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Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The …

Plasmid conjugation is a major route for the dissemination of antibiotic resistances and adaptive genes among bacterial populations. Obtaining precise conjugation rates is thus key to understanding how antibiotic resistances spread. Plasmid conjugation is typically modeled as a density-dependent process, where the formation of new transconjugants is proportional to the rate of encounters between donor and recipient bacteria. By analyzing conjugation dynamics at different cell concentrations, here we show that this assumption only holds at low bacterial densities. At higher concentrations, plasmid transmission switches from a density-dependent process to a frequency-dependent one. Mathematical modeling revealed that plasmid conjugation follows a Holling's Type II functional response, characterized by two fundamental parameters: the searching rate and the handling time. These parameters represent, respectively, the density and frequency dependent limits for plasmid transmission. Our results demonstrate that these parameters are characteristic of the transfer machinery, rather than the entire plasmid genome, and that they are robust to environmental and transcriptional perturbation. Precise parameterization of plasmid conjugation will contribute to a better understanding of the propagation dynamics of antimicrobial resistances.

Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).

Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve …

Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve …

Public health genomic surveillance systems typically measure genome relatedness and infer molecular epidemiological relationships using chromosomal loci alone - an approximation of vertical evolution, or homology-by-descent. The accessory genome, composed of plasmids and other mobile genetic elements, reflects horizontal gene transfer and serves as an important mechanism of bacterial evolution, enabling rapid adaptation. Measuring homology in the accessory genome - homology-by-admixture - could offer important molecular epidemiological information for public health application. We applied Jaccard Index and a novel genome length distance metric to compute pangenome relatedness for the globally-important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both homology-by-descent and homology-by-admixture in a reticulate network. Jaccard Index Network Analysis revealed structure in the Typhi pangenome that can be harnessed to enhance discriminatory power for surveillance, track antimicrobial resistance, and refine our understanding of homology for outbreak management and prevention. This offers a more intricate, multidimensional framework for understanding pathogen evolution.

High throughput sequencing has recently revealed the presence of Tetragenococcus-related DNA sequences in dairy environments such as brine and cheeses. In the present work, a selective medium was developed to isolate Tetragenococcus spp. from two ripened, traditional, Spanish, blue-veined cheese varieties made from raw milk. The strains recovered belonged to either Tetragenococcus koreensis or Tetragenococcus halophilus species. Twenty of these isolates (15 of T. koreensis and 5 of T. halophilus) were then subjected to a battery of phenotypic and genetic tests, and six strains (4 T. koreensis and 2 T. halophilus) to genome sequencing. Wide genetic and phenotypic diversity was noted. All strains grew poorly in milk, producing small quantities of lactic and acetic acids. Most strains used lactose as a carbon source and ferment milk citrate. In agreement, genome analysis detected in the genome of the six strains analyzed gene clusters harboring several lactose/galactose-related genes and genes encoding citrate metabolic enzymes (permease, citrate lyase, and oxaloacetate decarboxylase). Most of the tested strains were resistant to erythromycin and clindamycin, and a few to other antimicrobial agents, but neither known mutations nor acquired genes conferring resistance to antibiotics were identified in their genomes. Neither were genes coding for pathogenicity or virulence factors detected. Decarboxylase-encoding genes involved in biogenic amine production were not identified, in keeping with the strains' negative biogenic amine-producer phenotype. Genome comparison revealed vast arrays of genes (similar in number to those …

Genetic interventions on microbiomes, for clinical or biotechnological purposes, remain challenging. Conjugation-based delivery of genetic cargo is still unspecific and limited by low conjugation rates. Here we report an approach to overcome these problems, based on a synthetic bacterial adhesion system. Mating assemblers consist on a synthetic adhesion formed by the expression on the surface of donor and target cells of specific nanobodies (Nb) and their cognate antigen (Ag). The Nb–Ag bridge increased 1–3 logs transfer of a variety of plasmids, especially in liquid media, confirming that cell-cell docking is a main determinant limiting mating efficiency. Synthetic cell-to-cell adhesion allows efficient conjugation to targeted recipients, enhancing delivery of desired genes to a predefined subset of prey species, or even specific pathogenic strains such as enterohemorrhagic Escherichia coli (EHEC), within a …

Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to conjugate autonomously, the others being eventually mobilizable by conjugation. To understand the evolution of plasmid mobility, we studied plasmid size, gene repertoires, and conjugation-related genes. Plasmid gene repertoires were found to vary rapidly in relation to the evolutionary rate of relaxases, for example, most pairs of plasmids with 95% identical relaxases have fewer than 50% of homologs. Among 249 recent transitions of mobility type, we observed a clear excess of plasmids losing the capacity to conjugate. These transitions are associated with even greater changes in gene repertoires, possibly mediated by transposable elements, including pseudogenization of the conjugation locus, exchange of replicases reducing the problem of incompatibility, and …

Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix–turn–helix domains. We then probed and confirmed that ArdK shows affinity for an …

Alpha-linolenic acid and stearidonic acid are precursors of omega-3 polyunsaturated fatty acids, essential nutrients in the human diet. The ability of cyanobacteria to directly convert atmospheric carbon dioxide into bio-based compounds makes them promising microbial chassis to sustainably produce omega-3 fatty acids. However, their potential in this area remains unexploited, mainly due to important gaps in our knowledge of fatty acid synthesis pathways. To gain insight into the cyanobacterial fatty acid biosynthesis pathways, we analyzed two enzymes involved in the elongation cycle, FabG and FabZ, in Synechococcus elongatus PCC 7942. Overexpression of these two enzymes led to an increase in C18 fatty acids, key intermediates in omega-3 fatty acid production. Nevertheless, coexpression of these enzymes with desaturases DesA and DesB from Synechococcus sp. PCC 7002 did not improve alpha-linolenic acid production, possibly due to their limited role in fatty acid synthesis. In any case, efficient production of stearidonic acid was not achieved by cloning DesD from Synechocystis sp. PCC 6803 in combination with the aforementioned DesA and DesB, reaching maximum production at 48 h post induction. According to current knowledge, this is the first report demonstrating that S. elongatus PCC 7942 can be used as an autotrophic chassis to produce stearidonic acid.

Despite being linked to a number of recent poultry-associated outbreaks in the United States, few reference genomes are available for Salmonella enterica serotype Hadar. Here, we address this need by reporting 18 Salmonella Hadar genomes from samples collected from patients in the United States between 2014 and 2020.

Plasmids transmissible by conjugation are responsible for disseminating antibiotic-resistance genes, making plasmid detection relevant for pathogen tracking. We describe the use of a multiplex PCR method for the experimental identification of specific plasmid taxonomic units (PTUs) of transmissible plasmids. The PCR primers were designed to target conserved segments of the relaxase MOB gene of PTUs encoding adaptive traits for enterobacteria (antimicrobial resistance, virulence, and metabolism). In this way, PlasTax-PCR detects the presence of these plasmids and allows their direct assignation to a PTU.

Low-copy-number plasmids require sophisticated genetic devices to achieve efficient segregation of plasmid copies during cell division. Plasmid R388 uses a unique segregation mechanism, based on StbA, a small multifunctional protein. StbA is the key protein in a segregation system not involving a plasmid-encoded NTPase partner, it regulates the expression of several plasmid operons, and it is the main regulator of plasmid conjugation. The mechanisms by which StbA, together with the centromere-like sequence stbS, achieves segregation, is largely uncharacterized. To better understand the molecular basis of R388 segregation, we determined the crystal structure of the conserved N-terminal domain of StbA to 1.9 Å resolution. It folds into an HTH DNA-binding domain, structurally related to that of the PadR subfamily II of transcriptional regulators. StbA is organized in two domains. Its N-terminal domain carries …

Between 2018 and 2019, Salmonella enterica serotype Reading caused a large, multistate outbreak linked to contact with raw turkey products in the United States. Here, we provide five Salmonella Reading reference genomes collected from US patients between 2016 and 2018.

Challenge 8: Synthetic life | DIGITAL.CSIC Skip navigation Logo pequeño DigitalCISC Producción CSIC Áreas e Institutos Navegar ítems por: Fecha Publicación Autor Título Palabras Clave Autor con perfil Proyecto de investigación Grupo de investigación Agencia Financiadora Fecha Envío Pasarela Estadísticas Contacto Servicios Mi DIGITAL.CSIC Suscripciones Editar perfil 1.DIGITAL.CSIC 2.Humanidades y Ciencias Sociales 3.Centro de Ciencias Humanas y Sociales - Instituto de Filosofía (CCHS-IFS) 4.(CCHS-IFS) Libros y partes de libros Por favor, use este identificador para citar o enlazar a este item: http://hdl.handle.net/10261/261347 COMPARTIR / EXPORTAR: logo share SHARE BASE Comparte tu historia de Acceso Abierto Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL | DATACITE Refman EndNote Bibtex RefWorks Excel CSV PDF DataCite Send via email Título: …

Los plásmidos median la transferencia genética horizontal de genes de virulencia, resistencia a antibióticos y otros factores adaptativos entre las poblaciones bacterianas. El análisis de la composición genómica de 10.000 plásmidos de referencia y su identidad por pares de secuencias proporcionó un mapa global del plasmidoma procariótico (1). En este mapa, los plásmidos se organizan en grupos discretos a los que hemos denominado unidades taxonómicas plasmídicas (o PTUs por las siglas en inglés de Plasmid Taxonomic Units), las cuales muestran alta identidad promedio de nucleótidos entre sus miembros. En este conjunto de datos identificamos un total de 276 PTUs en el dominio Bacteria, 83 de ellos en el orden Enterobacterales, y definimos el rango de hospedador característico de cada PTU. Más del 60% de los plásmidos en el mapa global están ubicados en grupos cuyo rango de hospedador supera la barrera de especie. La información generada se recogió en una web interactiva (https://castillo.dicom.unican.es/PlasmidID) que sirvió de base para desarrollar la herramienta bioinformática COPLA (2), un algoritmo automático para asignar la PTU a un plásmido en función de su secuencia (https://castillo.dicom.unican.es/ copla). Proponemos una clasificación taxonómica jerarquizada que incluye clases (por homología de la relaxasa MOB), familias (por homología del sistema conjugativo MPF) y especies o PTUs (por homología del esqueleto plasmídico).1. Redondo-Salvo S et al. Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids. Nature Communications. 2020 Jul 17;11(1):3602.2 …

The Salmonella enterica plasmidome | DIGITAL.CSIC Skip navigation Logo pequeño DigitalCISC Producción CSIC Áreas e Institutos Navegar ítems por: Fecha Publicación Autor Título Palabras Clave Autor con perfil Proyecto de investigación Grupo de investigación Agencia Financiadora Fecha Envío Pasarela Estadísticas Contacto Servicios Mi DIGITAL.CSIC Suscripciones Editar perfil 1.DIGITAL.CSIC 2.Biología y Biomedicina 3.Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) 4.(IBBTEC) Comunicaciones congresos Por favor, use este identificador para citar o enlazar a este item: http://hdl.handle.net/10261/262995 COMPARTIR / EXPORTAR: logo share SHARE BASE Comparte tu historia de Acceso Abierto Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL | DATACITE Refman EndNote Bibtex RefWorks Excel CSV PDF DataCite Send via email Título: The …

Background Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence. Results We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its …

El Sistema de Secreción Tipo VI (T6SS) es un complejo multiproteico presente en bacterias Gramnegativas que permite inyectar toxinas de una manera dependiente de contacto a otras células, tanto procariotas como eucariotas. Su papel es crítico en la competición en comunidades microbianas y en la patogenicidad. La presencia de este sistema en plataformas móviles tales como plásmidos, parece anecdótica ya que, hasta ahora, la mayoría de T6SSs funcionales descritos son cromosómicos. Sin embargo, nuestro análisis de la base de datos plasmídica NCBI RefSeq identificó una cantidad significativa de plásmidos que codifican T6SSs. La mayoría de estos plásmidos codifican, además, la maquinaria necesaria para ser transmitidos mediante conjugación, incorporando esta arma al proceso de transferencia genética horizontal. Hemos comprobado la actividad antibacteriana de uno de estos T6SSs codificado en un plásmido conjugativo. Esto plantea la pregunta de cómo influye esta actividad antibacteriana en la transferencia del propio plásmido y viceversa, pero sobre todo, cómo los plásmidos conjugativos que codifican para este T6SS son capaces de decidir entre matar a una célula vecina o utilizarla como receptora.