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  1. Article ; Online: Construction of a Transposon Mutant Library in the Pathogen Agrobacterium tumefaciens C58 and Identification of Genes Involved in Gall Niche Exploitation and Colonization.

    Torres, Marta / Gonzalez-Mula, Almudena / Naquin, Delphine / Faure, Denis

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2605, Page(s) 209–226

    Abstract: Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease on a wide range of host species by transferring and integrating a part of its own DNA (T-DNA) into the plant genome. The genes responsible of the above-mentioned processes are ... ...

    Abstract Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease on a wide range of host species by transferring and integrating a part of its own DNA (T-DNA) into the plant genome. The genes responsible of the above-mentioned processes are well characterized. However, a large number of the mechanisms involved in exploitation and colonization of the galls (also named plant tumors) remain unknown. Due to recent development of "transposon-sequencing" (Tn-Seq) techniques, a high-throughput screening and identification of the different genes involved in such mechanisms is now possible. In this chapter, we describe the detailed methodology used to construct a transposon library in A. tumefaciens and to conduct a Tn-Seq approach to discover genes involved in plant tumor exploitation and colonization.
    MeSH term(s) Agrobacterium tumefaciens/genetics ; Plant Tumors/genetics ; Plant Tumors/microbiology ; Gene Library ; Plants/genetics ; Genome, Plant
    Language English
    Publishing date 2022-12-15
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2871-3_11
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Dissimilar gene repertoires of

    Robic, Kévin / Munier, Euphrasie / Effantin, Géraldine / Lachat, Joy / Naquin, Delphine / Gueguen, Erwan / Faure, Denis

    Frontiers in plant science

    2023  Volume 14, Page(s) 1154110

    Abstract: ... ...

    Abstract Dickeya
    Language English
    Publishing date 2023-05-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1154110
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont

    Jouan, Romain / Lextrait, Gaëlle / Lachat, Joy / Yokota, Aya / Cossard, Raynald / Naquin, Delphine / Timchenko, Tatiana / Kikuchi, Yoshitomo / Ohbayashi, Tsubasa / Mergaert, Peter

    ISME communications

    2024  Volume 4, Issue 1, Page(s) ycad001

    Abstract: Caballeronia ... ...

    Abstract Caballeronia insecticola
    Language English
    Publishing date 2024-01-10
    Publishing country England
    Document type Journal Article
    ISSN 2730-6151
    ISSN (online) 2730-6151
    DOI 10.1093/ismeco/ycad001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Agrobacterium tumefaciens fitness genes involved in the colonization of plant tumors and roots

    Torres, Marta / Jiquel, Audren / Jeanne, Etienne / Naquin, Delphine / Dessaux, Yves / Faure, Denis

    The new phytologist. 2022 Jan., v. 233, no. 2

    2022  

    Abstract: Agrobacterium tumefaciens colonizes the galls (plant tumors) it causes, and the roots of host and nonhost plants. Transposon‐sequencing (Tn‐Seq) was used to discover A.tumefaciens genes involved in reproductive success (fitness genes) on Solanum ... ...

    Abstract Agrobacterium tumefaciens colonizes the galls (plant tumors) it causes, and the roots of host and nonhost plants. Transposon‐sequencing (Tn‐Seq) was used to discover A.tumefaciens genes involved in reproductive success (fitness genes) on Solanum lycopersicum and Populus trichocarpa tumors and S.lycopersicum and Zea mays roots. The identified fitness genes represent 3–8% of A. tumefaciens genes and contribute to carbon and nitrogen metabolism, synthesis and repair of DNA, RNA and proteins and envelope‐associated functions. Competition assays between 12 knockout mutants and wild‐type confirmed the involvement of 10 genes (trpB, hisH, metH, cobN, ntrB, trxA, nrdJ, kamA, exoQ, wbbL) in A.tumefaciens fitness under both tumor and root conditions. The remaining two genes (fecA, noxA) were important in tumors only. None of these mutants was nonpathogenic, but four (hisH, trpB, exoQ, ntrB) exhibited impaired virulence. Finally, we used this knowledge to search for chemical and biocontrol treatments that target some of the identified fitness pathways and report reduced tumorigenesis and impaired establishment of A.tumefaciens on tomato roots using tannic acid or Pseudomonas protegens, which affect iron assimilation. This work revealed A.tumefaciens pathways that contribute to its competitive survival in plants and highlights a strategy to identify plant protection approaches against this pathogen.
    Keywords Agrobacterium radiobacter ; DNA ; Populus trichocarpa ; Pseudomonas protegens ; RNA ; Solanum lycopersicum ; Zea mays ; biological control ; carbon ; carcinogenesis ; neoplasms ; nitrogen metabolism ; pathogens ; plant protection ; reproductive success ; tannins ; tomatoes ; virulence
    Language English
    Dates of publication 2022-01
    Size p. 905-918.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.17810
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Construction and characterization of a saturated Tn-seq library of

    Trotereau, Jérôme / Jouan, Romain / Naquin, Delphine / Branger, Maxime / Schouler, Catherine / Velge, Philippe / Mergaert, Peter / Virlogeux-Payant, Isabelle

    Microbiology resource announcements

    2023  Volume 12, Issue 11, Page(s) e0036523

    Abstract: Salmonella ... ...

    Abstract Salmonella enterica
    Language English
    Publishing date 2023-10-05
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00365-23
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  6. Article: Genomics in the long-read sequencing era.

    van Dijk, Erwin L / Naquin, Delphine / Gorrichon, Kévin / Jaszczyszyn, Yan / Ouazahrou, Rania / Thermes, Claude / Hernandez, Céline

    Trends in genetics : TIG

    2023  Volume 39, Issue 9, Page(s) 649–671

    Abstract: Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, ... ...

    Abstract Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.
    MeSH term(s) Humans ; High-Throughput Nucleotide Sequencing/methods ; Genomics/methods ; Sequence Analysis, DNA/methods ; Computational Biology ; Gene Expression Profiling/methods
    Language English
    Publishing date 2023-05-23
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2023.04.006
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2272: Show issues Location:
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  7. Article ; Online: Agrobacterium tumefaciens fitness genes involved in the colonization of plant tumors and roots.

    Torres, Marta / Jiquel, Audren / Jeanne, Etienne / Naquin, Delphine / Dessaux, Yves / Faure, Denis

    The New phytologist

    2021  Volume 233, Issue 2, Page(s) 905–918

    Abstract: Agrobacterium tumefaciens colonizes the galls (plant tumors) it causes, and the roots of host and nonhost plants. Transposon-sequencing (Tn-Seq) was used to discover A.tumefaciens genes involved in reproductive success (fitness genes) on Solanum ... ...

    Abstract Agrobacterium tumefaciens colonizes the galls (plant tumors) it causes, and the roots of host and nonhost plants. Transposon-sequencing (Tn-Seq) was used to discover A.tumefaciens genes involved in reproductive success (fitness genes) on Solanum lycopersicum and Populus trichocarpa tumors and S.lycopersicum and Zea mays roots. The identified fitness genes represent 3-8% of A. tumefaciens genes and contribute to carbon and nitrogen metabolism, synthesis and repair of DNA, RNA and proteins and envelope-associated functions. Competition assays between 12 knockout mutants and wild-type confirmed the involvement of 10 genes (trpB, hisH, metH, cobN, ntrB, trxA, nrdJ, kamA, exoQ, wbbL) in A.tumefaciens fitness under both tumor and root conditions. The remaining two genes (fecA, noxA) were important in tumors only. None of these mutants was nonpathogenic, but four (hisH, trpB, exoQ, ntrB) exhibited impaired virulence. Finally, we used this knowledge to search for chemical and biocontrol treatments that target some of the identified fitness pathways and report reduced tumorigenesis and impaired establishment of A.tumefaciens on tomato roots using tannic acid or Pseudomonas protegens, which affect iron assimilation. This work revealed A.tumefaciens pathways that contribute to its competitive survival in plants and highlights a strategy to identify plant protection approaches against this pathogen.
    MeSH term(s) Agrobacterium tumefaciens/genetics ; Carbon ; Lycopersicon esculentum/genetics ; Lycopersicon esculentum/microbiology ; Plant Roots/genetics ; Plant Tumors/genetics ; Plant Tumors/microbiology ; Virulence/genetics
    Chemical Substances Carbon (7440-44-0)
    Language English
    Publishing date 2021-11-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.17810
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

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  8. Article ; Online: Pervasive transcription enhances the accessibility of H-NS-silenced promoters and generates bistability in

    Figueroa-Bossi, Nara / Sánchez-Romero, María Antonia / Kerboriou, Patricia / Naquin, Delphine / Mendes, Clara / Bouloc, Philippe / Casadesús, Josep / Bossi, Lionello

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 30, Page(s) e2203011119

    Abstract: ... ...

    Abstract In
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation, Bacterial ; Gene Silencing ; Promoter Regions, Genetic ; Salmonella/genetics ; Salmonella/pathogenicity ; Single-Cell Analysis ; Transcription, Genetic ; Virulence/genetics
    Chemical Substances Bacterial Proteins ; DNA-Binding Proteins ; H-NS protein, bacteria ; Spi1 protein, Salmonella
    Language English
    Publishing date 2022-07-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2203011119
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  9. Article: The Third Revolution in Sequencing Technology.

    van Dijk, Erwin L / Jaszczyszyn, Yan / Naquin, Delphine / Thermes, Claude

    Trends in genetics : TIG

    2018  Volume 34, Issue 9, Page(s) 666–681

    Abstract: Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete genome sequences to be deciphered for the first time. A second revolution came when next-generation sequencing (NGS) technologies appeared, which made genome ... ...

    Abstract Forty years ago the advent of Sanger sequencing was revolutionary as it allowed complete genome sequences to be deciphered for the first time. A second revolution came when next-generation sequencing (NGS) technologies appeared, which made genome sequencing much cheaper and faster. However, NGS methods have several drawbacks and pitfalls, most notably their short reads. Recently, third-generation/long-read methods appeared, which can produce genome assemblies of unprecedented quality. Moreover, these technologies can directly detect epigenetic modifications on native DNA and allow whole-transcript sequencing without the need for assembly. This marks the third revolution in sequencing technology. Here we review and compare the various long-read methods. We discuss their applications and their respective strengths and weaknesses and provide future perspectives.
    MeSH term(s) DNA/analysis ; DNA/genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing/methods ; High-Throughput Nucleotide Sequencing/trends ; Humans ; Sequence Analysis, DNA/methods ; Whole Exome Sequencing/methods ; Whole Exome Sequencing/trends
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2018-06-22
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2018.05.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Jg. 1995 - 2021: Lesesall (2.OG)
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  10. Article ; Online: Plesiomonas shigelloides, an Atypical Enterobacterales with a Vibrio-Related Secondary Chromosome.

    Adam, Yazid / Brezellec, Pierre / Espinosa, Elena / Besombes, Amelie / Naquin, Delphine / Paly, Evelyne / Possoz, Christophe / van Dijk, Erwin / Barre, Francois-Xavier / Ferat, Jean-Luc

    Genome biology and evolution

    2022  Volume 14, Issue 2

    Abstract: About 10% of bacteria have a multichromosome genome with a primary replicon of bacterial origin, called the chromosome, and other replicons of plasmid origin, the chromids. Studies on multichromosome bacteria revealed potential points of coordination ... ...

    Abstract About 10% of bacteria have a multichromosome genome with a primary replicon of bacterial origin, called the chromosome, and other replicons of plasmid origin, the chromids. Studies on multichromosome bacteria revealed potential points of coordination between the replication/segregation of chromids and the progression of the cell cycle. For example, replication of the chromid of Vibrionales (called Chr2) is initiated upon duplication of a sequence carried by the primary chromosome (called Chr1), in such a way that replication of both replicons is completed synchronously. Also, Chr2 uses the Chr1 as a scaffold for its partition in the daughter cells. How many of the features detected so far are required for the proper integration of a secondary chromosome in the cell cycle? How many more features remain to be discovered? We hypothesized that critical features for the integration of the replication/segregation of a given chromid within the cell cycle program would be conserved independently of the species in which the chromid has settled. Hence, we searched for a chromid related to that found in Vibrionales outside of this order. We identified one in Plesiomonas shigelloides, an aquatic and pathogenic enterobacterium that diverged early within the clade of Enterobacterales. Our results suggest that the chromids present in P. shigelloides and Vibrionales derive from a common ancestor. We initiated in silico genomic and proteomic comparative analyses of P. shigelloides, Vibrionales, and Enterobacterales that enabled us to establish a list of features likely involved in the maintenance of the chromid within the host cell cycle.
    MeSH term(s) Chromosomes, Bacterial/genetics ; Genome, Bacterial ; Plesiomonas/genetics ; Proteomics ; Vibrio/genetics
    Language English
    Publishing date 2022-01-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2495328-3
    ISSN 1759-6653 ; 1759-6653
    ISSN (online) 1759-6653
    ISSN 1759-6653
    DOI 10.1093/gbe/evac011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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