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Max Mergeay - One of the best experts on this subject based on the ideXlab platform.
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Cupriavidus metallidurans ch34 a historical perspective on its discovery characterization and metal resistance
FEMS Microbiology Ecology, 2021Co-Authors: Max Mergeay, Rob Van HoudtAbstract:Cupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of C. metallidurans research starting from its isolation in 1976. This minireview describes the early research and legacy tools used to study its metal resistance determinants, characteristic megaplasmids, ecological niches and environmental applications.
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spontaneous mutation in the agrrs two component regulatory system of Cupriavidus metallidurans results in enhanced silver resistance
Metallomics, 2019Co-Authors: K. Mijnendonckx, Pieter Monsieurs, A. Provoost, Natalie Leys, Max Mergeay, Paul Janssen, Muntasir Ali, Daniel Charlier, Rob Van HoudtAbstract:The uncontrolled and widespread use of (nano)silver compounds has led to the increased release of these compounds into the environment, raising concerns about their negative impact on ecosystems. Concomitantly, silver resistance determinants are widely spread among environmental and clinically relevant bacteria although the underlying mechanisms are not yet fully understood. We show that Cupriavidus metallidurans is able to adapt to toxic silver concentrations. However, none of the known silver resistance determinants present in C. metallidurans are involved in the adaptative response. Instead, increased silver resistance is achieved by the concerted action of a two-component system AgrR–AgrS, previously not associated with metal resistance, and two periplasmic proteins PrsQ1 and PrsQ2. Both proteins belong to an unique group of small, uncharacterized, secreted proteins restricted to the genera Cupriavidus and Ralstonia. This system gives C. metallidurans the ability to withstand much higher silver concentrations. The latter could be facilitated by the accumulation of silver ions and the formation of silver nanoparticles.
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paleomicrobiology to investigate copper resistance in bacteria isolation and description of Cupriavidus necator b9 in the soil of a medieval foundry
Environmental Microbiology, 2017Co-Authors: David Gillan, A. Provoost, Max Mergeay, Camille Van Camp, Nicolas Thomas, Laurent Vermard, Gabriel Billon, Ruddy WattiezAbstract:Summary Remains of a medieval foundry were excavated by archaeologists in 2013 in Verdun (France). Ancient workshops specialized in brass and copper alloys were found with an activity between 13th to 16th c. Levels of Cu, Zn and Pb reached 20000, 7000 and 6000 mg kg−1 (dw), respectively, in several soil horizons. The objective of the present work was to examine the microbial community in this contaminated site. A total of 8–22 106 reads were obtained by shotgun metagenomics in 4 soil horizons. Bioinformatic analyses suggest the presence of complex bacterial communities dominated by Proteobacteria. The structure of the community was not affected by metals, contrary to the set of metal-resistance genes. Using selective media, a novel strain of Cupriavidus necator (eutrophus), strain B9, was isolated. Its genome was sequenced and a novel metal resistance gene cluster with Hg resistance genes (merRTPCA) followed by 24 copper-resistance genes (actP, cusCBAF, silP, copK1, copH4QLOFGJH3IDCBARS, copH2H1, copK2) was found. This cluster is partly homologous to the cop genes of Cupriavidus gilardii CR3 and C. metallidurans CH34. Proteomics indicated that the four copH genes were differentially expressed: CopH1 and CopH2 were mostly induced by Cd while CopH4 was highly expressed by Cu. This article is protected by copyright. All rights reserved.
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metal response in Cupriavidus metallidurans volume ii insights into the structure function relationship of proteins
2015Co-Authors: Guy Vandenbussche, Max Mergeay, Rob Van HoudtAbstract:Bacteria such as Cupriavidus metallidurans have developed different strategies for tolerating toxic levels of metal ions. Metal ion resistance requires the contribution of multiple layers of mechanisms, the most efficient being the efflux of the noxious cations out of the cell regulated by transport systems. Structural and functional data from bacterial primary and secondary transporters are outlined and detailed for the corresponding C.metallidurans proteins. Next, the available high-resolution three-dimensional structures of C. metallidurans proteins involved in metal resistance mechanisms are reviewed and their structure-function relationship is discussed.
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response of Cupriavidus metallidurans ch34 to metals
2015Co-Authors: Pieter Monsieurs, Max Mergeay, Guy Vandenbussche, Jon L Hobman, Rob Van HoudtAbstract:Cupriavidus metallidurans CH34 displays resistance to a plethora of metals. Its response and underlying genetic determinants are dissected and detailed metal by metal (from arsenic to zinc). An important role for its megaplasmids pMOL28 and pMOL30 is shown, with high level resistance to cadmium, chromate, cobalt, copper, mercury, nickel, lead and zinc mediated by well-known genes for detoxification that are often accompanied by other functions linked to acute or chronic stress. Nevertheless, metal resistance determinants are also found on the chromid (e.g. to chromate, copper and zinc) as well as on a large genomic island integrated in the chromosome (e.g. to cadmium, lead and mercury). Even the core genome participates in certain responses such as to gold or selenium. Next, we summarized the environmental applications, which were developed based on the knowledge gained by studying these different determinants, and in particular biosensors and soil and water bioremediation. Finally, the general transcriptional response of C. metallidurans to sixteen different metals supplied at different concentrations (including acute stress) is discussed within the framework of its intricate regulatory network.
Rob Van Houdt - One of the best experts on this subject based on the ideXlab platform.
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Cupriavidus metallidurans ch34 a historical perspective on its discovery characterization and metal resistance
FEMS Microbiology Ecology, 2021Co-Authors: Max Mergeay, Rob Van HoudtAbstract:Cupriavidus metallidurans, and in particular type strain CH34, became a model bacterium to study bacterial resistance to metals. Although nowadays the routine use of a wide variety of omics and molecular techniques allow refining, deepening and expanding our knowledge on adaptation and resistance to metals, these were not available at the onset of C. metallidurans research starting from its isolation in 1976. This minireview describes the early research and legacy tools used to study its metal resistance determinants, characteristic megaplasmids, ecological niches and environmental applications.
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spontaneous mutation in the agrrs two component regulatory system of Cupriavidus metallidurans results in enhanced silver resistance
Metallomics, 2019Co-Authors: K. Mijnendonckx, Pieter Monsieurs, A. Provoost, Natalie Leys, Max Mergeay, Paul Janssen, Muntasir Ali, Daniel Charlier, Rob Van HoudtAbstract:The uncontrolled and widespread use of (nano)silver compounds has led to the increased release of these compounds into the environment, raising concerns about their negative impact on ecosystems. Concomitantly, silver resistance determinants are widely spread among environmental and clinically relevant bacteria although the underlying mechanisms are not yet fully understood. We show that Cupriavidus metallidurans is able to adapt to toxic silver concentrations. However, none of the known silver resistance determinants present in C. metallidurans are involved in the adaptative response. Instead, increased silver resistance is achieved by the concerted action of a two-component system AgrR–AgrS, previously not associated with metal resistance, and two periplasmic proteins PrsQ1 and PrsQ2. Both proteins belong to an unique group of small, uncharacterized, secreted proteins restricted to the genera Cupriavidus and Ralstonia. This system gives C. metallidurans the ability to withstand much higher silver concentrations. The latter could be facilitated by the accumulation of silver ions and the formation of silver nanoparticles.
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the ability of basalt to leach nutrients and support growth of Cupriavidus metallidurans ch34 depends on basalt composition and element release
Geomicrobiology Journal, 2018Co-Authors: Bo Byloos, Rob Van Houdt, Harsh Maan, Nico Boon, Natalie LeysAbstract:The influence of different rock mineralogical compositions on element leaching and bio-weathering processes is poorly understood. Here, the role of basalt composition on nutrient leaching (calcium, iron, phosphorus or magnesium) and subsequent support of Cupriavidus metallidurans CH34 growth was evaluated. Seven different basalts were examined. In iron-limiting media, growth could be restored for all basalts tested, while only two basalts could restore growth in magnesium-limiting medium. Only for magnesium growth complementation was correlated with the composition of the basalts tested. Our results showed that basalt composition can affect leaching and availability of different elements, in turn, affecting bacterial growth.
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metal response in Cupriavidus metallidurans volume ii insights into the structure function relationship of proteins
2015Co-Authors: Guy Vandenbussche, Max Mergeay, Rob Van HoudtAbstract:Bacteria such as Cupriavidus metallidurans have developed different strategies for tolerating toxic levels of metal ions. Metal ion resistance requires the contribution of multiple layers of mechanisms, the most efficient being the efflux of the noxious cations out of the cell regulated by transport systems. Structural and functional data from bacterial primary and secondary transporters are outlined and detailed for the corresponding C.metallidurans proteins. Next, the available high-resolution three-dimensional structures of C. metallidurans proteins involved in metal resistance mechanisms are reviewed and their structure-function relationship is discussed.
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response of Cupriavidus metallidurans ch34 to metals
2015Co-Authors: Pieter Monsieurs, Max Mergeay, Guy Vandenbussche, Jon L Hobman, Rob Van HoudtAbstract:Cupriavidus metallidurans CH34 displays resistance to a plethora of metals. Its response and underlying genetic determinants are dissected and detailed metal by metal (from arsenic to zinc). An important role for its megaplasmids pMOL28 and pMOL30 is shown, with high level resistance to cadmium, chromate, cobalt, copper, mercury, nickel, lead and zinc mediated by well-known genes for detoxification that are often accompanied by other functions linked to acute or chronic stress. Nevertheless, metal resistance determinants are also found on the chromid (e.g. to chromate, copper and zinc) as well as on a large genomic island integrated in the chromosome (e.g. to cadmium, lead and mercury). Even the core genome participates in certain responses such as to gold or selenium. Next, we summarized the environmental applications, which were developed based on the knowledge gained by studying these different determinants, and in particular biosensors and soil and water bioremediation. Finally, the general transcriptional response of C. metallidurans to sixteen different metals supplied at different concentrations (including acute stress) is discussed within the framework of its intricate regulatory network.
Naoto Ogawa - One of the best experts on this subject based on the ideXlab platform.
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complete genome sequence of 3 chlorobenzoate degrading bacterium Cupriavidus necator nh9 and reclassification of the strains of the genera Cupriavidus and ralstonia based on phylogenetic and whole genome sequence analyses
Frontiers in Microbiology, 2019Co-Authors: Ryota Moriuchi, Hideo Dohra, Yu Kanesaki, Naoto OgawaAbstract:Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain’s ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 Mb and 3.4 Mb) and two circular plasmids (427 kb and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia. As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.
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Data_Sheet_1_Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses.PDF
2019Co-Authors: Ryota Moriuchi, Hideo Dohra, Yu Kanesaki, Naoto OgawaAbstract:Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain's ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 and 3.4 Mb) and two circular plasmids (427 and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia. As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.
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Table_4_Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses.XLSX
2019Co-Authors: Ryota Moriuchi, Hideo Dohra, Yu Kanesaki, Naoto OgawaAbstract:Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain's ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 and 3.4 Mb) and two circular plasmids (427 and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia. As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.
Lionel Moulin - One of the best experts on this subject based on the ideXlab platform.
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novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus stm 6070 a new species of mimosa pudica microsymbiont isolated from heavy metal rich mining site soil
BMC Genomics, 2020Co-Authors: Agnieszka Klonowska, Lionel Moulin, Julie Ardley, Florence Braun, Margaret Gollagher, Jaco Daniel Zandberg, Dora Marinova, Marcel Huntemann, T B K Reddy, Neha VargheseAbstract:Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
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Biodiversity of Mimosa pudica rhizobial symbionts (Cupriavidus taiwanensis, Rhizobium mesoamericanum) in New Caledonia and their adaptation to heavy metal-rich soils
FEMS Microbiology Ecology, 2012Co-Authors: Agnieszka Klonowska, Pierre Tisseyre, Clemence Chaintreuil, Lucie Miche, Rémy Melkonian, Gisele Laguerre, Brigitte Brunel, Marc Ducousso, Lionel MoulinAbstract:Rhizobia are soil bacteria able to develop a nitrogen-fixing symbiosis with legumes. They are taxonomically spread among the alpha and beta subclasses of the Proteobacteria. Mimosa pudica, a tropical invasive weed, has been found to have an affinity for beta-rhizobia, including species within the Burkholderia and Cupriavidus genera. In this study, we describe the diversity of M. pudica symbionts in the island of New Caledonia, which is characterized by soils with high heavy metal content, especially of Ni. By using a plant-trapping approach on four soils, we isolated 96 strains, the great majority of which belonged to the species Cupriavidus taiwanensis (16S rRNA and recA gene phylogenies). A few Rhizobium strains in the newly described species Rhizobium mesoamericanum were also isolated. The housekeeping and nod gene phylogenies supported the hypothesis of the arrival of the C. taiwanensis and R. mesoamericanum strains together with their host at the time of the introduction of M. pudica in New Caledonia (NC) for its use as a fodder. The C. taiwanensis strains exhibited various tolerances to Ni, Zn and Cr, suggesting their adaptation to the specific environments in NC. Specific metal tolerance marker genes were found in the genomes of these symbionts, and their origin was investigated by phylogenetic analyses.
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legume nodulating betaproteobacteria diversity host range and future prospects
Molecular Plant-microbe Interactions, 2011Co-Authors: Prasad Gyaneshwar, Lionel Moulin, Wenming Chen, Cyril Bontemps, Ann M Hirsch, Geoffrey N Elliott, Paulina Estradade Los Santos, E Gross, Fabio Bueno Dos Reis, Janet I SprentAbstract:Rhizobia form specialized nodules on the roots of legumes (family Fabaceae) and fix nitrogen in exchange for carbon from the host plant. Although the majority of legumes form symbioses with members of genus Rhizobium and its relatives in class Alphaproteobacteria, some legumes, such as those in the large genus Mimosa, are nodulated predominantly by betaproteobacteria in the genera Burkholderia and Cupriavidus. The principal centers of diversity of these bacteria are in central Brazil and South Africa. Molecular phylogenetic studies have shown that betaproteobacteria have existed as legume symbionts for approximately 50 million years, and that, although they have a common origin, the symbiosis genes in both subclasses have evolved separately since then. Additionally, some species of genus Burkholderia, such as B. phymatum, are highly promiscuous, effectively nodulating several important legumes, including common bean (Phaseolus vulgaris). In contrast to genus Burkholderia, only one species of genus Cupriavidus (C. taiwanensis) has so far been shown to nodulate legumes. The recent availability of the genome sequences of C. taiwanensis, B. phymatum, and B. tuberum has paved the way for a more detailed analysis of the evolutionary and mechanistic differences between nodulating strains of alpha- and betaproteobacteria. Initial analyses of genome sequences have suggested that plant-associated Burkholderia spp. have lower G+C contents than Burkholderia spp. that are opportunistic human pathogens, thus supporting previous suggestions that the plant- and human-associated groups of Burkholderia actually belong in separate genera.
Ryota Moriuchi - One of the best experts on this subject based on the ideXlab platform.
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complete genome sequence of 3 chlorobenzoate degrading bacterium Cupriavidus necator nh9 and reclassification of the strains of the genera Cupriavidus and ralstonia based on phylogenetic and whole genome sequence analyses
Frontiers in Microbiology, 2019Co-Authors: Ryota Moriuchi, Hideo Dohra, Yu Kanesaki, Naoto OgawaAbstract:Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain’s ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 Mb and 3.4 Mb) and two circular plasmids (427 kb and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia. As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.
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Data_Sheet_1_Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses.PDF
2019Co-Authors: Ryota Moriuchi, Hideo Dohra, Yu Kanesaki, Naoto OgawaAbstract:Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain's ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 and 3.4 Mb) and two circular plasmids (427 and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia. As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.
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Table_4_Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses.XLSX
2019Co-Authors: Ryota Moriuchi, Hideo Dohra, Yu Kanesaki, Naoto OgawaAbstract:Cupriavidus necator NH9, a 3-chlorobenzoate (3-CB)-degrading bacterium, was isolated from soil in Japan. In this study, the complete genome sequence of NH9 was obtained via PacBio long-read sequencing to better understand the genetic components contributing to the strain's ability to degrade aromatic compounds, including 3-CB. The genome of NH9 comprised two circular chromosomes (4.3 and 3.4 Mb) and two circular plasmids (427 and 77 kb) containing 7,290 coding sequences, 15 rRNA and 68 tRNA genes. Kyoto Encyclopedia of Genes and Genomes pathway analysis of the protein-coding sequences in NH9 revealed a capacity to completely degrade benzoate, 2-, 3-, or 4-hydroxybenzoate, 2,3-, 2,5-, or 3,4-dihydroxybenzoate, benzoylformate, and benzonitrile. To validate the identification of NH9, phylogenetic analyses (16S rRNA sequence-based tree and multilocus sequence analysis) and whole-genome sequence analyses (average nucleotide identity, percentage of conserved proteins, and tetra-nucleotide analyses) were performed, confirming that NH9 is a C. necator strain. Over the course of our investigation, we noticed inconsistencies in the classification of several strains that were supposed to belong to the two closely-related genera Cupriavidus and Ralstonia. As a result of whole-genome sequence analysis of 46 Cupriavidus strains and 104 Ralstonia strains, we propose that the taxonomic classification of 41 of the 150 strains should be changed. Our results provide a clear delineation of the two genera based on genome sequences, thus allowing taxonomic identification of strains belonging to these two genera.
