<i>Dickeya</i>
            Plant Pathogens

Hugouvieux‐Cotte‐Pattat, Nicole; Condemine, Guy; Gueguen, Erwan; Shevchik, Vladimir E.

doi:10.1002/9780470015902.a0028932

Cited by 16 publications

(23 citation statements)

References 47 publications

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“…It encodes three genes involved in pectin degradation: pelD, paeY and pemA. In the initial step of pectinolysis occuring in plants, paeY (acetylesterase) and pemA (methylesterase) remove acetyl and methyl groups from pectin, which can then be efficiently degraded by the pectate lyase pelD (3). The pelD gene is essentially transcribed as a monocistronic RNA, although its terminator (predicted as intrinsic) can be overstepped to generate a polycistronic transcript comprising the three genes (71).…”

Section: Transcriptional Read-through the Root Of Transcription Extementioning

confidence: 99%

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Mapping the complex transcriptional landscape of the phytopathogenic bacteriumDickeya dadantii

Forquet

Jiang

Nasser

et al. 2020

Preprint

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Dickeya dadantii is a phytopathogenic bacterium that causes soft rot in a wide range of plant hosts worldwide and a model organism for studying gene regulation during the pathogenic process. The present study provides a comprehensive and annotated transcriptomic map of D. dadantii obtained by a computational method combining three independent transcriptomic datasets covering a wide range of conditions which closely reproduce the variations of transcription occurring in the course of plant infection: (1) paired-end RNA-seq data for a precise reconstruction of the RNA landscape, (2) DNA microarray data reflecting gene response to sudden environmental shocks mimicking conditions encountered by bacteria in the plant, (3) dRNA-seq data for a specific high-resolution mapping of transcription start sites. We define transcription units throughout the genome, and map the associated transcription start and termination sites with a quantitative magnitude analysis. Our results show that transcription units sometimes coincide with predicted operons but are generally longer, most of them exhibiting internal promoters and terminators that generate alternative transcripts of variable gene composition. We characterize the occurrence of transcriptional read-through at terminators, which might play a basal regulation role and explain the extent of transcription beyond the scale of operons. We finally highlight the presence of noncontiguous operons and excludons in D. dadantii genome, novel genomic arrangements that might contribute to the basal coordination of transcription. The highlighted transcriptional organization may allow D. dadantii finely adjusting its gene expression program for a rapid adaptation to fast changing environment relevant to plant infection. Importance: this is the first transcriptomic map of a phytopathogen, characterized under physiological conditions encountered by the bacteria during the infection process. It might therefore significantly contribute to further progress in the field of phytopathogenicity. Our findings also provide insights into basal rules of coordination of transcription that might be valid for other bacteria, and may raise interest in the field of microbiology in general. In particular, we demonstrate that gene expression is coordinated at the scale of transcription units rather than operons, which are larger functional genomic units capable of generating transcripts with variable gene composition for a fine-tuning of gene expression in response to environmental changes. In line with recent studies, our findings indicate that the canonical operon model is insufficient to explain the complexity of bacterial transcriptomes.

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Section: Transcriptional Read-through the Root Of Transcription Extementioning

confidence: 99%

“…Bacteria of the Dickeya genus are Gram-negative phytopathogens that cause soft rot in a wide range of plant hosts worldwide (1)(2)(3). This severe disease leads to tissue maceration and eventually plant death (4).…”

Section: Introductionmentioning

confidence: 99%

Mapping the complex transcriptional landscape of the phytopathogenic bacteriumDickeya dadantii

Forquet

Jiang

Nasser

et al. 2020

Preprint

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“…Bacterial phytopathogens of the genus Dickeya and Pectobacterium are pectinolytic necrotrophic bacteria with a broad host plant spectrum (Charkowski et al, 2012;Hugouvieux-Cotte-Pattat et al, 2020). These members of the family Pectobacteriaceae (Van cause substantial agricultural losses worldwide by affecting many vegetables, ornamentals and crops, of which the potato is the most important economically.…”

Section: Introductionmentioning

confidence: 99%

A natural single nucleotide mutation in the small regulatory RNA ArcZ ofDickeya solaniswitches off the antimicrobial activities against yeast and bacteria

Effantin

eacute

Hugouvieux‐Cotte‐Pattat

et al. 2021

Preprint

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The necrotrophic plant pathogenic bacterium Dickeya solani is a new invader of potato agrosystem in Europe. All isolated strains of D. solani contain several large polyketide/fatty acid/non-ribosomal peptide synthetase clusters. Analogy with genes described in other bacteria, suggests that two clusters are involved in the production of secondary metabolites of the oocydin and zeamine family. In this study, we constructed by an approach of reverse genetics mutants affected in the three secondary metabolite clusters ssm, ooc and zms in order to compare the phenotype of the D. solani strain D s0432-1 with its derived mutants. We demonstrated that the zeamine cluster inhibits growth of gram-positive and gram-negative bacteria. It is also implicated in a toxicity against aphids. The oocydin cluster inhibits growth of fungi of the phylum Ascomycota. Finally, we unveiled the function of a new secondary metabolite cluster (ssm, for solani secondary metabolite), only conserved in some Dickeya species. This cluster produces a secondary metabolite inhibiting yeasts. D. solani therefore produces several molecules that are toxic to a wide range of living and potentially interacting organisms, from bacteria to insects. The expression of these secondary metabolite pathways could contribute to the rapid spread of D. solani in Europe.

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“…The type 2 secretion system (T2SS) is widespread in proteobacteria and secretes folded proteins that play a pivotal role in colonization of different niches, survival, competition and pathogenicity (8)(9)(10)(11)(12). The plant pathogenic γ-proteobacterium D. dadantii uses the T2SS, called Out, to secrete pectinases in the infected plant tissues causing soft rot disease in numerous plants and root-vegetables (13,14).…”

Section: Introductionmentioning

confidence: 99%

Scaffolding protein GspB/OutB facilitates assembly of the Dickeya dadantii type 2 secretion system by anchoring the outer membrane secretin pore to the inner membrane and to the peptidoglycan cell wall

Zhang

Rycroft

et al. 2021

Preprint

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SummaryThe phytopathogenic proteobacterium Dickeya dadantii secretes an array of plant cell wall degrading enzymes and other virulence factors via the type 2 secretion system (T2SS). T2SSs are widespread among important plant, animal and human bacterial pathogens. This multi-protein complex spans the double membrane cell envelope and secretes fully folded proteins through a large outer membrane pore formed by 15 subunits of the secretin GspD. Secretins are also found in the type 3 secretion system and the type 4 pili. Usually, specialized lipoproteins termed as pilotins assist the targeting and assembly of secretins into the outer membrane. Here, we show that in Dickeya, the pilotin acts in concert with the scaffolding protein GspB. Deletion of gspB profoundly impacts secretin assembly, pectinase secretion, and virulence. Structural studies reveal that GspB possesses a conserved periplasmic Homology Region domain that interacts directly with the N-terminal secretin domain. Site-specific photo cross-linking unravels molecular details of the GspB-GspD complex in vivo. We show that GspB facilitates outer membrane targeting and assembly of the secretin pores and anchors them to the inner membrane while the C-terminal extension of GspB scaffolds the secretin channel in the peptidoglycan cell wall. Phylogenetic analysis shows that in other bacteria, GspB homologs vary in length and domain composition and act in concert with either a cognate ATPase GspA or a pilotin GspS.ImportanceGram-negative bacteria have two cell membranes sandwiching a peptidoglycan net that form together a robust protective cell envelope. To translocate effector proteins across this multilayer envelope, bacteria have evolved several specialized secretion systems. In the type 2 secretion system and some other bacterial machineries, secretins form large multimeric pores that allow transport of effector proteins or filaments across the outer membrane. The secretins are essential for nutrient acquisition and pathogenicity and constitute a target for development of new antibacterials. Targeting of secretin subunits into the outer membrane is often facilitated by a special class of lipoproteins called pilotins. Here, we show that in Dickeya and some other bacteria, the scaffolding protein GspB acts in concert with pilotin, facilitating the assembly of the secretin pore and its anchoring to both the inner membrane and the bacterial cell wall. GspB homologs of varied domain composition are present in many other T2SSs.

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Dickeya Plant Pathogens

Cited by 16 publications

References 47 publications

Mapping the complex transcriptional landscape of the phytopathogenic bacteriumDickeya dadantii

Mapping the complex transcriptional landscape of the phytopathogenic bacteriumDickeya dadantii

A natural single nucleotide mutation in the small regulatory RNA ArcZ ofDickeya solaniswitches off the antimicrobial activities against yeast and bacteria

Scaffolding protein GspB/OutB facilitates assembly of the Dickeya dadantii type 2 secretion system by anchoring the outer membrane secretin pore to the inner membrane and to the peptidoglycan cell wall

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