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The collection of articles published in this eBook represent different facets of the interactions between pathogens and their host concerning the battle for iron. Pathogens have developed different strategies to acquire iron from their host. These include the production of siderophores, heme acquisition and ferrous iron uptake.

Infection --- nutritional immunity --- Virulence --- Bacterial Pathogenesis --- bacterioferritin --- iron acquisition --- siderophore

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La pyoverdine est un sidérophore, molécule capable de chélater le fer, principalement produite par les bactéries appartenant au groupe des Pseudomonas fluorescents. Récemment, le mécanisme de biosynthèse de ce chromopeptide a été entièrement décodé. 
Ce travail est consacré à l’analyse du mécanisme de biosynthèse de l’isopyoverdine produite par la bactérie Pseudomonas putida BTP1. Cette molécule diffère de la pyoverdine par la liaison de la chaine peptidique au chromophore, celle-ci se trouve liée au carbone C3 du chromophore à la place du carbone C1 pour les pyoverdines. 
Une analyse bio-informatique a été réalisée pour déterminer les différences entre les gènes impliqués dans la formation de l’isopyoverdine de P. putida BTP1 et de la pyoverdine chez d’autres souches. Cette analyse a montré notamment que le gène pvdP de BTP1, impliqué dans la maturation et la cyclisation du chromophore, possède un pourcentage d’identité assez faible quand il est comparé au même gène provenant de souches produisant de la pyoverdine. De plus, en étudiant la structure primaire, secondaire et tertiaire de l’enzyme PvdP, des différences notables sont apparues principalement dans le domaine N-terminal de la protéine. 
Sur la base des résultats obtenus, un mutant de BTP1 délété du gène pvdP susceptible d’être responsable de la synthèse d’une isopyoverdine à la place d’une pyoverdine a donc été construit. Ce mutant a ensuite été complémenté avec le même gène d’intérêt provenant soit de P. putida BTP1, soit d’une souche produisant de la pyoverdine. Des cinétiques de croissance microbienne et de production du sidérophore de ces différents mutants ont été réalisées sur trois milieux de culture différents. Les surnageants de culture ont été analysés par LC-QTOF-MS. Le surnageant du mutant délété du gène pvdP ne fluoresce plus du fait qu’il produit le précurseur de l’isopyoverdine, la ferribactine, ne possédant pas un chromophore mature synonyme de fluorescence. Le mutant complémenté par le gène pvdP de la souche P. putida BTP1 et de la souche P. putida KT2440 permet de faire réapparaitre la fluorescence et de confirmer par analyse par LC-QTOF-MS la présence d’un pic correspondant au poids moléculaire de l’isopyoverdine produite par la souche sauvage de BTP1. 
En conclusion, l’enzyme PvdP pourrait être responsable de la formation de l’isopyoverdine de BTP1. Une confirmation de cette hypothèse pourrait être établie en purifiant les sidérophores produits par les différentes souches mutantes et en comparant leur structure par résonance magnétique nucléaire, seule technique permettant de faire la différence entre une pyoverdine et une isopyoverdine. Pyoverdine is a siderophore, a molecule capable of chelating iron, mainly produced by bacteria belonging to the fluorescent Pseudomonas group. Recently, the biosynthetic mechanism of this chromopeptide has been fully decoded. 
This work is devoted to the analysis of the biosynthetic mechanism of isopyoverdine produced by the bacterium Pseudomonas putida BTP1. This molecule differs from pyoverdine by the binding of the peptide chain to the chromophore, which is linked to the C3 carbon of the chromophore instead of the C1 carbon for pyoverdines. 
A bioinformatics analysis was performed to determine the differences between the genes involved in the formation of isopyoverdine in P. putida BTP1 and pyoverdine in other strains. In particular, this analysis showed that the pvdP gene of BTP1, involved in the maturation and cyclisation of the chromophore, has a rather low percentage of identity when compared to the same gene from pyoverdine producing strains. Furthermore, when studying the primary, secondary and tertiary structure of the PvdP enzyme, notable differences appeared mainly in the N-terminal domain of the protein. 
Based on the results obtained, a BTP1 mutant deleted from the pvdP gene that could be responsible for the synthesis of an isopyoverdine instead of a pyoverdine was constructed. This mutant was then complemented with the same gene of interest from either P. putida BTP1 or a pyoverdine producing strain. Microbial growth and siderophore production kinetics of these different mutants were performed on three different culture media. The culture supernatants were analysed by LC-QTOF-MS. The supernatant of the pvdP gene-deleted mutant no longer fluoresces because it produces the isopyoverdine precursor, ferribactin, which does not possess a mature chromophore synonymous with fluorescence. The mutant complemented with the pvdP gene of P. putida BTP1 and P. putida KT2440 allows the fluorescence to reappear and to confirm by LC-QTOF-MS analysis the presence of a peak corresponding to the molecular weight of the isopyoverdine produced by the wild type BTP1 strain 
In conclusion, the PvdP enzyme could be responsible for the formation of isopyoverdine from BTP1. A confirmation of this hypothesis could be established by purifying the siderophores produced by the different mutant strains and by comparing their structure by nuclear magnetic resonance, the only technique that can distinguish between a pyoverdine and an isopyoverdine.

Isopyoverdine --- Biosynthèse --- BTP1 --- Sidérophore --- PvdP --- Sciences du vivant > Biochimie, biophysique & biologie moléculaire --- Sciences du vivant > Biotechnologie

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Plante --- plants --- Nutrition des plantes --- plant nutrition --- Iron --- Maladie des plantes --- Plant diseases --- Micro-organisme --- microorganisms --- Sidérophore --- Siderophores --- Réponse de la plante --- Plant response --- Pseudomonaceae --- Promoteur de croissance animale --- animal growth promoters --- Substance de croissance végétale --- plant growth substances --- -Plant diseases --- -Plants, Effect of iron on --- -Siderophores --- -Microbial iron chelates --- Siderochromes --- Iron chelates --- Microbial metabolites --- Plants, Effect of iron on --- Plants --- Botany --- Communicable diseases in plants --- Crop diseases --- Crops --- Diseases of plants --- Microbial diseases in plants --- Pathological botany --- Pathology, Vegetable --- Phytopathology --- Plant pathology --- Vegetable pathology --- Agricultural pests --- Crop losses --- Diseased plants --- Phytopathogenic microorganisms --- Plant pathologists --- Plant quarantine --- Native element minerals --- Transition metals --- Siderophile elements --- Physiological effect --- -Congresses --- Congresses --- Effect of trace elements on --- Pathology --- Diseases and pests --- Diseases --- Wounds and injuries --- Plant and Crop Sciences. Diseases, Pests and Disorders of Plants --- Effect of iron on --- Diseases, Pests and Disorders of Plants (General) --- -Physiological effect --- Diseases, Pests and Disorders of Plants (General). --- Nato workshop

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Beyond being the most important natural compound source, actinomycetes are the origin of up to two-thirds of all clinically used antibiotics. Currently, new antimicrobials are urgently needed, as infections caused by antibiotic-resistant pathogens are on the rise. In the identification of new antibiotics, many scientists are currently investigating biosynthetic aspects of antibiotic production in actinomycetes. Since the emergence of next-generation sequencing technologies, the field of antibiotics research has experienced a remarkable revival. These bacteria have the potential to produce more antibiotics than previously thought possible. Some antibiotics are produced in standard media, while others require the presence of a specific signaling molecule in the medium. Others, however, are only produced when the native regulation of the biosynthesis gene cluster is overruled. This book covers topics in the field of antibiotic-producing actinomycetes. The following tops are addressed: - Approaches to access novel antibiotic producers for novel natural compounds - Omics and genome mining approaches for the discovery of novel natural compounds - Analyses and genetic engineering of antibiotic biosynthesis - Regulation of the secondary metabolism in actinomycetes

Research & information: general --- Biology, life sciences --- Streptomyces --- biogeography --- comparative genomics --- diversification --- secondary metabolite biosynthetic gene clusters --- SMGC --- natural products --- streptomyces --- rishirilide --- biosynthesis --- polyketides --- polynucleotide phosphorylase --- ribonuclease --- regulation --- promoter --- RNA decay --- polyadenylation --- (p)ppGpp --- antibiotic --- antibiotics --- geomicrobiology --- Illumina sequencing --- microbiome diversity --- Actinobacteria --- Cave microbiology --- secondary metabolite --- rare Actinobacteria --- Amycolatopsis --- unculturability --- siderophore --- glycopeptide antibiotics --- dbv cluster --- regulatory genes --- StrR --- LAL --- LuxR solo --- dalbavancin --- A40926 --- Streptomyces lividans --- secretion pathways --- secretory proteins --- signal peptides --- actinomycetes --- teicoplanin --- van resistance genes --- Streptomyces tsukubaensis --- tacrolimus --- FK506 --- omics --- screening --- secondary metabolism --- differentiation --- elicitors --- morphology --- liquid cultures --- metagenomics --- rare actinomycetes --- dereplication --- metabolomics --- genome mining --- secondary metabolites --- novel compounds --- physicochemical screening --- physical and chemical properties --- structural diversity --- biological activity --- Actinoallomurus --- antibiotics polyethers --- lysolipin --- minimal PKS II --- cyclases --- benz[a]naphthacene quinone --- tridecaketide --- aromatic polyketide --- pentacyclic angular polyphenol --- extended polyketide chain --- actinobacteria --- β-lactamase --- resistance --- β-lactamase inhibitor --- polyketide synthases --- acyltransferases --- engineering --- new bioactive compounds --- symbiosis --- drug discovery --- chemical ecology --- culture-based approaches --- strain --- specialized metabolites --- biosynthetic gene cluster --- n/a

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The application of genomic, transcriptomic, and proteomic analyses brings new dimensions to our understanding of the biology of phototrophic bacteria. Comparing gene sequences of photosynthetic reaction center proteins and a key enzyme of bacteriochlorophyll biosynthesis from more than 150 genomes demonstrates the ancient roots of phototrophic bacteria. The presence and phylogeny of biosynthetic pathways of the compatible solutes ectoine and glycine betaine define groups of marine and halophilic phototrophic bacteria. The wide range of ecological niches conquered during evolution is demonstrated by the adaptation of cyanobacterial genera Scytonema, Tolypothrix, and Nostoc to different temperature ranges and the adaptation of Heliorestis species to alkaline habitats. Differences between phototrophic purple bacteria from marine and freshwater habitats are reflected in the preference for sulfidic and non-sulfidic niches. Also, a high proportion of siderophore producers was found among isolates from freshwater sources opposed to those from salty habitats . The primary colonization of carbonate rocks by a group of novel endolithic cyanobacteria and the following successions were studied over 9 months. The genomic characterization of the aerobic Dinoroseobacter strain AAP5, the strictly anaerobic and syntrophic Prosthecochloris ethylica, and the strictly anaerobic Heliorestis convoluta is reported. Significant differences in relation to oxygen are reflected in oxygen production by some species, oxygen tolerance over a wide range of concentrations, and the use of oxygen for energy generation or a strictly anaerobic lifestyle. Relations to oxygen are highlighted in papers on photooxidative stress, regulation of iron–sulfur cluster formation, and interactions of redox regulators. In situ metatranscriptomic and proteomic studies demonstrate the high metabolic flexibility of Chloroflexus aggregans in a hot spring microbial mat and show its adaptation to the changing conditions over day and night periods by a well-coordinated regulation of key metabolic processes for both phototrophic and chemotrophic growth.

phylogeny --- photosynthetic reaction center proteins --- bacteriochlorophyll biosynthesis --- phototrophic purple bacteria --- evolution of anoxygenic photosynthesis --- iron-sulfur cluster --- isc genes --- suf genes --- antisense promoters --- OxyR --- IscR --- Irr --- anoxygenic phototrophic bacteria --- purple nonsulfur bacteria --- massive blooms --- pufM gene --- Rhodovulum --- phylogenomics --- bioerosion --- anoxygenic phototroph --- microbiome --- euendolith --- Rhodobacter capsulatus --- Rhodobacter sphaeroides --- photooxidative stress --- transcriptomics --- proteomics --- stress defense --- heliobacteria --- Heliorestis convoluta --- alkaliphilic bacteria --- soda lake --- bacteriochlorophyll g --- biological soil crust --- drylands --- niche partitioning --- nitrogen fixing cyanobacteria --- Alphaproteobacteria --- Rhodobacteraceae --- nitric oxide --- quorum sensing --- gene transfer agent --- motility --- Crp/Fnr --- Dnr --- RegA --- ChpT --- green sulfur bacteria --- syntrophy --- e-pili --- adhesion protein --- photosynthetic symbionts --- large multiheme cytochrome --- metagenomic binning --- genomes of photosynthetic bacteria --- glycine betaine biosynthesis --- ectoine biosynthesis --- osmotic adaptation --- phylogeny of osmolyte biosynthesis --- filamentous anoxygenic phototroph --- microbial mats --- hot springs --- metatranscriptomics --- energy metabolism --- carbon fixation --- aerobic anoxygenic phototrophic bacteria --- bacteriochlorophyll a --- photosynthesis genes --- rhodopsin --- Sphingomonadaceae --- aerobic anoxygenic phototrophs --- siderophore --- metallophore --- CAS assay --- Chromocurvus halotolerans strain EG19 --- n/a