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A mesophilic, anaerobic, endospore-forming, fermentative bacterium designated strain 8C15bT was isolated from bank sediment of the Bach Dang Estuary, Haiphong, Vietnam. The Bach Dang Estuary, where Haiphong harbour is located, is subject to strong anthropogenic influence, resulting in high concentrations of black carbon and heavy metals. Strain 8C15bT grew optimally at 30â°C, pH 7.5 and with 2.5â% (w/v) NaCl. The main cellular fatty acids consisted of iso-C15â:â0 (51â%), iso-C15:1 ω7c (32â%) and iso-C13â:â0 (5â%). Genomic considerations of strain 8C15bT and comparisons with the phylogenetically closest strains of the genus Tepidibacter provide evidence that Tepidibacter thalassicus SC562T (=DSM 15285T), Tepidibacter formicigenes DV1184T (=DSM 15518T), Tepidibacter mesophilus B1T (=JCM 16806T) and strain 8C15bT could be differentiated at the species level. We propose the name Tepidibacter aestuarii sp. nov. for the type strain 8C15bT (=JCM 35983T=KCTC 25692T). Finally, the nickel-tolerance properties of strain 8C15bT are highlighted in this study.
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Estuarios , Ácidos Grasos , Ácidos Grasos/química , Vietnam , Análisis de Secuencia de ADN , Filogenia , Composición de Base , ADN Bacteriano/genética , ARN Ribosómico 16S/genética , Técnicas de Tipificación Bacteriana , Fosfolípidos/químicaRESUMEN
Herein, we report a rapid and scalable continuous-flow photocatalytic approach for the carbamoylation of nitrones. This protocol makes use of readily available 4-amido-1,4 dihydropyridines as carbamoyl radical precursors. The scope of this transformation exhibits high compatibility with complex structures containing amino acids, peptides, and glycosides. Importantly, the developed method allows a photocatalytic synthetic strategy in combination with flow conditions, maximizing the potential and efficiency for the synthesis of valuable α-(N-hydroxy)amino amides.
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C-Glycosyl compounds have gained considerable attention over the last few decades due to their high chemical stability and promising applications in drug discovery. Herein we disclose an operationally simple, metal-free, photocatalytic approach for the glycosylation of azomethine imines using 4-glycosyl-1,4-dihydropyridines (DHPs) as radical precursors. The protocol features mild reaction conditions, scalability, broad substrate scope, and good functional group tolerance. Moreover, the resulting pyrazolidinone moiety can be easily deprotected, acylated or reduced into a glycosyl ß-alanine analog.
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Self-transmissible mobile genetic elements drive horizontal gene transfer between prokaryotes. Some of these elements integrate in the chromosome, whereas others replicate autonomously as plasmids. Recent works showed the existence of few differences, and occasional interconversion, between the two types of elements. Here, we enquired on why evolutionary processes have maintained the two types of mobile genetic elements by comparing integrative and conjugative elements (ICE) with extrachromosomal ones (conjugative plasmids) of the highly abundant MPFT conjugative type. We observed that plasmids encode more replicases, partition systems, and antibiotic resistance genes, whereas ICEs encode more integrases and metabolism-associated genes. ICEs and plasmids have similar average sizes, but plasmids are much more variable, have more DNA repeats, and exchange genes more frequently. On the other hand, we found that ICEs are more frequently transferred between distant taxa. We propose a model where the different genetic plasticity and amplitude of host range between elements explain the co-occurrence of integrative and extrachromosomal elements in microbial populations. In particular, the conversion from ICE to plasmid allows ICE to be more plastic, while the conversion from plasmid to ICE allows the expansion of the element's host range.
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Conjugación Genética , Secuencias Repetitivas Esparcidas , Plásmidos , Proteobacteria/genéticaRESUMEN
Restriction-modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.
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Bacterias/genética , Bacterias/inmunología , Transferencia de Gen Horizontal , Inmunidad Innata , Genoma Bacteriano , Recombinación HomólogaRESUMEN
The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.
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Enzimas de Restricción-Modificación del ADN/genética , Genoma Arqueal , Genoma Bacteriano , Secuencias Repetitivas Esparcidas , Sistemas CRISPR-Cas , Evolución Molecular , Transferencia de Gen Horizontal , Profagos/genéticaRESUMEN
Genomic instability is recognized as one of the most important hurdles in the expanding field of stem cell-based therapies. In the recent years, an accumulating body of evidence has shown that human stem cells undergo a diverse program of biological changes upon ex vivo cultivation that include numerical and structural chromosomal abnormalities, point mutations, variation of telomere length, and epigenetic instability. As the field moves forward, the growing awareness of the risk factors associated with human genome plasticity strongly advocates for the use of extensive genetic screening as part of a quality control platform to attest to the safety of stem cell-based products. Here we present a timely and comprehensive review that addresses the current status and emerging trends of the field, ultimately underscoring the need to implement new regulatory standards able to streamline the route to therapeutic applications.
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Diferenciación Celular/genética , Aberraciones Cromosómicas , Inestabilidad Genómica/genética , Células Madre Pluripotentes Inducidas/citología , Trasplante de Células Madre , Animales , Humanos , Trasplante de Células Madre/métodos , Telómero/genéticaRESUMEN
Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a meta-analysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3' region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability.
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Bacteriófagos/genética , Elementos Transponibles de ADN , ADN Bacteriano/genética , ADN Viral/genética , Escherichia coli/genética , Mutagénesis Insercional , Plásmidos/genéticaRESUMEN
Bacteria have developed various defense mechanisms to avoid infection and killing in response to the fast evolution and turnover of viruses and other genetic parasites. Such pan-immune system (defensome) encompasses a growing number of defense lines that include well-studied innate and adaptive systems such as restriction-modification, CRISPR-Cas and abortive infection, but also newly found ones whose mechanisms are still poorly understood. While the abundance and distribution of defense systems is well-known in complete and culturable genomes, there is a void in our understanding of their diversity and richness in complex microbial communities. Here we performed a large-scale in-depth analysis of the defensomes of 7759 high-quality bacterial population genomes reconstructed from soil, marine, and human gut environments. We observed a wide variation in the frequency and nature of the defensome among large phyla, which correlated with lifestyle, genome size, habitat, and geographic background. The defensome's genetic mobility, its clustering in defense islands, and genetic variability was found to be system-specific and shaped by the bacterial environment. Hence, our results provide a detailed picture of the multiple immune barriers present in environmentally distinct bacterial communities and set the stage for subsequent identification of novel and ingenious strategies of diversification among uncultivated microbes.
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Bacterias , Genoma Bacteriano , Humanos , Bacterias/genética , Metagenómica , Tamaño del Genoma , Sistemas CRISPR-CasRESUMEN
The kinetics of sulfur transfer from titanocene (poly)sulfides (RCp2TiS5, Cp2TiS4CMe2, Cp2Ti(SAr)2, Cp2TiCl(SAr)) to sulfenyl chlorides (S2Cl2, RSCl) have been investigated by a combination of stopped-flow UV-Vis/NMR reaction monitoring, titration assays, numerical kinetic modelling and KS-DFT calculations. The reactions are rapid, proceeding to completion over timescales of milliseconds to minutes, via a sequence of two S-S bond-forming steps (k 1, k 2). The archetypical polysulfides Cp2TiS5 (1a) and Cp2TiS4C(Me2) (2a) react with disulfur dichloride (S2Cl2) through rate-limiting intermolecular S-S bond formation (k 1) followed by a rapid intramolecular cyclization (k 2, with k 2 â« k 1 [RSCl]). The monofunctional sulfenyl chlorides (RSCl) studied herein react in two intermolecular S-S bond forming steps proceeding at similar rates (k 1 ≈ k 2). Reactions of titanocene bisthiophenolates, Cp2Ti(SAr)2 (5), with both mono- and di-functional sulfenyl chlorides result in rapid accumulation of the monothiophenolate, Cp2TiCl(SAr) (6) (k 1 > k 2). Across the range of reactants studied, the rates are relatively insensitive to changes in temperature and in the electronics of the sulfenyl chloride, moderately sensitive to the electronics of the titanocene (poly)sulfide (ρ (Ti-(SAr)) ≈ -2.0), and highly sensitive to the solvent polarity, with non-polar solvents (CS2, CCl4) leading to the slowest rates. The combined sensitivities are the result of a concerted, polarized and late transition state for the rate-limiting S-S bond forming step, accompanied by a large entropic penalty. Each substitution step {[Ti]-SR' + Cl-SR â [Ti]-Cl + RS-SR'} proceeds via titanium-assisted Cl-S cleavage to generate a transient pentacoordinate complex, Cl-[Cp2TiX]-S(R')-SR, which then undergoes rapid Ti-S dissociation.
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Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.
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Antozoos , Microbiota , Animales , Arrecifes de Coral , Océano Pacífico , Biodiversidad , Peces , PlanctonRESUMEN
Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.
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Antozoos , Arrecifes de Coral , Animales , Biodiversidad , EcosistemaRESUMEN
The preparation of amide-containing compounds is among the most interesting and challenging topics for the synthetic community. Such relevance is given by their reactive aspects explored in the context of organic synthesis and by the direct application of these compounds as pharmaceuticals and useful materials, and their key roles in biological structures. A simple and straightforward strategy for the amide moiety installation is the use of carbamoyl radicals - this nucleophilic one-electron intermediate is prone to undergo a series of transformations, providing a range of structurally relevant derivatives. In this review, we summarize the latest advances in the field from the perspective of photoinduced protocols. To this end, their synthetic applications are organized accordingly to the nature of the radical precursor (formamides through HAT, 4-substituted-1,4-dihydropyridines, oxamic acids, and N-hydroxyphthalimido esters), the mechanistic aspects also being highlighted. The discussion also includes a recent approach proceeding via photolytic C-S cleavage of dithiocarbamate-carbamoyl intermediates. By exploring fundamental concepts, this material aims to offer an understanding of the topic, which will encourage and facilitate the design of new synthetic strategies applying the carbamoyl radical.
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Formamidas , Carbamilación de Proteína , Amidas , Técnicas de Química SintéticaRESUMEN
We report the complete genome sequence of Tepidibacter sp. strain 8C15b, isolated from bank sediments of Haiphong Bay, Vietnam. The genome includes a 3,628,320-bp circular chromosome and a plasmid of 38,213 bp.
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Epigenetic DNA methylation in bacteria has been traditionally studied in the context of antiparasitic defense and as part of the innate immune discrimination between self and nonself DNA. However, sequencing advances that allow genome-wide analysis of DNA methylation at the single-base resolution are nowadays expanding and have propelled a modern epigenomic revolution in our understanding of the extent, evolution, and physiological relevance of methylation. Indeed, as the number of mapped bacterial methylomes recently surpassed 4,000, increasing evidence supports roles for methylation in gene expression regulation, virulence, and host colonization, among others. In this paper, I summarize lessons taken from high-dimensional methylome data analyses and recent efforts that we and others are developing to leverage such findings into meaningful biological insights and overarching frameworks. Ultimately, I highlight anticipated research avenues and technological developments likely to unfold in the coming years.
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An increasing number of studies have reported that bacterial DNA methylation has important functions beyond the roles in restriction-modification systems, including the ability of affecting clinically relevant phenotypes such as virulence, host colonization, sporulation, biofilm formation, among others. Although insightful, such studies have a largely ad hoc nature and would benefit from a systematic strategy enabling a joint functional characterization of bacterial methylomes by the microbiology community. In this opinion article, we propose that highly conserved DNA methyltransferases (MTases) represent a unique opportunity for bacterial epigenomic studies. These MTases are rather common in bacteria, span various taxonomic scales, and are present in multiple human pathogens. Apart from well-characterized core DNA MTases, like those from Vibrio cholerae, Salmonella enterica, Clostridioides difficile, or Streptococcus pyogenes, multiple highly conserved DNA MTases are also found in numerous human pathogens, including those belonging to the genera Burkholderia and Acinetobacter. We discuss why and how these MTases can be prioritized to enable a community-wide, integrative approach for functional epigenomic studies. Ultimately, we discuss how some highly conserved DNA MTases may emerge as promising targets for the development of novel epigenetic inhibitors for biomedical applications.
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Bacterias/enzimología , Bacterias/genética , Proteínas Bacterianas/metabolismo , Metilasas de Modificación del ADN/metabolismo , Animales , Bacterias/metabolismo , Infecciones Bacterianas/microbiología , Proteínas Bacterianas/genética , Metilación de ADN , Metilasas de Modificación del ADN/genética , Epigénesis Genética , HumanosRESUMEN
A versatile and robust photocatalytic methodology to install the amide functional group into azomethine imine ions is described. This protocol is distinguished by its broad scope and mild reaction conditions, which are well suited for the preparation of structurally complex compounds in the form of amino acids, peptides, and small drug-like molecules. Moreover, the generated pyrazolidinone core could be easily converted into ß-alanine analogues.
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Structural instability has been frequently observed in natural plasmids and vectors used for protein expression or DNA vaccine development. However, there is a lack of information concerning hotspot mapping, namely, DNA repeats or sequences identical to the host genome. This led us to evaluate the abundance and distribution of direct, inverted, and tandem repeats with high recombination potential in 36 natural plasmids from ten bacterial genera, as well as in several widely used bacterial and mammalian expression vectors. In natural plasmids, we observed an overrepresentation of close direct repeats in comparison to inverted ones and a preferential location of repeats with high recombination potential in intergenic regions, suggesting a highly plastic and dynamic behavior. In plasmid vectors, we found a high density of repeats within eukaryotic promoters and non-coding sequences. As a result of this in silico analysis, we detected a spontaneous recombination between two 21-bp direct repeats present in the human cytomegalovirus early enhancer/promoter (huCMV EEP) of the pCIneo plasmid. This finding is of particular importance, as the huCMV EEP is one of the most frequently used regulatory elements in plasmid vectors. Because pDNA integration into host gDNA can have adverse consequences in terms of plasmid processing and host safety, we also mapped several regions with high probability to mediate integration into the Escherichia coli or human genomes. Like repeated regions, some of these were located in non-coding regions of the plasmids, thus being preferential targets to be removed.
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Bacterias/genética , Inestabilidad Genómica , Plásmidos/genética , Secuencias Repetitivas de Ácidos Nucleicos , Secuencia de Bases , Genoma Humano , Humanos , Datos de Secuencia MolecularRESUMEN
An amendment to this paper has been published and can be accessed via a link at the top of the paper.