain PsJN is a well-studied plant-associated bacterium known to induce resistance against biotic and abiotic stresses. In this work, we described the spontaneous appearance of mucoid variants in PsJN from static cultures. We showed that the conversion from the wild-type (WT) form to variants (V) correlates with an overproduction of EPS, an enhanced ability to form biofilm and , and a reduced swimming motility. Our results revealed also that these phenotypes are in part associated with spontaneous mutations in an iron-sulfur cluster. Overall, the data provided here allow a better understanding of the adaptive mechanisms likely developed by PsJN in a heterogeneous environment.
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http://dx.doi.org/10.1128/AEM.02670-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532049PMC
June 2019

Integrative and deconvolution omics approaches to uncover the Agrobacterium tumefaciens lifestyle in plant tumors.

Plant Signal Behav 2019 17;14(3):e1581562. Epub 2019 Feb 17.

a Institute for integrative biology of the cell (I2BC), CNRS CEA Univ. Paris-Sud , University Paris-Saclay , Gif-sur-Yvette , France.

Agrobacterium tumefaciens is a plant pathogen which provokes galls on roots and stems (crown-gall disease) and colonizes them. Two approaches combining omics were used to decipher the lifestyle of A. tumefaciens in plant tumors: an integrative approach when omics were used on A. tumefaciens cells collected from plant tumors, a deconvolution approach when omics were used on A. tumefaciens cells exploiting a single tumor metabolite in pure culture assay. This addendum highlights some recent results on the biotroph lifestyle of A. tumefaciens in plant tumors.
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http://dx.doi.org/10.1080/15592324.2019.1581562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6422367PMC
February 2020

Common and distinctive adaptive traits expressed in Dickeya dianthicola and Dickeya solani pathogens when exploiting potato plant host.

Environ Microbiol 2019 03 27;21(3):1004-1018. Epub 2019 Jan 27.

Sorbonne Université, INRA, Institute of Ecology and Environmental sciences-Paris, 4 place Jussieu, F-75252, Paris, France.

Blackleg and soft rot are devastating diseases on potato stem and tuber caused by Pectobacterium and Dickeya pectinolytic enterobacteria. In European potato cultures, D. dianthicola and D. solani species successively emerged in the past decades. Ecological traits associated to their settlement remain elusive, especially in the case of the recent invader D. solani. In this work, we combined genomic, metabolic and transcriptomic comparisons to unravel common and distinctive genetic and functional characteristics between two D. solani and D. dianthicola isolates. The two strains differ by more than a thousand genes that are often clustered in genomic regions (GRs). Several GRs code for transport and metabolism functions that correlate with some of the differences in metabolic abilities identified between the two Dickeya strains. About 800 D. dianthicola and 1100 D. solani genes where differentially expressed in macerated potato tubers as compared to when growing in rich medium. These include several genes located in GRs, pointing to a potential role in host interaction. In addition, some genes common to both species, including virulence genes, differed in their expression. This work highlighted distinctive traits when D. dianthicola and D. solani exploit the host as a resource.
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http://dx.doi.org/10.1111/1462-2920.14519DOI Listing
March 2019

Transfer of the waterfall source isolate Pectobacterium carotovorum M022 to Pectobacterium fontis sp. nov., a deep-branching species within the genus Pectobacterium.

Int J Syst Evol Microbiol 2019 Feb 2;69(2):470-475. Epub 2019 Jan 2.

1​Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.

Pectobacterium carotovorum M022 has been isolated from a waterfall source in Selangor district (Malaysia). Using genomic and phenotypic tests, we re-examined the taxonomical position of this strain. Based on 14 concatenated housekeeping genes (fusA, rpoD, rpoS, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB), multi-locus sequence analysis revealed that strain M022 falls into a novel clade separated from the other Pectobacterium species. The in silico DNA-DNA hybridization and average nucleotide identity values were lower than the 70 and 95 % threshold values, respectively. In addition, by combining genomic and phenotypic tests, strain M022 may be distinguished from the other Pectobacterium isolates by its incapacity to grow on d(+)-xylose, l-rhamnose, cellobiose and lactose. Strain M022 (=CFBP 8629=LMG 30744) is proposed as the type strain of the Pectobacteriumfontis sp. nov.
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http://dx.doi.org/10.1099/ijsem.0.003180DOI Listing
February 2019

The biotroph Agrobacterium tumefaciens thrives in tumors by exploiting a wide spectrum of plant host metabolites.

New Phytol 2019 04 3;222(1):455-467. Epub 2019 Jan 3.

Institute for Integrative Biology of the Cell (I2BC), CNRS CEA University Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, F-91190, France.

Agrobacterium tumefaciens is a niche-constructing biotroph that exploits host plant metabolites. We combined metabolomics, transposon-sequencing (Tn-seq), transcriptomics, and reverse genetics to characterize A. tumefaciens pathways involved in the exploitation of resources from the Solanum lycopersicum host plant. Metabolomics of healthy stems and plant tumors revealed the common (e.g. sucrose, glutamate) and enriched (e.g. opines, γ-aminobutyric acid (GABA), γ-hydroxybutyric acid (GHB), pyruvate) metabolites that A. tumefaciens could use as nutrients. Tn-seq and transcriptomics pinpointed the genes that are crucial and/or upregulated when the pathogen grew on either sucrose (pgi, kdgA, pycA, cisY) or GHB (blcAB, pckA, eno, gpsA) as a carbon source. While sucrose assimilation involved the Entner-Doudoroff and tricarboxylic acid (TCA) pathways, GHB degradation required the blc genes, TCA cycle, and gluconeogenesis. The tumor-enriched metabolite pyruvate is at the node connecting these pathways. Using reverse genetics, we showed that the blc, pckA, and pycA loci were important for aggressiveness (tumor weight), proliferation (bacterial charge), and/or fitness (competition between the constructed mutants and wild-type) of A. tumefaciens in plant tumors. This work highlighted how a biotroph mobilizes its central metabolism for exploiting a wide diversity of resources in a plant host. It further shows the complementarity of functional genome-wide scans by transcriptomics and Tn-seq to decipher the lifestyle of a plant pathogen.
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http://dx.doi.org/10.1111/nph.15598DOI Listing
April 2019

Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan.

Int J Syst Evol Microbiol 2018 Nov 21;68(11):3551-3556. Epub 2018 Sep 21.

2​Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.

Pectobacterium isolates SS95, SS54 and SS56 were collected from a potato field in the Chiniot district in the plains of the Punjab province, Pakistan. Sequencing of the gapA barcode revealed that these strains belong to a novel phylogenetic group separated from P.ectobacterium wasabiae and Pectobacterium parmentieri species. Furthermore, multilocus sequence analyses of 13 housekeeping genes (fusA, rpoD, acnA, purA, gyrB, recA, mdh, mtlD, groEL, secY, glyA, gapA and rplB) clearly distinguished the type strain, SS95, from its closest relatives, i.e. P. parmentieri RNS 08-42-1A and P. wasabiae CFBP3304, as well as from all the other known Pectobacteriumspecies. In silico DNA-DNA hybridization (<44.1 %) and average nucleotide identity (<90.75 %) values of strain SS95 compared with other Pectobacterium type strains supported the delineation of a new species. Genomic and phenotypic comparisons permitted the identification of additional traits that distinguished the Pakistani isolates from all other known Pectobacterium type strains. The name Pectobacterium punjabense sp. nov. is proposed for this taxon with the type strain SS95 (=CFBP 8604=LMG 30622).
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http://dx.doi.org/10.1099/ijsem.0.003029DOI Listing
November 2018

Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems.

New Phytol 2018 06;218(4):1321-1324

Aix Marseille University, CEA, CNRS, Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment (LEMiRE), UMR7265 BVME, F-13108, Saint-Paul-lez-Durance, France.

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http://dx.doi.org/10.1111/nph.15199DOI Listing
June 2018

Lifestyle of the biotroph Agrobacterium tumefaciens in the ecological niche constructed on its host plant.

New Phytol 2018 07 27;219(1):350-362. Epub 2018 Apr 27.

Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, F-91190, France.

Agrobacterium tumefaciens constructs an ecological niche in its host plant by transferring the T-DNA from its Ti plasmid into the host genome and by diverting the host metabolism. We combined transcriptomics and genetics for understanding the A. tumefaciens lifestyle when it colonizes Arabidopsis thaliana tumors. Transcriptomics highlighted: a transition from a motile to sessile behavior that mobilizes some master regulators (Hfq, CtrA, DivK and PleD); a remodeling of some cell surface components (O-antigen, succinoglucan, curdlan, att genes, putative fasciclin) and functions associated with plant defense (Ef-Tu and flagellin pathogen-associated molecular pattern-response and glycerol-3-phosphate and nitric oxide signaling); and an exploitation of a wide variety of host resources, including opines, amino acids, sugars, organic acids, phosphate, phosphorylated compounds, and iron. In addition, construction of transgenic A. thaliana lines expressing a lactonase enzyme showed that Ti plasmid transfer could escape host-mediated quorum-quenching. Finally, construction of knock-out mutants in A. tumefaciens showed that expression of some At plasmid genes seemed more costly than the selective advantage they would have conferred in tumor colonization. We provide the first overview of A. tumefaciens lifestyle in a plant tumor and reveal novel signaling and trophic interplays for investigating host-pathogen interactions.
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http://dx.doi.org/10.1111/nph.15164DOI Listing
July 2018

Complete Chromosome and Plasmid Sequences of Two Plant Pathogens, Dickeya solani Strains D s0432-1 and PPO 9019.

Genome Announc 2018 Apr 26;6(17). Epub 2018 Apr 26.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France

species are emerging bacterial pathogens of Here, we announce the complete genome sequences of two strains, D s0432-1 and PPO 9019. Strain PPO 9019 represents the first described member of the genus with an extrachromosomal genetic element.
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http://dx.doi.org/10.1128/genomeA.00233-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920179PMC
April 2018

Quorum Sensing and Quorum Quenching in : A "Go/No Go System"?

Genes (Basel) 2018 Apr 16;9(4). Epub 2018 Apr 16.

Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Avenue de la terrasse, 91198 Gif sur Yvette CEDEX, France.

The pathogen induces gall formation on a wide range of dicotyledonous plants. In this bacteria, most pathogenicity determinants are borne on the tumour inducing (Ti) plasmid. The conjugative transfer of this plasmid between agrobacteria is regulated by quorum sensing (QS). However, processes involved in the disturbance of QS also occur in this bacteria under the molecular form of a protein, TraM, inhibiting the sensing of the QS signals, and two lactonases BlcC (AttM) and AiiB that degrade the acylhomoserine lactone (AHL) QS signal. In the model strain C58, several data, once integrated, strongly suggest that the QS regulation may not be reacting only to cell concentration. Rather, these QS elements in association with the quorum quenching (QQ) activities may constitute an integrated and complex “go/no go system” that finely controls the biologically costly transfer of the Ti plasmid in response to multiple environmental cues. This decision mechanism permits the bacteria to sense whether it is in a gall or not, in a living or decaying tumor, in stressed plant tissues, etc. In this scheme, the role of the lactonases selected and maintained in the course of Ti plasmid and agrobacterial evolution appears to be pivotal.
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http://dx.doi.org/10.3390/genes9040210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924552PMC
April 2018

Complete Genome Sequences of the Plant Pathogens RNS 08.23.3.1.A and RNS04.9.

Genome Announc 2018 Jan 25;6(4). Epub 2018 Jan 25.

Institute for Integrative Biology of the Cell (I2BC), CEA CNRS Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France

spp. are bacterial pathogens causing soft-rot and blackleg diseases on a wide range of ornamental plants and crops. In this paper, we announce the PacBio complete genome sequences of the plant pathogens RNS 08.23.3.1.A (PRI3337) and RNS04.9.
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http://dx.doi.org/10.1128/genomeA.01447-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786673PMC
January 2018

Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.

Sci Rep 2017 12 21;7(1):18033. Epub 2017 Dec 21.

Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette, 91198, France.

Agrobacterium pathogens of octopine- and nopaline-types force host plants to produce either octopine or nopaline compounds, which they use as nutrients. Two Agrobacterium ABC-transporters and their cognate periplasmic binding proteins (PBPs) OccJ and NocT import octopine and nopaline/octopine, respectively. Here, we show that both octopine transport and degradation confer a selective advantage to octopine-type A. tumefaciens when it colonizes plants. We report the X-ray structures of the unliganded PBP OccJ and its complex with octopine as well as a structural comparison with NocT and the related PBP LAO from Salmonella enterica, which binds amino acids (lysine, arginine and ornithine). We investigated the specificity of OccJ, NocT and LAO using several ligands such as amino acids, octopine, nopaline and octopine analogues. OccJ displays a high selectivity and nanomolar range affinity for octopine. Altogether, the structural and affinity data allowed to define an octopine binding signature in PBPs and to construct a OccJ mutant impaired in octopine binding, a selective octopine-binding NocT and a non-selective octopine-binding LAO by changing one single residue in these PBPs. We proposed the PBP OccJ as a major trait in the ecological specialization of octopine-type Agrobacterium pathogens when they colonize and exploit the plant host.
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http://dx.doi.org/10.1038/s41598-017-18243-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5740067PMC
December 2017

A gapA PCR-sequencing Assay for Identifying the Dickeya and Pectobacterium Potato Pathogens.

Plant Dis 2017 Jul 3;101(7):1278-1282. Epub 2017 May 3.

Institute for Integrative Biology of the Cell, CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France.

Several pectinolytic Pectobacterium and Dickeya species and subspecies are causative agents of blackleg and soft rot diseases on potato plants and tubers. Rapid and accurate identification of these taxa is a crucial issue for the production and international trade of potato seed-tubers. Here, we developed a PCR-sequencing tool to easily characterize the different Pectobacterium and Dickeya taxa. The gapA gene sequences from 53 published genomes were aligned and a phylogeny tree was constructed. A set of 35 signature nucleotides was discovered to distinguish the Pectobacterium and Dickeya genera, species, and subspecies. Then, a PCR-primer couple was designed for amplifying the gapA gene in pectinolytic enterobacteria. The primers were tested on 22 isolates recovered from blackleg symptoms in several potato fields. Amplicons were sequenced and signature-nucleotides were analyzed. A phylogeny that includes gapA sequence specimens confirmed the taxonomical identification of these environmental isolates.
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http://dx.doi.org/10.1094/PDIS-12-16-1810-REDOI Listing
July 2017

Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate.

AMB Express 2017 Dec 26;7(1):138. Epub 2017 Jun 26.

Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.

Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.
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http://dx.doi.org/10.1186/s13568-017-0437-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484659PMC
December 2017

Quorum-quenching limits quorum-sensing exploitation by signal-negative invaders.

Sci Rep 2017 01 5;7:40126. Epub 2017 Jan 5.

Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France.

Some bacteria produce and perceive quorum-sensing (QS) signals that coordinate several behaviours, including the costly processes that are exoenzyme production and plasmid transfer. In the case of plasmid transfer, the emergence of QS signal-altered invaders and their policing are poorly documented. In Agrobacterium tumefaciens, the virulence Ti-plasmid encodes both synthesis and sensing of QS-signals, which promote its transfer from a donor to a recipient cell. Here, we reported that QS-altered A. tumefaciens mutants arose during experimental evolution. All showed improved growth compared to their ancestor. Genome sequencing revealed that, though some had lost the Ti-plasmid, most were defective for QS-signal synthesis and Ti-plasmid conjugation (traR mutations) and one exhibited a QS-signal exploitation behaviour, using signal produced by other cells to enhance its own Ti-plasmid transfer. We explored mechanisms that can limit this QS-hijacking. We showed that the A. tumefaciens capacity to inactivate QS-signals by expressing QS-degrading enzyme could attenuate dissemination of the QS signal-negative Ti-plasmids. This work shows that enzymatic QS-disruption whether encoded by the QS-producing Ti-plasmid itself, by a companion plasmid in the same donor cells, or by one in the recipient cells, in all cases can serve as a mechanism for controlling QS exploitation by QS signal-negative mutants.
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http://dx.doi.org/10.1038/srep40126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5215187PMC
January 2017

Complete genome anatomy of the emerging potato pathogen type strain IPO 2222.

Stand Genomic Sci 2016 29;11:87. Epub 2016 Nov 29.

Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette cedex, France.

Several species of the genus provoke soft rot and blackleg diseases on a wide range of plants and crops. has been identified as the causative agent of diseases outbreaks on potato culture in Europe for the last decade. Here, we report the complete genome of the IPO 2222. Using PacBio and Illumina technologies, a unique circular chromosome of 4,919,833 bp was assembled. The G + C content reaches 56% and the genomic sequence contains 4,059 predicted proteins. The ANI values calculated for IPO 2222 vs. other available genomes was over 99.9% indicating a high genetic homogeneity within species.
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http://dx.doi.org/10.1186/s40793-016-0208-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127095PMC
November 2016

Fitness costs restrict niche expansion by generalist niche-constructing pathogens.

ISME J 2017 02 1;11(2):374-385. Epub 2016 Nov 1.

Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.

We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant hosts that provide different nutrients: nopaline or octopine, respectively. Previous studies revealed that nopaline-type pathogens may expand their niche to also assimilate octopine in the presence of nopaline, but consequences of this phenomenon on pathogen dynamics in planta were not known. Here, we provided molecular insight into how the transport protein NocT can bind octopine as well as nopaline, contributing to niche expansion. We further showed that despite the ability for niche expansion, nopaline-type pathogens had no competitive advantage over octopine-type pathogens in co-infected plants. We also demonstrated that a single nucleotide polymorphism in the nocR gene was sufficient to allow octopine assimilation by nopaline-type strains even in absence of nopaline. The evolved nocR bacteria had higher fitness than their ancestor in octopine-rich transgenic plants but lower fitness in tumors induced by octopine-type pathogens. Overall, this work elucidates the specialization of A. tumefaciens to particular opine niches and explains why generalists do not always spread despite the advantage associated with broader nutritional niches.
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http://dx.doi.org/10.1038/ismej.2016.137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5270578PMC
February 2017

Comprehensive genomic and phenotypic metal resistance profile of Pseudomonas putida strain S13.1.2 isolated from a vineyard soil.

AMB Express 2016 Dec 12;6(1):95. Epub 2016 Oct 12.

Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.

Trace metals are required in many cellular processes in bacteria but also induce toxic effects to cells when present in excess. As such, various forms of adaptive responses towards extracellular trace metal ions are essential for the survival and fitness of bacteria in their environment. A soil Pseudomonas putida, strain S13.1.2 has been isolated from French vineyard soil samples, and shown to confer resistance to copper ions. Further investigation revealed a high capacity to tolerate elevated concentrations of various heavy metals including nickel, cobalt, cadmium, zinc and arsenic. The complete genome analysis was conducted using single-molecule real-time (SMRT) sequencing and the genome consisted in a single chromosome at the size of 6.6 Mb. Presence of operons and gene clusters such as cop, cus, czc, nik, and asc systems were detected and accounted for the observed resistance phenotypes. The unique features in terms of specificity and arrangements of some genetic determinants were also highlighted in the study. Our findings has provided insights into the adaptation of this strain to accumulation and persistence of copper and other heavy metals in vineyard soil environment.
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http://dx.doi.org/10.1186/s13568-016-0269-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5059233PMC
December 2016

Transfer of the potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov.

Int J Syst Evol Microbiol 2016 Dec 26;66(12):5379-5383. Epub 2016 Sep 26.

Institute of Integrative Biology of the Cell (I2BC), CEA CNRS Univ. Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette, France.

Pectobacterium wasabiae was originally isolated from Japanese horseradish (Eutrema wasabi), but recently some Pectobacterium isolates collected from potato plants and tubers displaying blackleg and soft rot symptoms were also assigned to P. wasabiae. Here, combining genomic and phenotypical data, we re-evaluated their taxonomic position. PacBio and Illumina technologies were used to complete the genome sequences of P. wasabiae CFBP 3304T and RNS 08-42-1A. Multi-locus sequence analysis showed that the P. wasabiae strains RNS 08-42-1A, SCC3193, CFIA1002 and WPP163, which were collected from potato plant environment, constituted a separate clade from the original Japanese horseradish P. wasabiae. The taxonomic position of these strains was also supported by calculation of the in-silico DNA-DNA hybridization, genome average nucleotide indentity, alignment fraction and average nucleotide indentity values. In addition, they were phenotypically distinguished from P. wasabiae strains by producing acids from (+)-raffinose, α-d(+)-α-lactose, d(+)-galactose and (+)-melibiose but not from methyl α-d-glycopyranoside, (+)-maltose or malonic acid. The name Pectobacterium parmentieri sp. nov. is proposed for this taxon; the type strain is RNS 08-42-1AT (=CFBP 8475T=LMG 29774T).
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http://dx.doi.org/10.1099/ijsem.0.001524DOI Listing
December 2016

Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.

J Biol Chem 2016 Oct 8;291(43):22638-22649. Epub 2016 Sep 8.

From the Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France

Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. Opines are either sugar phosphodiesters or the products of condensed amino acids with ketoacids or sugars. They are Agrobacterium nutrients and imported into the bacterial cell via periplasmic-binding proteins (PBPs) and ABC-transporters. Mannopine, an opine from the mannityl-opine family, is synthesized from an intermediate named deoxy-fructosyl-glutamine (DFG), which is also an opine and abundant Amadori compound (a name used for any derivative of aminodeoxysugars) present in decaying plant materials. The PBP MotA is responsible for mannopine import in mannopine-assimilating agrobacteria. In the nopaline-opine type agrobacteria strain, SocA protein was proposed as a putative mannopine binding PBP, and AttC protein was annotated as a mannopine binding-like PBP. Structural data on mannityl-opine-PBP complexes is currently lacking. By combining affinity data with analysis of seven x-ray structures at high resolution, we investigated the molecular basis of MotA, SocA, and AttC interactions with mannopine and its DFG precursor. Our work demonstrates that AttC is not a mannopine-binding protein and reveals a specific binding pocket for DFG in SocA with an affinity in nanomolar range. Hence, mannopine would not be imported into nopaline-type agrobacteria strains. In contrast, MotA binds both mannopine and DFG. We thus defined one mannopine and two DFG binding signatures. Unlike mannopine-PBPs, selective DFG-PBPs are present in a wide diversity of bacteria, including Actinobacteria, α-,β-, and γ-proteobacteria, revealing a common role of this Amadori compound in pathogenic, symbiotic, and opportunistic bacteria.
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http://dx.doi.org/10.1074/jbc.M116.745562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5077200PMC
October 2016

Transcriptome analysis revealed that a quorum sensing system regulates the transfer of the pAt megaplasmid in Agrobacterium tumefaciens.

BMC Genomics 2016 08 20;17:661. Epub 2016 Aug 20.

Institut for integrative biology of the cell, CEA, CNRS, Université Paris-sud, Université Paris-Saclay, 91198, Gif sur Yvette, CEDEX, France.

Background: Agrobacterium tumefaciens strain P4 is atypical, as the strain is not pathogenic and produces a for this species unusual quorum sensing signal, identified as N-(3-hydroxy-octanoyl)-homoserine lactone (3OH,C8-HSL).

Results: By sequence analysis and cloning, a functional luxI-like gene, named cinI, has been identified on the At plasmid of A. tumefaciens strain P4. Insertion mutagenesis in the cinI gene and transcriptome analyses permitted the identification of 32 cinI-regulated genes in this strain, most of them encoding proteins responsible for the conjugative transfer of pAtP4. Among these genes were the avhB genes that encode a type 4 secretion system (T4SS) involved in the formation of the conjugation apparatus, the tra genes that encode the DNA transfer and replication (Dtr) machinery and cinI and two luxR orthologs. These last two genes, cinR and cinX, exhibit an unusual organization, with the cinI gene surrounded by the two luxR orthologs. Conjugation experiments confirmed that the conjugative transfer of pAtP4 is regulated by 3OH,C8-HSL. Root colonization experiments indicated that the quorum sensing regulation of the conjugation of the pAtP4 does not confer a gain or a loss of fitness to the bacterial host in the tomato plant rhizosphere.

Conclusion: This work is the first identification of the occurrence of a quorum sensing regulation of the pAt conjugation phenomenon in Agrobacterium.
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http://dx.doi.org/10.1186/s12864-016-3007-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4992315PMC
August 2016