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Robic K, Munier E, Effantin G, Lachat J, Naquin D, Gueguen E, Faure D. Dissimilar gene repertoires of Dickeya solani involved in the colonization of lesions and roots of Solanum tuberosum. Front Plant Sci 2023; 14:1154110. [PMID: 37223796 PMCID: PMC10202176 DOI: 10.3389/fpls.2023.1154110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023]
Abstract
Dickeya and Pectobacterium species are necrotrophic pathogens that macerate stems (blackleg disease) and tubers (soft rot disease) of Solanum tuberosum. They proliferate by exploiting plant cell remains. They also colonize roots, even if no symptoms are observed. The genes involved in pre-symptomatic root colonization are poorly understood. Here, transposon-sequencing (Tn-seq) analysis of Dickeya solani living in macerated tissues revealed 126 genes important for competitive colonization of tuber lesions and 207 for stem lesions, including 96 genes common to both conditions. Common genes included acr genes involved in the detoxification of plant defense phytoalexins and kduD, kduI, eda (=kdgA), gudD, garK, garL, and garR genes involved in the assimilation of pectin and galactarate. In root colonization, Tn-seq highlighted 83 genes, all different from those in stem and tuber lesion conditions. They encode the exploitation of organic and mineral nutrients (dpp, ddp, dctA, and pst) including glucuronate (kdgK and yeiQ) and synthesis of metabolites: cellulose (celY and bcs), aryl polyene (ape), and oocydin (ooc). We constructed in-frame deletion mutants of bcsA, ddpA, apeH, and pstA genes. All mutants were virulent in stem infection assays, but they were impaired in the competitive colonization of roots. In addition, the ΔpstA mutant was impaired in its capacity to colonize progeny tubers. Overall, this work distinguished two metabolic networks supporting either an oligotrophic lifestyle on roots or a copiotrophic lifestyle in lesions. This work revealed novel traits and pathways important for understanding how the D. solani pathogen efficiently survives on roots, persists in the environment, and colonizes progeny tubers.
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Affiliation(s)
- Kévin Robic
- French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Euphrasie Munier
- French Federation of Seed Potato Growers (FN3PT/inov3PT), Paris, France
| | - Géraldine Effantin
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP, Lyon, France
| | - Joy Lachat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Erwan Gueguen
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP, Lyon, France
| | - Denis Faure
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Brual T, Effantin G, Baltenneck J, Attaiech L, Grosbois C, Royer M, Cigna J, Faure D, Hugouvieux-Cotte-Pattat N, Gueguen E. A natural single nucleotide mutation in the small regulatory RNA ArcZ of Dickeya solani switches off the antimicrobial activities against yeast and bacteria. PLoS Genet 2023; 19:e1010725. [PMID: 37104544 PMCID: PMC10168573 DOI: 10.1371/journal.pgen.1010725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/09/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
The necrotrophic plant pathogenic bacterium Dickeya solani emerged in the potato agrosystem in Europe. All isolated strains of D. solani contain several large polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) gene clusters. Analogy with genes described in other bacteria suggests that the clusters ooc and zms are involved in the production of secondary metabolites of the oocydin and zeamine families, respectively. A third cluster named sol was recently shown to produce an antifungal molecule. In this study, we constructed mutants impaired in each of the three secondary metabolite clusters sol, ooc, and zms to compare first the phenotype of the D. solani wild-type strain D s0432-1 with its associated mutants. We demonstrated the antimicrobial functions of these three PKS/NRPS clusters against bacteria, yeasts or fungi. The cluster sol, conserved in several other Dickeya species, produces a secondary metabolite inhibiting yeasts. Phenotyping and comparative genomics of different D. solani wild-type isolates revealed that the small regulatory RNA ArcZ plays a major role in the control of the clusters sol and zms. A single-point mutation, conserved in some Dickeya wild-type strains, including the D. solani type strain IPO 2222, impairs the ArcZ function by affecting its processing into an active form.
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Affiliation(s)
- Typhaine Brual
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP LYON, France
| | - Géraldine Effantin
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP LYON, France
| | - Julie Baltenneck
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP LYON, France
| | - Laetitia Attaiech
- CIRI, Centre International de Recherche en Infectiologie, Team "Horizontal gene transfer in bacterial pathogens" (Horigene), Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Cloé Grosbois
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP LYON, France
| | | | - Jérémy Cigna
- French Federation of Seed Potato Growers (FN3PT-inov3PT), Paris, France
| | - Denis Faure
- Paris-Saclay University, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Erwan Gueguen
- Univ Lyon, Université Claude Bernard Lyon1, CNRS, INSA Lyon, UMR5240 MAP LYON, France
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Gault M, Effantin G, Rodrigue A. Ni exposure impacts the pool of free Fe and modifies DNA supercoiling via metal-induced oxidative stress in Escherichia coli K-12. Free Radic Biol Med 2016; 97:351-361. [PMID: 27375130 DOI: 10.1016/j.freeradbiomed.2016.06.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/23/2016] [Accepted: 06/28/2016] [Indexed: 12/16/2022]
Abstract
The biology of nickel has been widely studied in mammals because of its carcinogenic properties, whereas few studies have been performed in microorganisms. In the present work, changes accompanying stress caused by nickel were evaluated at the cellular level using RNA-Seq in Escherichia coli K-12. Interestingly, a very large number of genes were found to be deregulated by Ni stress. Iron and oxidative stress homeostasis maintenance were among the most highly enriched functional categories, and genes involved in periplasmic copper efflux were among the most highly upregulated. These results suggest that the deregulation of Fe and Cu homeostatic genes is caused by a release of free Cu and Fe ions in the cell which in turn activate the Cu and Fe homeostatic systems. The content of Cu was not significantly affected upon the addition of Ni to the growth medium, nor were the Cus and CopA Cu-efflux systems important for the survival of bacteria under Ni stress In contrast the addition of Ni slightly decreased the amount of cellular Fe and activated the transcription of Fur regulated genes in a Fur-dependent manner. Cu or Fe imbalance together with oxidative stress might affect the structure of DNA. Further experiments revealed that Ni alters the state of DNA folding by causing a relaxed conformation, a phenomenon that is reversible by addition of the antioxidant Tiron or the Fe chelator Dip. The Tiron-reversible DNA relaxation was also observed for Fe and to a lesser extent with Cu but not with Co. DNA supercoiling is well recognized as an integral aspect of gene regulation. Moreover our results show that Ni modifies the expression of several nucleoid-associated proteins (NAPs), important agents of DNA topology and global gene regulation. This is the first report describing the impact of metal-induced oxidative on global regulatory networks.
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Affiliation(s)
- Manon Gault
- Microbiologie, Adaptation et Pathogénie, UMR5240, INSA Lyon, Université Lyon 1, CNRS, Université de Lyon, F-69621 Villeurbanne, France
| | - Géraldine Effantin
- Microbiologie, Adaptation et Pathogénie, UMR5240, INSA Lyon, Université Lyon 1, CNRS, Université de Lyon, F-69621 Villeurbanne, France
| | - Agnès Rodrigue
- Microbiologie, Adaptation et Pathogénie, UMR5240, INSA Lyon, Université Lyon 1, CNRS, Université de Lyon, F-69621 Villeurbanne, France.
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Lallemand M, Login FH, Guschinskaya N, Pineau C, Effantin G, Robert X, Shevchik VE. Dynamic interplay between the periplasmic and transmembrane domains of GspL and GspM in the type II secretion system. PLoS One 2013; 8:e79562. [PMID: 24223969 PMCID: PMC3815138 DOI: 10.1371/journal.pone.0079562] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/24/2013] [Indexed: 11/29/2022] Open
Abstract
The type II secretion system (T2SS) is a multiprotein nanomachine that transports folded proteins across the outer membrane of gram-negative bacteria. The molecular mechanisms that govern the secretion process remain poorly understood. The inner membrane components GspC, GspL and GspM possess a single transmembrane segment (TMS) and a large periplasmic region and they are thought to form a platform of unknown function. Here, using two-hybrid and pull-down assays we performed a systematic mapping of the GspC/GspL/GspM interaction regions in the plant pathogen Dickeya dadantii. We found that the TMS of these components interact with each other, implying a complex interaction network within the inner membrane. We also showed that the periplasmic, ferredoxin-like, domains of GspL and GspM drive homo- and heterodimerizations of these proteins. Disulfide bonding analyses revealed that the respective domain interfaces include the equivalent secondary-structure elements, suggesting alternating interactions of the periplasmic domains, L/L and M/M versus L/M. Finally, we found that displacements of the periplasmic GspM domain mediate coordinated shifts or rotations of the cognate TMS. These data suggest a plausible mechanism for signal transmission between the periplasmic and the cytoplasmic portions of the T2SS machine.
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Affiliation(s)
- Mathilde Lallemand
- INSA-Lyon, Villeurbanne, France
- CNRS, UMR5240, Microbiologie Adaptation et Pathogénie, Lyon, France
| | - Frédéric H. Login
- Université Lyon 1, Lyon, France
- CNRS, UMR5240, Microbiologie Adaptation et Pathogénie, Lyon, France
| | - Natalia Guschinskaya
- Université Lyon 1, Lyon, France
- CNRS, UMR5240, Microbiologie Adaptation et Pathogénie, Lyon, France
| | - Camille Pineau
- INSA-Lyon, Villeurbanne, France
- CNRS, UMR5240, Microbiologie Adaptation et Pathogénie, Lyon, France
| | | | - Xavier Robert
- Université Lyon 1, Lyon, France
- Laboratory for Biocrystallography and Structural Biology of Therapeutic Targets, Molecular and Structural Bases of Infectious Diseases, CNRS UMR5086, Lyon, France
| | - Vladimir E. Shevchik
- Université Lyon 1, Lyon, France
- INSA-Lyon, Villeurbanne, France
- CNRS, UMR5240, Microbiologie Adaptation et Pathogénie, Lyon, France
- * E-mail:
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Prigent-Combaret C, Zghidi-Abouzid O, Effantin G, Lejeune P, Reverchon S, Nasser W. The nucleoid-associated protein Fis directly modulates the synthesis of cellulose, an essential component of pellicle-biofilms in the phytopathogenic bacterium Dickeya dadantii. Mol Microbiol 2012; 86:172-86. [PMID: 22925161 DOI: 10.1111/j.1365-2958.2012.08182.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacteria use biofilm structures to colonize surfaces and to survive in hostile conditions, and numerous bacteria produce cellulose as a biofilm matrix polymer. Hence, expression of the bcs operon, responsible for cellulose biosynthesis, must be finely regulated in order to allow bacteria to adopt the proper surface-associated behaviours. Here we show that in the phytopathogenic bacterium, Dickeya dadantii, production of cellulose is required for pellicle-biofilm formation and resistance to chlorine treatments. Expression of the bcs operon is growth phase-regulated and is stimulated in biofilms. Furthermore, we unexpectedly found that the nucleoid-associated protein and global regulator of virulence functions, Fis, directly represses bcs operon expression by interacting with an operator that is absent from the bcs operon of animal pathogenic bacteria and the plant pathogenic bacterium Pectobacterium. Moreover, production of cellulose enhances plant surface colonization by D. dadantii. Overall, these data suggest that cellulose production and biofilm formation may be important factors for surface colonization by D. dadantii and its subsequent survival in hostile environments. This report also presents a new example of how bacteria can modulate the action of a global regulator to co-ordinate basic metabolism, virulence and modifications of lifestyle.
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Effantin G, Rivasseau C, Gromova M, Bligny R, Hugouvieux-Cotte-Pattat N. Massive production of butanediol during plant infection by phytopathogenic bacteria of the genera Dickeya and Pectobacterium. Mol Microbiol 2011; 82:988-97. [PMID: 22032684 DOI: 10.1111/j.1365-2958.2011.07881.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Plant pathogenic bacteria of the genera Dickeya and Pectobacterium are broad-host-range necrotrophs which cause soft-rot diseases in important crops. A metabolomic analysis, based on (13)C-NMR spectroscopy, was used to characterize the plant-bacteria interaction. Metabolic profiles revealed a decline in plant sugars and amino acids during infection and the concomitant appearance of a compound identified as 2,3-butanediol. Butanediol is the major metabolite found in macerated tissues of various host plants. It is accumulated during the symptomatic phase of the disease. Different species of Dickeya or Pectobacterium secrete high levels of butanediol during plant infection. Butanediol has been described as a signalling molecule involved in plant/bacterium interactions and, notably, able to induce plant systemic resistance. The bud genes, involved in butanediol production, are conserved in the phytopathogenic enterobacteria of the genera Dickeya, Pectobacterium, Erwinia, Pantoea and Brenneria. Inactivation of the bud genes of Dickeya dadantii revealed that the virulence of budA, budB and budR mutants was clearly reduced. The genes budA, budB and budC are highly expressed during plant infection. These data highlight the importance of butanediol metabolism in limiting acidification of the plant tissue during the development of the soft-rot disease caused by pectinolytic enterobacteria.
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Affiliation(s)
- Géraldine Effantin
- Université de Lyon, Université Lyon 1, INSA-Lyon, Microbiologie Adaptation et Pathogénie, CNRS UMR5240, Domaine Scientifique de la Doua, 69622 Villeurbanne, France
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Reverchon S, Van Gijsegem F, Effantin G, Zghidi-Abouzid O, Nasser W. Systematic targeted mutagenesis of the MarR/SlyA family members of Dickeya dadantii 3937 reveals a role for MfbR in the modulation of virulence gene expression in response to acidic pH. Mol Microbiol 2010; 78:1018-37. [PMID: 21062374 DOI: 10.1111/j.1365-2958.2010.07388.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pathogenicity of Dickeya dadantii is a process involving several factors, such as plant cell wall-degrading enzymes and adaptation systems to adverse conditions encountered in the apoplast. Regulators of the MarR family control a variety of biological processes, including adaptation to hostile environments and virulence. Analysis of the members of this family in D. dadantii led to the identification of a new regulator, MfbR, which controls virulence. MfbR represses its own expression but activates genes encoding plant cell wall-degrading enzymes. Purified MfbR increases the binding of RNA polymerase at the virulence gene promoters and inhibits transcription initiation at the mfbR promoter. MfbR activity appeared to be modulated by acidic pH, a stress encountered by pathogens during the early stages of infection. Expression of mfbR and its targets, during infection, showed that MfbR is unable to activate virulence genes in acidic conditions at an early step of infection. In contrast, alkalinization of the apoplast, during an advanced stage of infection, led to the potentialization of MfbR activity resulting in plant cell wall degrading enzyme production. This report presents a new example of how pathogens adjust virulence-associated factors during the time-course of an infection.
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Effantin G, Boulanger P, Neumann E, Letellier L, Conway JF. Bacteriophage T5 Structure Reveals Similarities with HK97 and T4 Suggesting Evolutionary Relationships. J Mol Biol 2006; 361:993-1002. [PMID: 16876823 DOI: 10.1016/j.jmb.2006.06.081] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 06/30/2006] [Indexed: 11/29/2022]
Abstract
Evolutionary relationships between viruses may be obscure by protein sequence but unmasked by structure. Analysis of bacteriophage T5 by cryo-electron microscopy and protein sequence analysis reveals analogies with HK97 and T4 that suggest a mosaic of such connections. The T5 capsid is consistent with the HK97 capsid protein fold but has a different geometry, incorporating three additional hexamers on each icosahedral facet. Similarly to HK97, the T5 major capsid protein has an N-terminal extension, or Delta-domain that is missing in the mature capsid, and by analogy with HK97, may function as an assembly or scaffold domain. This Delta-domain is predicted to be largely coiled-coil, as for that of HK97, but is approximately 70% longer correlating with the larger capsid. Thus, capsid architecture appears likely to be specified by the Delta-domain. Unlike HK97, the T5 capsid binds a decoration protein in the center of each hexamer similarly to the "hoc" protein of phage T4, suggesting a common role for these molecules. The tail-tube has unusual trimeric symmetry that may aid in the unique two-stage DNA-ejection process, and joins the tail-tip at a disk where tail fibers attach. This intriguing mix of characteristics embodied by phage T5 offers insights into virus assembly, subunit function, and the evolutionary connections between related viruses.
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Affiliation(s)
- G Effantin
- Laboratoire de Microscopie Electronique Structurale, Institut de Biologie Structurale J.-P. Ebel, UMR 5075 CNRS-CEA-UJF, 38027 Grenoble, France
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Abstract
We report here on the isolation and primary characterization of the yohM gene of Escherichia coli. We show that yohM encodes a membrane-bound polypeptide conferring increased nickel and cobalt resistance in E. coli. yohM was specifically induced by nickel or cobalt but not by cadmium, zinc, or copper. Mutation of yohM increased the accumulation of nickel inside the cell, whereas cells harboring yohM in multicopy displayed reduced intracellular nickel content. Our data support the hypothesis that YohM is the first described efflux system for nickel and cobalt in E. coli. We propose rcnA (resistance to cobalt and nickel) as the new denomination of yohM.
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Affiliation(s)
- Agnès Rodrigue
- Unité de Microbiologie et Génétique, Unité Mixte de Recherche 5122, Centre National de la Recherche Scientifique, Institut National des Sciences, Applquée de Lyon I, Villeurbanne, France.
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