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Green bonds are an increasingly used instrument to catalyze cash flows towards a low-carbon economy. Nonetheless, the existence of an actual price advantage is still uncertain. This research paper aims to assess whether there is a green bond premium (“greenium”) for green bonds relative to conventional bonds with similar characteristics, and how liquidity may affect the determination of a price advantage. It analyzes the yield differentials between green and conventional bonds using three different methods. First, a Nelson-Siegel-Svensson method is executed, estimating the premium both as the yield spreads and as the differentials in Z-spreads. Using a matching method and creating a sample of green and synthetic conventional bonds, the second methodology consists in calculating the distances between each categories’ yield for the same duration. Finally, a fixed-effect regression is performed to better control the liquidity bias. In the first case, a positive premium emerges when analyzing the yield spreads (+37, 89 basis points) and the Z-spreads (+10.62 basis points). The second method mitigates the liquidity risk by creating a sample of synthetic bonds and reveals a yield spread of –15.89 basis points. Lastly, the regression method shows a negative greenium equal to –17,1487 basis points. Thus, a greenium emerges from all the three different methods, but its nature, sign, and real determinants are still uncertain. It is, therefore, not possible to conclude a definite price advantage for issuers of green bonds.

The Mediterranean Sea is an almost completely closed basin connecting several countries. Its configuration leads to its peculiarity and richness, but the intensive activities within the basin and along the coast aggravate the ecological conditions. The existing regulatory European Framework for environmental protection has already been in place through a series of legal instruments for almost 20 years. In this context, open science could play a fundamental role. The existing data must become findable, accessible, interoperable, and reusable (FAIR) to provide stakeholders and decision-makers with the instruments to understand how to improve the available information and support decisions based on the best set of existing information. Since 2009, the European Marine Observation and Data Network, EMODnet, has provided access to high-quality marine information supporting research and stakeholders’ mission and objectives. Data related to pollution are collated, validated, and published using standard protocols, formats, and vocabularies, thus becoming FAIR. For marine litter, a detailed and qualified data management system for macro- and microlitter in diverse compartments was structured. Some of these data and metadata were already used to calculate the first coastline litter baselines based on harmonized and FAIR datasets (2012–2016). The availability of these data related to the Mediterranean area is relevant, but additional work is required.

The Vfm Quorum Sensing (QS) system is preponderant for the virulence of different species of phytopathogenic bacteria of the genus Dickeya. The vfm gene cluster includes 26 genes involved in the biosynthesis, sensing or transduction of the Vfm signal. The transduction of the Vfm signal was shown to result into the activation of the promoter of the gene vfmE encoding a transcriptional regulator of the AraC family which itself activates the promoter of genes encoding the plant cell wall degrading enzymes (PCWDEs). The transcriptional regulator VfmE was shown to also activate promoters of the vfm gene cluster, allowing an exponential auto-induction of the Vfm QS system. Additionally, the activity of the transcriptional regulator VfmE was shown to also be controlled by Vfm-independent regulatory pathways involving the secondary messenger c-di-GMP and/or transcriptional regulators encoded outside of the vfm gene cluster. Here, we used a reporter gene fused to the promoter of the gene vfmE and compared the activity of the vfmE promoter among strains of Dickeya.

The Vfm quorum sensing (QS) system is preponderant for the virulence of different species of the bacterial genus Dickeya. The vfm gene cluster encodes 26 genes involved in the production, sensing or transduction of the QS signal. To date, the Vfm QS signal has escaped detection by analytical chemistry methods. However, we report here a strain-specific polymorphism in the biosynthesis genes vfmO and vfmP, which is predicted to be related to the production of different analogues of the QS signal. Consequently, the Vfm communication could be impossible between strains possessing different variants of the genes vfmO/P. We constructed three Vfm QS biosensor strains possessing different vfmO/P variants and compared these biosensors for their responses to samples prepared from 34 Dickeya strains possessing different vfmO/P variants. A pattern of specificity was demonstrated, providing evidence that the polymorphism in the genes vfmO/P determines the biosynthesis of different analogues of the QS signal. Unexpectedly, this vfmO/P-dependent pattern of specificity is linked to a polymorphism in the ABC transporter gene vfmG, suggesting an adaptation of the putative permease VfmG to specifically bind different analogues of the QS signal. Accordingly, we discuss the possible involvement of VfmG as co-sensor of the Vfm two-component regulatory system.

Nonribosomal peptides are microbial secondary metabolites exhibiting a tremendous structural diversity and a broad range of biological activities useful in the medical and agro-ecological fields. They are built up by huge multimodular enzymes called nonribosomal peptide synthetases. These synthetases are organized in modules constituted of adenylation, thiolation, and condensation core domains. As such, each module governs, according to the collinearity rule, the incorporation of a monomer within the growing peptide. The release of the peptide from the assembly chain is finally performed by a terminal core thioesterase domain. Secondary domains with modifying catalytic activities such as epimerization or methylation are sometimes included in the assembly lines as supplementary domains. This assembly line structure is analyzed by bioinformatics tools to predict the sequence and structure of the final peptides according to the sequence of the corresponding synthetases. However, a constantly expanding literature unravels new examples of nonribosomal synthetases exhibiting very rare domains and noncanonical organizations of domains and modules, leading to several amazing strategies developed by microorganisms to synthesize nonribosomal peptides. In this review, through several examples, we aim at highlighting these noncanonical pathways in order for the readers to perceive their complexity.

The Vfm quorum sensing (QS) system is preponderant for the virulence of different species of the bacterial genus Dickeya. The vfm gene cluster encodes 26 genes involved in the production, sensing or transduction of the QS signal. To date, the Vfm QS signal has escaped detection by analytical chemistry methods. However, we report here a strain-specific polymorphism in the biosynthesis genes vfmO and vfmP, which is predicted to be related to the production of different analogues of the QS signal. Consequently, the Vfm communication could be impossible between strains possessing different variants of the genes vfmO/P. We constructed three Vfm QS biosensor strains possessing different vfmO/P variants and compared these biosensors for their responses to samples prepared from 34 Dickeya strains possessing different vfmO/P variants. A pattern of specificity was demonstrated, providing evidence that the polymorphism in the genes vfmO/P determines the biosynthesis of different analogues of the QS signal. Unexpectedly, this vfmO/P-dependent pattern of specificity is linked to a polymorphism in the ABC transporter gene vfmG, suggesting an adaptation of the putative permease VfmG to specifically bind different analogues of the QS signal. Accordingly, we discuss the possible involvement of VfmG as co-sensor of the Vfm two-component regulatory system.

Nonribosomal peptides are microbial secondary metabolites exhibiting a tremendous structural diversity and a broad range of biological activities useful in the medical and agro-ecological fields. They are built up by huge multimodular enzymes called nonribosomal peptide synthetases. These synthetases are organized in modules constituted of adenylation, thiolation, and condensation core domains. As such, each module governs, according to the collinearity rule, the incorporation of a monomer within the growing peptide. The release of the peptide from the assembly chain is finally performed by a terminal core thioesterase domain. Secondary domains with modifying catalytic activities such as epimerization or methylation are sometimes included in the assembly lines as supplementary domains. This assembly line structure is analyzed by bioinformatics tools to predict the sequence and structure of the final peptides according to the sequence of the corresponding synthetases. However, a constantly expanding literature unravels new examples of nonribosomal synthetases exhibiting very rare domains and noncanonical organizations of domains and modules, leading to several amazing strategies developed by microorganisms to synthesize nonribosomal peptides. In this review, through several examples, we aim at highlighting these noncanonical pathways in order for the readers to perceive their complexity.

This document describes the data management and computation methods used to produce the EMODnet Chemistry seafloor litter visualization products. The heterogeneities in the data described above induced some normalization depending on the product. The data used for the EMODnet Marine Litter Products have been homogenized and filtered in order to allow comparisons among countries. Thus, EMODnet Marine Litter products might not be comparable with source data accessible through other platforms.

This document describes the data management and computation methods used to produce the EMODnet Chemistry beach litter visualization products. The heterogeneities in the data described above induced some normalization depending on the product. The data used for the EMODnet Marine Litter Products have been homogenized and filtered in order to allow comparisons among countries. Thus, EMODnet Marine Litter products might not be comparable with source data available on other platforms.

This document describes the data management and computation methods used to produce the EMODnet Chemistry seafloor litter visualization products. The heterogeneities in the data described above induced some normalization depending on the product. The data used for the EMODnet Marine Litter Products have been homogenized and filtered in order to allow comparisons among countries. Thus, EMODnet Marine Litter products might not be comparable with source data accessible through other platforms.

This document describes the data management and computation methods used to produce the EMODnet Chemistry beach litter visualization products. The heterogeneities in the data described above induced some normalization depending on the product. The data used for the EMODnet Marine Litter Products have been homogenized and filtered in order to allow comparisons among countries. Thus, EMODnet Marine Litter products might not be comparable with source data available on other platforms.

This document describes the data management and computation methods used to produce the EMODnet Chemistry beach litter visualization products. The heterogeneities in the data described above induced some normalization depending on the product. The data used for the EMODnet Marine Litter Products have been homogenized and filtered in order to allow comparisons among countries. Thus, EMODnet Marine Litter products might not be comparable with source data available on other platforms.

This document describes the data management and computation methods used to produce the EMODnet Chemistry seafloor litter visualization products. The heterogeneities in the data described above induced some normalization depending on the product. The data used for the EMODnet Marine Litter Products have been homogenized and filtered in order to allow comparisons among countries. Thus, EMODnet Marine Litter products might not be comparable with source data accessible through other platforms.

The pulmonary hypoplasia and anasarca syndrome (PHA) is a congenital lethal disorder, which until now has been reported in cattle and sheep. PHA is characterized by extensive subcutaneous fetal edema combined with hypoplasia or aplasia of the lungs and dysplasia of the lymphatic system. PHA is assumed to be of genetic etiology. This study presents the occurrence of PHA in two different cattle breeds and their genetic causation. Two PHA cases from one sire were observed in Slovenian Cika cattle. Under the assumption of monogenic inheritance, genome-wide homozygosity mapping scaled down the critical regions to 3% of the bovine genome including a 43.6 Mb-sized segment on chromosome 6. Whole-genome sequencing of one case, variant filtering against controls and genotyping of a larger cohort of Cika cattle led to the detection of a likely pathogenic protein-changing variant perfectly associated with the disease: a missense variant on chromosome 6 in ADAMTS3 (NM_001192797.1: c.1222C>T), which affects an evolutionary conserved residue (NP_001179726.1: p.(His408Tyr)). A single PHA case was found in Danish Holstein cattle and was whole-genome sequenced along with its parents. However, as there was no plausible private protein-changing variant, mining for structural variation revealed a likely pathogenic trisomy of the entire chromosome 20. The identified ADAMTS3 associated missense variant and the trisomy 20 are two different genetic causes, which shows a compelling genetic heterogeneity for bovine PHA.

Large-scale implementation of (plant) microbial fuel cells is greatly limited by high electrode costs. In this work, the potential of exploiting electrochemically active self-assembled biofilms in fabricating three-dimensional bioelectrodes for (plant) microbial fuel cells with minimum use of electrode materials was studied. Three-dimensional robust bioanodes were successfully developed with inexpensive polyurethane foams (PU) and activated carbon (AC). The PU/AC electrode bases were fabricated via a water-based sorption of AC particles on the surface of the PU cubes. The electrical current was enhanced by growth of bacteria on the PU/AC bioanode while sole current collectors produced minor current. Growth and electrochemical activity of the biofilm were shown with SEM imaging and DNA sequencing of the microbial community. The electric conductivity of the PU/AC electrode enhanced over time during bioanode development. The maximum current and power density of an acetate fed MFC reached 3 mA·m−2 projected surface area of anode compartment and 22 mW·m−3 anode compartment. The field test of the Plant-MFC reached a maximum performance of 0.9 mW·m−2 plant growth area (PGA) at a current density of 5.6 mA·m−2 PGA. A paddy field test showed that the PU/AC electrode was suitable as an anode material in combination with a graphite felt cathode. Finally, this study offers insights on the role of electrochemically active biofilms as natural enhancers of the conductivity of electrodes and as transformers of inert low-cost electrode materials into living electron acceptors.

Albicidin is produced by the sugarcane pathogenic bacterium Xanthomonas albilineans and is a potent antibiotic specifically targeting the bacterial DNA gyrase with an IC50 value in the nanomolar range. The structure of albicidin, which has remained unsolved for more than three decades since its first description, has been solved by a combination of extensive NMR and HR-MS/MS experiments. An inherent problem for the structure elucidation was the low amount of the albicidin production in cell culture. The low production forced us to cultivate several hundred liters in order to purify a few milligrams required for NMR experiments. In comparison, LC-HR-MS/MS has the great advantage of several orders of magnitude and high sensitivity. Thus, this approach requires much less material. But more importantly, purification of compounds is not necessary for structural analysis. Due to the application of targeted LC-MS/MS experiments, we were able to propose the structure of N-terminal carba- S158 moylated and b-methoxylated albicidin derivatives. Both of them are currently chemically synthesized and studied in a medicinal chemistry campaign. In order to search for more pharmaceutically relevant albicidin derivatives, we applied non-targeted LC-HR-MS/MS approaches combined with mass spectral networking, a recently introduced approach for non-targeted MS/MS data-analysis. However, as for the structural elucidation of albicidin, the even lower concentrated derivatives resulted in difficulties to obtain useful MS/ MS spectra. Since we typically operate the mass spectrometer in data-dependent acquisition mode (DDA), it inherently selects high abundant compounds of cell extracts for MS/ MS scans and possibly ignore low abundant compounds. The same goes for the network analysis which is based on similarity of MS/MS spectra and may not take potential ion species into account. To overcome this problem, we implemented a bioactivity-guided fractionation by solid phase extraction and semi

Albicidin is a potent antibiotic and phytotoxin produced by the sugarcane pathogenic bacterium Xanthomonas albilineans which targets the plant and bacterial DNA gyrase.[1] The infection occurs through the xylem vessels of the plants where the pathogen induces chlorosis which is characterized by white-pencil streaks.[2] Albicidin is encoded in the alb gene cluster, a polyketide synthase non-ribosomal peptide synthetase hybrid (PKS-NRPS). In addition to the PKS-NRPS megasynthetase machinery their existing several tailoring and post-NRPS proteins, whose function in connection with the processing of albicidin is unclear.[3] We could characterize a new albicidin derivative with a combination of tandem mass spectrometry, in vitro and knockout experiments from cultures of a Xanthomonas overproducer which is carbamoylated at the N-terminal coumaric acid. The putative ATP-dependent O-carbamoyltransferase Alb15, present in the biosynthesis gene cluster of albicidin, is responsible for the derivatization. Cloning and Expression of Alb15 in Escherichia coli and in vitro reconstitution of the carbamoyltransferase activity confirmed albicidin as the target substrate. The chemical synthesis of carbamoyl-albicidin enabled us to carry out bioactivity assays by means of in vitro gyrase inhibition and antibacterial assays. Carbamoyl-albicidin showed a significantly higher inhibitory efficiency against bacterial gyrase (∼8 nM vs 49 nM) then albicidin, which identifies the carbamoyl group as an important structural feature of albicidin maturation.

Albicidin is a potent antibiotic and phytotoxin produced by the sugarcane pathogenic bacterium Xanthomonas albilineans which targets the plant and bacterial DNA gyrase.[1] The infection occurs through the xylem vessels of the plants where the pathogen induces chlorosis which is characterized by white-pencil streaks.[2] Albicidin is encoded in the alb gene cluster, a polyketide synthase non-ribosomal peptide synthetase hybrid (PKS-NRPS). In addition to the PKS-NRPS megasynthetase machinery their existing several tailoring and post-NRPS proteins, whose function in connection with the processing of albicidin is unclear.[3] We could characterize a new albicidin derivative with a combination of tandem mass spectrometry, in vitro and knockout experiments from cultures of a Xanthomonas overproducer which is carbamoylated at the N-terminal coumaric acid. The putative ATP-dependent O-carbamoyltransferase Alb15, present in the biosynthesis gene cluster of albicidin, is responsible for the derivatization. Cloning and Expression of Alb15 in Escherichia coli and in vitro reconstitution of the carbamoyltransferase activity confirmed albicidin as the target substrate. The chemical synthesis of carbamoyl-albicidin enabled us to carry out bioactivity assays by means of in vitro gyrase inhibition and antibacterial assays. Carbamoyl-albicidin showed a significantly higher inhibitory efficiency against bacterial gyrase (∼8 nM vs 49 nM) then albicidin, which identifies the carbamoyl group as an important structural feature of albicidin maturation.

Albicidin is produced by the sugarcane pathogenic bacterium Xanthomonas albilineans and is a potent antibiotic specifically targeting the bacterial DNA gyrase with an IC50 value in the nanomolar range. The structure of albicidin, which has remained unsolved for more than three decades since its first description, has been solved by a combination of extensive NMR and HR-MS/MS experiments. An inherent problem for the structure elucidation was the low amount of the albicidin production in cell culture. The low production forced us to cultivate several hundred liters in order to purify a few milligrams required for NMR experiments. In comparison, LC-HR-MS/MS has the great advantage of several orders of magnitude and high sensitivity. Thus, this approach requires much less material. But more importantly, purification of compounds is not necessary for structural analysis. Due to the application of targeted LC-MS/MS experiments, we were able to propose the structure of N-terminal carba- S158 moylated and b-methoxylated albicidin derivatives. Both of them are currently chemically synthesized and studied in a medicinal chemistry campaign. In order to search for more pharmaceutically relevant albicidin derivatives, we applied non-targeted LC-HR-MS/MS approaches combined with mass spectral networking, a recently introduced approach for non-targeted MS/MS data-analysis. However, as for the structural elucidation of albicidin, the even lower concentrated derivatives resulted in difficulties to obtain useful MS/ MS spectra. Since we typically operate the mass spectrometer in data-dependent acquisition mode (DDA), it inherently selects high abundant compounds of cell extracts for MS/ MS scans and possibly ignore low abundant compounds. The same goes for the network analysis which is based on similarity of MS/MS spectra and may not take potential ion species into account. To overcome this problem, we implemented a bioactivity-guided fractionation by solid phase extraction and semi

We report the high-quality draft genome sequence of Xanthomonas sacchari strain LMG 476, isolated from sugarcane. The genome comparison of this strain with a previously sequenced X. sacchari strain isolated from a distinct environmental source should provide further insights into the adaptation of this species to different habitats and its evolution. (Résumé d'auteur)

Xanthomonas albilineans is the bacterium responsible for leaf scald, a lethal disease of sugarcane. Within the Xanthomonas genus, X. albilineans exhibits distinctive genomic characteristics including the presence of significant genome erosion, a non-ribosomal peptide synthesis (NRPS) locus involved in albicidin biosynthesis, and a type 3 secretion system (T3SS) of the Salmonella pathogenicity island-1 (SPI-1) family. We sequenced two X. albilineans-like strains isolated from unusual environments, i.e., from dew droplets on sugarcane leaves and from the wild grass Paspalum dilatatum, and compared these genomes sequences with those of two strains of X. albilineans and three of Xanthomonas sacchari. Average nucleotide identity (ANI) and multi-locus sequence analysis (MLSA) showed that both X. albilineans-like strains belong to a new species close to X. albilineans that we have named “Xanthomonas pseudalbilineans”. X. albilineans and “X. pseudalbilineans” share many genomic features including (i) the lack of genes encoding a hypersensitive response and pathogenicity type 3 secretion system (Hrp-T3SS), and (ii) genome erosion that probably occurred in a common progenitor of both species. Our comparative analyses also revealed specific genomic features that may help X. albilineans interact with sugarcane, e.g., a PglA endoglucanase, three TonB-dependent transporters and a glycogen metabolism gene cluster. Other specific genomic features found in the “X. pseudalbilineans” genome may contribute to its fitness and specific ecological niche.

Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. Compared to other species of Xanthomonas, X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy. Its genome, which has experienced significant erosion, has unique genomic features. It lacks two loci required for pathogenicity in other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis and the Hrp-T3SS (hypersensitive response and pathogenicity-type three secretion system) gene clusters. Instead, X. albilineans harbors in its genome an SPI-1 (Salmonella pathogenicity island-1) T3SS gene cluster usually found in animal pathogens. X. albilineans produces a potent DNA gyrase inhibitor called albicidin, which blocks chloroplast differentiation, resulting in the characteristic white foliar stripe symptoms. The antibacterial activity of albicidin also confers on X. albilineans a competitive advantage against rival bacteria during sugarcane colonization. Recent chemical studies have uncovered the unique structure of albicidin and allowed us to partially elucidate its fascinating biosynthesis apparatus, which involves an enigmatic hybrid PKS/NRPS (polyketide synthase/non-ribosomal peptide synthetase) machinery.

Xanthomonas albilineans is the bacterium responsible for leaf scald, a lethal disease of sugarcane. Within the Xanthomonas genus, X. albilineans exhibits distinctive genomic characteristics including the presence of significant genome erosion, a non-ribosomal peptide synthesis (NRPS) locus involved in albicidin biosynthesis, and a type 3 secretion system (T3SS) of the Salmonella pathogenicity island-1 (SPI-1) family. We sequenced two X. albilineans-like strains isolated from unusual environments, i.e., from dew droplets on sugarcane leaves and from the wild grass Paspalum dilatatum, and compared these genomes sequences with those of two strains of X. albilineans and three of Xanthomonas sacchari. Average nucleotide identity (ANI) and multi-locus sequence analysis (MLSA) showed that both X. albilineans-like strains belong to a new species close to X. albilineans that we have named “Xanthomonas pseudalbilineans”. X. albilineans and “X. pseudalbilineans” share many genomic features including (i) the lack of genes encoding a hypersensitive response and pathogenicity type 3 secretion system (Hrp-T3SS), and (ii) genome erosion that probably occurred in a common progenitor of both species. Our comparative analyses also revealed specific genomic features that may help X. albilineans interact with sugarcane, e.g., a PglA endoglucanase, three TonB-dependent transporters and a glycogen metabolism gene cluster. Other specific genomic features found in the “X. pseudalbilineans” genome may contribute to its fitness and specific ecological niche.

Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. Compared to other species of Xanthomonas, X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy. Its genome, which has experienced significant erosion, has unique genomic features. It lacks two loci required for pathogenicity in other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis and the Hrp-T3SS (hypersensitive response and pathogenicity-type three secretion system) gene clusters. Instead, X. albilineans harbors in its genome an SPI-1 (Salmonella pathogenicity island-1) T3SS gene cluster usually found in animal pathogens. X. albilineans produces a potent DNA gyrase inhibitor called albicidin, which blocks chloroplast differentiation, resulting in the characteristic white foliar stripe symptoms. The antibacterial activity of albicidin also confers on X. albilineans a competitive advantage against rival bacteria during sugarcane colonization. Recent chemical studies have uncovered the unique structure of albicidin and allowed us to partially elucidate its fascinating biosynthesis apparatus, which involves an enigmatic hybrid PKS/NRPS (polyketide synthase/non-ribosomal peptide synthetase) machinery.

We report the high-quality draft genome sequence of Xanthomonas sacchari strain LMG 476, isolated from sugarcane. The genome comparison of this strain with a previously sequenced X. sacchari strain isolated from a distinct environmental source should provide further insights into the adaptation of this species to different habitats and its evolution.

The present invention relates to a antibiotically active compounds characterized by general formula (I), wherein X1, BB, BC, BD, BE and X2 are building blocks with D1, D2, D3, D4 or D5 being linkers which comprise carbon, sulphur, nitrogen, phosphor and/or oxygen atoms and which are covalently connecting the moities BA and BB, BB and BC, BC and BD, BD and BE and BE and BF, respectively, and wherein in particular the building block BC comprises an amino acid derivative. The invention relates further to said compounds for use in a method of treatment of diseases, in particular for use in a method of treatment of bacterial infections.

The present invention relates to a antibiotically active compounds characterized by general formula (I), wherein X1, BB, BC, BD, BE and X2 are building blocks with D1, D2, D3, D4 or D5 being linkers which comprise carbon, sulphur, nitrogen, phosphor and/or oxygen atoms and which are covalently connecting the moities BA and BB, BB and BC, BC and BD, BD and BE and BE and BF, respectively, and wherein in particular the building block BC comprises an amino acid derivative. The invention relates further to said compounds for use in a method of treatment of diseases, in particular for use in a method of treatment of bacterial infections.

Background: Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results: We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters and share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or the secretion of peptides. In silico prediction of peptide structures according to NRPS architecture suggests eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas translucens and X. oryzae pv. oryzicola. Further genome mining revealed other novel NRPS gen

Background Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Results Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. Conclusions This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.

Background: To date, the only known small molecule synthesized by non-ribosomal peptide synthesis (NRPS) in the genus Xanthomonas is the phytotoxin albicidin produced by Xanthomonas albilineans, the causal agent of sugarcane leaf scald disease. Recent analyses of available genomic sequences indicated that X. albilineans, as well as Xanthomonas oryzae and Xanthomonas translucens, possess a novel NRPS gene cluster called META-B whose architecture is strainspecific (each sequenced strain is predicted to synthesize a different peptide) and doesn´t resemble to any NRPS gene cluster described to date. Because the META-B NRPS gene cluster is specific to three phylogenetically distant species of Xanthomonas associated with monocotyledonous plants, we assume a putative involvement of the new family of small molecules produced by this gene cluster in plant-bacteria interactions. Objectives: We aimed at isolating and characterizing the small molecule encoded by the META-B NRPS gene cluster of X. albilineans in order to study its putative involvement in plant-bacteria interactions. Methods: We developed a META-B overproducing X. albilineans strain by over-expressing the AraC transcriptional regulator which is present within the META-B NRPS gene cluster. HPLC profiles obtained from cultures of wild type vs the AraC over-expressing strain were compared. Peaks with significantly increased amplitude in the HPLC profile from the AraC over-expressing strain were collected and their content analyzed by mass spectrometry. Conclusions: We identified a peptide with a nominal molecular mass > 2 kDa and with an amino acid sequence (MS/MS experiments) which excellently matches the one predicted by A-domain specificities of META-B NRPS genes. (Texte intégral)

Background Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Results Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. Conclusions This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.

Background: Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. Results: We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters and share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or the secretion of peptides. In silico prediction of peptide structures according to NRPS architecture suggests eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas translucens and X. oryzae pv. oryzicola. Further genome mining revealed other novel NRPS gen

Background: To date, the only known small molecule synthesized by non-ribosomal peptide synthesis (NRPS) in the genus Xanthomonas is the phytotoxin albicidin produced by Xanthomonas albilineans, the causal agent of sugarcane leaf scald disease. Recent analyses of available genomic sequences indicated that X. albilineans, as well as Xanthomonas oryzae and Xanthomonas translucens, possess a novel NRPS gene cluster called META-B whose architecture is strainspecific (each sequenced strain is predicted to synthesize a different peptide) and doesn´t resemble to any NRPS gene cluster described to date. Because the META-B NRPS gene cluster is specific to three phylogenetically distant species of Xanthomonas associated with monocotyledonous plants, we assume a putative involvement of the new family of small molecules produced by this gene cluster in plant-bacteria interactions. Objectives: We aimed at isolating and characterizing the small molecule encoded by the META-B NRPS gene cluster of X. albilineans in order to study its putative involvement in plant-bacteria interactions. Methods: We developed a META-B overproducing X. albilineans strain by over-expressing the AraC transcriptional regulator which is present within the META-B NRPS gene cluster. HPLC profiles obtained from cultures of wild type vs the AraC over-expressing strain were compared. Peaks with significantly increased amplitude in the HPLC profile from the AraC over-expressing strain were collected and their content analyzed by mass spectrometry. Conclusions: We identified a peptide with a nominal molecular mass > 2 kDa and with an amino acid sequence (MS/MS experiments) which excellently matches the one predicted by A-domain specificities of META-B NRPS genes. (Texte intégral)

Xanthomonas albilineans is a xylem-invading pathogen that causes leaf scald, a lethal disease of sugarcane. Unlike other xanthomonads, X. albilineans exhibits a large intra-species variability which was previously observed with different genetic markers (PFGE for Pulsed Field Gel Electrophoresis and MLSA for Multi Locus Sequence Analysis). The CRISPR systems (Clustered Regularly Interspaced Short Palindromic Repeats) are repetitive structures in bacteria and Archaea composed of exact 24- to 48-bp repeated sequences (or "repeats") separated by unique sequences of similar length (or "spacers"). Over 40 gene families, which are found nowhere except near these repeats, have been designated collectively as CRISPR-associated (cas) genes. CRISPR/cas systems participate in an antiviral response, probably by an RNA interference-like mechanism. Analysis of the variability of CRISPR spacers is currently used to perform diversity or epidemiological studies in bacteria. The genome sequence of X. albilineans revealed the occurrence of two different CRISPR/cas systems in this pathogen. The first system, called CRISPR-1, is associated with seven cas genes and contains repeats of 31 base pairs. It is similar to the CRISPR system found in several sequenced species of Xanthomonas. The second system, called CRISPR-2, is associated with six cas genes and contains repeats of 28 base pairs. There is only one Xanthomonas pathovar that is known to contain a similar CRISPR-2 system, namely X. campestris pv. raphani. In this study, we analyzed the polymorphism of the two different CRISPR/cas systems among 21 strains spanning the genetic diversity of X. albilineans. We have either sequenced PCR products resulting from amplification of spacers or cas genes, or used sequences from draft genome sequences. Whereas CRISPR-2 is ubiquitous within the 21 strains, CRISPR-1 is absent in three strains. The loss of CRISPR-1 by a common ancestor of these three strains is in accordance with the MLSA phyloge

Xanthomonads are plant-associated bacteria that establish neutral, commensal or pathogenic relationships with plants. The list of common characteristics shared by all members of the genus Xanthomonas is now well established based on the entire genome sequences that are currently available and that represent various species, numerous pathovars of X. axonopodis (sensu Vauterin et al., 2000), X. oryzae and X. campestris, and many strains within some pathovars. These ?-proteobacteria are motile by a single polar flagellum. Motility is an important feature involved in biofilm formation, plant colonization and hence considered as a pathogenicity factor. X. axonopodis pv. phaseoli var. fuscans (Xapf) is one of the causal agents of common bacterial blight of bean and 4834-R is a highly aggressive strain of this pathogen that was isolated from a seed-borne epidemic in France in 1998. We obtained a high quality assembled sequence of the genome of this strain with 454-Solexa and 2X Sanger sequencing. Housekeeping functions are conserved in this genome that shares core characteristics with genomes of other xanthomonads: the six secretion systems which have been described so far in Gram negative bacteria are all present, as well as their ubiquitous substrates or effectors and a rather usual number of mobile elements. Elements devoted to the adaptation to the environment constitute an important part of the genome with a chemotaxis island and dispersed MCPs, numerous two-component systems, and numerous TonB dependent transporters. Furthermore, numerous multidrug efflux systems and functions dedicated to biofilm formation that confer resistance to stresses are also present. An intriguing feature revealed by genome analysis is a long deletion of 35 genes (33 kbp) involved in flagellar biosynthesis. This deletion is replaced by an insertion sequence called ISXapf2. Genes such as flgB to flgL and fliC to fleQ which are involved in the flagellar structure (rod, P- and L-ring, hook, cap

Background Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenic X. albilineans strain GPE PC73 focused exclusively on distinctive genomic features shared with Xylella fastidiosa-another xylem-limited Xanthomonadaceae. The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features of X. albilineans, and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity. Results Comparative genomic analyses showed that most of the known pathogenicity factors from other Xanthomonas species are conserved in X. albilineans, with the notable absence of two major determinants of the "artillery" of other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity). Genomic features specific to X. albilineans that may contribute to specific adaptation of this pathogen to sugarcane xylem vessels were also revealed. SSH experiments led to the identification of 20 genes common to three highly pathogenic strains but missing in a less pathogenic strain. These 20 genes, which include four ABC transporter genes, a methyl-accepting chemotaxis protein gene and an oxidoreductase gene, could play a key role in pathogenicity. With the exception of hypothetical proteins revealed by our comparative genomic analyses and SSH experiments, no genes potentially involved in any offensive or counter-defensive mechanism specific to X. albilineans were identi

Co-ordinated efforts to collect and maintain cotton genetic resources have increased over the last 100 years to insure the worldwide economic value of cotton fibre and cotton by-products. The classified genetic resources of cotton are extensive and include five tetraploid species in the primary gene pool, 20 diploid species in the secondary gene pool, and 25 diploid species in the tertiary gene pool. There are at least eight major cotton collections worldwide and their status and contents are discussed. An overview of the collections suggest that there is a substantial coverage of the Gossypium genome but some recently identified species are not yet maintained and several species are underrepresented and threatened by loss of their natural habitat. Meeting the high demand for cotton genetic resources and increasing the coverage of the genus with decreasing budgets are a few of the challenges facing individual collections. These types of challenges and the opportunities for international collaboration that they create are discussed. One desirable outcome of co-ordinated efforts among collections would be finding gaps in the collections and sharing of the workload to conserve the genus. Multinational communication and collaboration are critical for the evaluation of rare and unique cotton germplasm and protection of the global cotton germplasm resources.

Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by non-ribosomal peptide synthesis (NRPS) in this genus is albicidin produced by Xanthomonas albilineans. The DNA gyrase inhibitor albicidin is not only an important virulence factor but also a possible lead structure for novel antibiotics. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. The most unexpected result of these analyses is that these two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters. Furthermore, these Xanthomonas spp. strains share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or for the secretion of peptides. In silico prediction of peptide structures according to the NRPS architecture accounts for eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas transluscens and X. oryzae pv. oryzicola. Further genome mining revealed (i) novel NRPS genes shared by Xanthomonas spp. strains GPE PC73 and XaS3 with the plant-associated bacterium Bradyrhizobium spp. strain BTAi and (ii) novel NRPS genes specific to X

Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by non-ribosomal peptide synthesis (NRPS) in this genus is albicidin produced by Xanthomonas albilineans. The DNA gyrase inhibitor albicidin is not only an important virulence factor but also a possible lead structure for novel antibiotics. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. The most unexpected result of these analyses is that these two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters. Furthermore, these Xanthomonas spp. strains share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or for the secretion of peptides. In silico prediction of peptide structures according to the NRPS architecture accounts for eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas transluscens and X. oryzae pv. oryzicola. Further genome mining revealed (i) novel NRPS genes shared by Xanthomonas spp. strains GPE PC73 and XaS3 with the plant-associated bacterium Bradyrhizobium spp. strain BTAi and (ii) novel NRPS genes specific to X

Background Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenic X. albilineans strain GPE PC73 focused exclusively on distinctive genomic features shared with Xylella fastidiosa-another xylem-limited Xanthomonadaceae. The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features of X. albilineans, and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity. Results Comparative genomic analyses showed that most of the known pathogenicity factors from other Xanthomonas species are conserved in X. albilineans, with the notable absence of two major determinants of the "artillery" of other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity). Genomic features specific to X. albilineans that may contribute to specific adaptation of this pathogen to sugarcane xylem vessels were also revealed. SSH experiments led to the identification of 20 genes common to three highly pathogenic strains but missing in a less pathogenic strain. These 20 genes, which include four ABC transporter genes, a methyl-accepting chemotaxis protein gene and an oxidoreductase gene, could play a key role in pathogenicity. With the exception of hypothetical proteins revealed by our comparative genomic analyses and SSH experiments, no genes potentially involved in any offensive or counter-defensive mechanism specific to X. albilineans were identi

Xanthomonads are plant-associated bacteria that establish neutral, commensal or pathogenic relationships with plants. The list of common characteristics shared by all members of the genus Xanthomonas is now well established based on the entire genome sequences that are currently available and that represent various species, numerous pathovars of X. axonopodis (sensu Vauterin et al., 2000), X. oryzae and X. campestris, and many strains within some pathovars. These ?-proteobacteria are motile by a single polar flagellum. Motility is an important feature involved in biofilm formation, plant colonization and hence considered as a pathogenicity factor. X. axonopodis pv. phaseoli var. fuscans (Xapf) is one of the causal agents of common bacterial blight of bean and 4834-R is a highly aggressive strain of this pathogen that was isolated from a seed-borne epidemic in France in 1998. We obtained a high quality assembled sequence of the genome of this strain with 454-Solexa and 2X Sanger sequencing. Housekeeping functions are conserved in this genome that shares core characteristics with genomes of other xanthomonads: the six secretion systems which have been described so far in Gram negative bacteria are all present, as well as their ubiquitous substrates or effectors and a rather usual number of mobile elements. Elements devoted to the adaptation to the environment constitute an important part of the genome with a chemotaxis island and dispersed MCPs, numerous two-component systems, and numerous TonB dependent transporters. Furthermore, numerous multidrug efflux systems and functions dedicated to biofilm formation that confer resistance to stresses are also present. An intriguing feature revealed by genome analysis is a long deletion of 35 genes (33 kbp) involved in flagellar biosynthesis. This deletion is replaced by an insertion sequence called ISXapf2. Genes such as flgB to flgL and fliC to fleQ which are involved in the flagellar structure (rod, P- and L-ring, hook, cap