Project description:Bacilli are genetically and physiologically diverse, ranging from innocuous to highly pathogenic. Here, we present annotated genome assemblies for 20 strains belonging to Bacillus anthracis, B. atrophaeus, B. cereus, B. licheniformis, B. macerans, B. megaterium, B. mycoides, and B. subtilis.
Project description:Mitochondrial DNA is maternally inherited and is shown to affect nuclear-cytoplasmic interactions in potato. Analyzing the mitogenome helps understand the evolutionary relationships and improve breeding programs in potato. We report complete mitogenome sequences from a panel of 13 potato accessions of various taxa. Each mitogenome has three independent circular molecules, except one of the S. bukasovii sample BUK2, which has a single circular molecule. Each mitogenome code for 37 non-redundant protein-coding genes, three rRNAs, 20 tRNAs, and 19 hypothetical open reading frames. Phylogenetic analysis reveals congruency between plastome and mitogenome phylogeny.
Project description:The chloroplasts are a crucial part of photosynthesizing plant cells and are extensively utilized in phylogenetic studies mainly due to their maternal inheritance. Characterization and analysis of complete plastome sequences is necessary to understand their diversity and evolutionary relationships. Here, a panel of thirteen plastomes from various potato taxa are presented. Though they are highly similar with respect to gene order and content, there is also a great extent of SNPs and InDels between them, with one of the Solanum bukasovii plastomes (BUK2) having the highest number of SNPs and InDels. Five different potato plastome types (C, S, A, W, W2) are present in the panel. Interestingly, the S. tuberosum subsp. tuberosum (TBR) accession has a W-type plastome, which is not commonly found in this species. The S-type plastome has a conserved 48 bp deletion not found in other types, which is responsible for the divergence of the S-type from the C-type plastome. Finally, a phylogenetic analysis shows that these plastomes cluster according to their types. Congruence between the nuclear genome and the plastome phylogeny of these accessions was seen, however with considerable differences, supporting the hypothesis of introgression and hybridization between potato species.
Project description:Hybrid assemblies are highly valuable for studies of Enterobacteriaceae due to their ability to fully resolve the structure of mobile genetic elements, such as plasmids, which are involved in the carriage of clinically important genes (e.g. those involved in antimicrobial resistance/virulence). The widespread application of this technique is currently primarily limited by cost. Recent data have suggested that non-inferior, and even superior, hybrid assemblies can be produced using a fraction of the total output from a multiplexed nanopore [Oxford Nanopore Technologies (ONT)] flowcell run. In this study we sought to determine the optimal minimal running time for flowcells when acquiring reads for hybrid assembly. We then evaluated whether the ONT wash kit might allow users to exploit shorter running times by sequencing multiple libraries per flowcell. After 24?h of sequencing, most chromosomes and plasmids had circularized and there was no benefit associated with longer running times. Quality was similar at 12?h, suggesting that shorter running times are likely to be acceptable for certain applications (e.g. plasmid genomics). The ONT wash kit was highly effective in removing DNA between libraries. Contamination between libraries did not appear to affect subsequent hybrid assemblies, even when the same barcodes were used successively on a single flowcell. Utilizing shorter run times in combination with between-library nuclease washes allows at least 36 Enterobacteriaceae isolates to be sequenced per flowcell, significantly reducing the per-isolate sequencing cost. Ultimately this will facilitate large-scale studies utilizing hybrid assembly, advancing our understanding of the genomics of key human pathogens.
Project description:Yersinia spp. are animal pathogens, some of which cause human disease. We sequenced 10 Yersinia isolates (from six species: Yersinia enterocolitica, Y. fredericksenii, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, and Y. ruckeri) to high-quality draft or complete status. The genomes range in size from 3.77 to 4.94 Mbp.
Project description:Rubber oxygenase A (RoxA) is one of only two known enzymes able to catalyze the oxidative cleavage of latex for biodegradation. RoxA acts as a processive dioxygenase to yield the predominant product 12-oxo-4,8-dimethyl-trideca-4,8-diene-1-al (ODTD), a tri-isoprene unit. Here we present a structural analysis of RoxA from Xanthomonas sp. strain 35Y at a resolution of 1.8 Å. The enzyme is a 75-kDa diheme c-type cytochrome with an unusually low degree of secondary structure. Analysis of the heme group arrangement and peptide chain topology of RoxA confirmed a distant kinship with diheme peroxidases of the CcpA family, but the proteins are functionally distinct, and the extracellular RoxA has evolved to have twice the molecular mass by successively accumulating extensions of peripheral loops. RoxA incorporates both oxygen atoms of its cosubstrate dioxygen into the rubber cleavage product ODTD, and we show that RoxA is isolated with O2 stably bound to the active site heme iron. Activation and cleavage of O2 require binding of polyisoprene, and thus the substrate needs to use hydrophobic access channels to reach the deeply buried active site of RoxA. The location and nature of these channels support a processive mechanism of latex cleavage.
Project description:Extraintestinal pathogenic Escherichia coli (ExPEC) is an important source of multidrug-resistant infections, particularly in hospitals. We report hybrid Nanopore-Illumina assemblies for 5 ExPEC isolates with various drug resistance profiles.
Project description:Iron is a vital nutrient to bacteria, not only in the basal metabolism but also for virulent species in infection and pathogenicity at their hosts. Despite its relevance, the role of iron in Xanthomonas citri infection, the etiological agent of citrus canker disease, is poorly understood in contrast to other pathogens, including other members of the Xanthomonas genus. In this review, we present iron assimilation pathways in X. citri including the ones for siderophore production and siderophore-iron assimilation, proven to be key factors to virulence in many organisms like Escherichia coli and Xanthomonas campestris. Based on classical iron-related proteins previously characterized in E. coli, Pseudomonas aeruginosa, and also Xanthomonadaceae, we identified orthologs in X. citri and evaluated their sequences, structural characteristics such as functional motifs, and residues that support their putative functions. Among the identified proteins are TonB-dependent receptors, periplasmic-binding proteins, active transporters, efflux pumps, and cytoplasmic enzymes. The role of each protein for the bacterium was analyzed and complemented with proteomics data previously reported. The global view of different aspects of iron regulation and nutrition in X. citri virulence and pathogenesis may help guide future investigations aiming the development of new drug targets against this important phytopathogen.
Project description:Neonatal meningitis-causing Escherichia coli isolates (SP-4, SP-5, SP-13, SP-46, and SP-65) were recovered between 1989 and 1997 from infants in the Netherlands. Here, we report the draft genome sequences of these five E. coli isolates, which are currently being used to validate food safety processing technologies.
Project description:The present article reports the development of soft nanohybrids comprising of single walled carbon nanotube (SWCNT) included silver nanoparticles (AgNPs) having superior antibacterial property. In this regard aqueous dispersing agent of carbon nanotube (CNT) containing a silver ion reducing unit was synthesised by the inclusion of tryptophan and tyrosine within the backbone of the amphiphile. The dispersions were characterized spectroscopically and microscopically using TEM, AFM and Raman spectroscopy. The nanotube-nanoparticle conjugates were prepared by the in situ photoreduction of AgNO3. The phenolate residue and the indole moieties of tyrosine and tryptophan, respectively reduces the sliver ion as well as acts as stabilizing agents for the synthesized AgNPs. The nanohybrids were characterized using TEM and AFM. The antibacterial activity of the nanohybrids was studied against Gram-positive (Bacillus subtilis and Micrococcus luteus) and Gram-negative bacteria (Escherichia coli and Klebsiella aerogenes). The SWCNT dispersions showed moderate killing ability (40-60%) against Gram-positive bacteria however no antibacterial activity was observed against the Gram negative ones. Interestingly, the developed SWCNT-amphiphile-AgNP nanohybrids exhibited significant killing ability (?90%) against all bacteria. Importantly, the cell viability of these newly developed self-assemblies was checked towards chinese hamster ovarian cells and high cell viability was observed after 24 h of incubation. This specific killing of bacterial cells may have been achieved due to the presence of higher -SH containing proteins in the cell walls of the bacteria. The developed nanohybrids were subsequently infused into tissue engineering scaffold agar-gelatin films and the films similarly showed bactericidal activity towards both kinds of bacterial strains while allowing normal growth of eukaryotic cells on the surface of the films.