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1.
Cell ; 186(1): 47-62.e16, 2023 01 05.
Artículo en Inglés | MEDLINE | ID: mdl-36608657

RESUMEN

Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.


Asunto(s)
Ecosistema , Genoma Bacteriano , Genoma Bacteriano/genética , Filogenia , Océanos y Mares , Genómica
2.
Proc Natl Acad Sci U S A ; 121(11): e2314606121, 2024 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-38446847

RESUMEN

Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.


Asunto(s)
Virus Gigantes , Estramenopilos , Virosis , Humanos , Virófagos , Virus Gigantes/genética , Estramenopilos/genética , Antivirales
3.
Proc Natl Acad Sci U S A ; 120(16): e2300465120, 2023 04 18.
Artículo en Inglés | MEDLINE | ID: mdl-37036967

RESUMEN

Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be "genomic fossils." Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses. These EVEs, composed of virophages, Polinton-like viruses, and related entities, have remained hitherto hidden owing to poor sequence conservation between virus groups and their repetitive nature that precluded accurate short-read assembly. We show that long-read sequencing technology is ideal for resolving virus insertions. Many protist EVEs appear intact, and most encode integrases, which suggests that they have actively colonized hosts across the tree of eukaryotes. We also found evidence for gene expression in host transcriptomes and that closely related virophage and Polinton-like virus genomes are abundant in viral metagenomes, indicating that many EVEs are probably functional viruses.


Asunto(s)
Eucariontes , Virus , Animales , Eucariontes/genética , Virus ADN/genética , Virus/genética , Virófagos , Genoma Viral/genética , Filogenia
4.
Proc Natl Acad Sci U S A ; 120(20): e2213271120, 2023 05 16.
Artículo en Inglés | MEDLINE | ID: mdl-37159478

RESUMEN

Marine picocyanobacteria Prochlorococcus and Synechococcus, the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, while studying the ability of picocyanobacteria to supplement photosynthetic carbon fixation with the use of exogenous organic carbon, we found the widespread occurrence of genes for breaking down chitin, an abundant source of organic carbon that exists primarily as particles. We show that cells that encode a chitin degradation pathway display chitin degradation activity, attach to chitin particles, and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated soluble form of chitin. Marine chitin is largely derived from arthropods, which underwent major diversifications 520 to 535 Mya, close to when marine picocyanobacteria are inferred to have appeared in the ocean. Phylogenetic analyses confirm that the chitin utilization trait was acquired at the root of marine picocyanobacteria. Together this leads us to postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Subsequently, transitioning to a constitutive planktonic life without chitin associations led to cellular and genomic streamlining along a major early branch within Prochlorococcus. Our work highlights how the emergence of associations between organisms from different trophic levels, and their coevolution, creates opportunities for colonizing new environments. In this view, the rise of ecological complexity and the expansion of the biosphere are deeply intertwined processes.


Asunto(s)
Quitosano , Prochlorococcus , Quitina , Ecosistema , Filogenia , Carbono , Plancton/genética , Prochlorococcus/genética
5.
Proc Natl Acad Sci U S A ; 119(11): e2113386119, 2022 03 15.
Artículo en Inglés | MEDLINE | ID: mdl-35254902

RESUMEN

SignificancePhosphonates are a class of phosphorus metabolites characterized by a highly stable C-P bond. Phosphonates accumulate to high concentrations in seawater, fuel a large fraction of marine methane production, and serve as a source of phosphorus to microbes inhabiting nutrient-limited regions of the oligotrophic ocean. Here, we show that 15% of all bacterioplankton in the surface ocean have genes phosphonate synthesis and that most belong to the abundant groups Prochlorococcus and SAR11. Genomic and chemical evidence suggests that phosphonates are incorporated into cell-surface phosphonoglycoproteins that may act to mitigate cell mortality by grazing and viral lysis. These results underscore the large global biogeochemical impact of relatively rare but highly expressed traits in numerically abundant groups of marine bacteria.


Asunto(s)
Organismos Acuáticos/metabolismo , Organofosfonatos/metabolismo , Organismos Acuáticos/genética , Bacterias/genética , Bacterias/metabolismo , Regulación Bacteriana de la Expresión Génica , Transferencia de Gen Horizontal , Genes Bacterianos , Modelos Biológicos , Prochlorococcus/genética , Prochlorococcus/metabolismo , Carácter Cuantitativo Heredable , Agua de Mar/microbiología
6.
Appl Environ Microbiol ; 90(4): e0012924, 2024 Apr 17.
Artículo en Inglés | MEDLINE | ID: mdl-38470030

RESUMEN

Archaeal viruses are among the most enigmatic members of the virosphere, and their diverse morphologies raise many questions about their infection mechanisms. The study of molecular mechanisms underlying virus-host interactions hinges upon robust model organisms with a system for gene expression and deletion. Currently, there are only a limited number of archaea that have associated viruses and have a well-developed genetic system. Here, we report the development of a genetic system for the euryarchaeon Haloferax gibbonsii LR2-5. This strain can be infected by multiple viruses and is a model for the study of virus-host interactions. We created a Hfx. gibbonsii LR2-5 ∆pyrE strain, resulting in uracil auxotrophy, which could be used as a selection marker. An expression plasmid carrying a pyrE gene from the well-established Haloferax volcanii system was tested for functionality. Expression of a GFP-MinD fusion under a tryptophan inducible promoter was fully functional and showed similar cellular localization as in Hfx. volcanii. Thus, the plasmids of the Hfx. volcanii system can be used directly for the Hfx. gibbonsii LR2-5 genetic system, facilitating the transfer of tools between the two. Finally, we tested for the functionality of gene deletions by knocking out two genes of the archaeal motility structure, the archaellum. These deletion mutants were as expected non-motile and the phenotype of one deletion could be rescued by the expression of the deleted archaellum gene from a plasmid. Thus, we developed a functional genetic toolbox for the euryarchaeal virus host Hfx. gibbonsii LR2-5, which will propel future studies on archaeal viruses. IMPORTANCE: Species from all domains of life are infected by viruses. In some environments, viruses outnumber their microbial hosts by a factor of 10, and viruses are the most important predators of microorganisms. While much has been discovered about the infection mechanisms of bacterial and eukaryotic viruses, archaeal viruses remain understudied. Good model systems are needed to study their virus-host interactions in detail. The salt-loving archaeon Haloferax gibbonsii LR2-5 has been shown to be infected by a variety of different viruses and, thus, is an excellent model to study archaeal viruses. By establishing a genetic system, we have significantly expanded the toolbox for this model organism, which will fuel our understanding of infection strategies of the underexplored archaeal viruses.


Asunto(s)
Proteínas Arqueales , Haloferax volcanii , Haloferax , Virus , Haloferax/genética , Eliminación de Gen , Haloferax volcanii/genética , Haloferax volcanii/metabolismo , Regiones Promotoras Genéticas , Virus/genética , Proteínas Arqueales/genética
7.
Bioinformatics ; 36(22-23): 5514-5515, 2021 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-33258916

RESUMEN

MOTIVATION: The generation of high-quality assemblies, even for large eukaryotic genomes, has become a routine task for many biologists thanks to recent advances in sequencing technologies. However, the annotation of these assemblies-a crucial step toward unlocking the biology of the organism of interest-has remained a complex challenge that often requires advanced bioinformatics expertise. RESULTS: Here, we present MOSGA (Modular Open-Source Genome Annotator), a genome annotation framework for eukaryotic genomes with a user-friendly web-interface that generates and integrates annotations from various tools. The aggregated results can be analyzed with a fully integrated genome browser and are provided in a format ready for submission to NCBI. MOSGA is built on a portable, customizable and easily extendible Snakemake backend, and thus, can be tailored to a wide range of users and projects. AVAILABILITY AND IMPLEMENTATION: We provide MOSGA as a web service at https://mosga.mathematik.uni-marburg.de and as a docker container at registry.gitlab.com/mosga/mosga: latest. Source code can be found at https://gitlab.com/mosga/mosga. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Genoma , Programas Informáticos , Eucariontes
8.
Nature ; 540(7632): 288-291, 2016 12 07.
Artículo en Inglés | MEDLINE | ID: mdl-27929021

RESUMEN

Endogenous viral elements are increasingly found in eukaryotic genomes, yet little is known about their origins, dynamics, or function. Here we provide a compelling example of a DNA virus that readily integrates into a eukaryotic genome where it acts as an inducible antiviral defence system. We found that the virophage mavirus, a parasite of the giant Cafeteria roenbergensis virus (CroV), integrates at multiple sites within the nuclear genome of the marine protozoan Cafeteria roenbergensis. The endogenous mavirus is structurally and genetically similar to eukaryotic DNA transposons and endogenous viruses of the Maverick/Polinton family. Provirophage genes are not constitutively expressed, but are specifically activated by superinfection with CroV, which induces the production of infectious mavirus particles. Virophages can inhibit the replication of mimivirus-like giant viruses and an anti-viral protective effect of provirophages on their hosts has been hypothesized. We find that provirophage-carrying cells are not directly protected from CroV; however, lysis of these cells releases infectious mavirus particles that are then able to suppress CroV replication and enhance host survival during subsequent rounds of infection. The microbial host-parasite interaction described here involves an altruistic aspect and suggests that giant-virus-induced activation of provirophages might be ecologically relevant in natural protist populations.


Asunto(s)
Genoma/genética , Virus Gigantes/fisiología , Interacciones Huésped-Parásitos , Estramenopilos/genética , Estramenopilos/virología , Virófagos/crecimiento & desarrollo , Integración Viral , Elementos Transponibles de ADN/genética , Regulación Viral de la Expresión Génica , Genoma Viral/genética , Virus Gigantes/genética , Virus Gigantes/crecimiento & desarrollo , Mimiviridae/crecimiento & desarrollo , Profagos/genética , Profagos/fisiología , Estramenopilos/crecimiento & desarrollo , Sobreinfección , Virión/crecimiento & desarrollo , Virófagos/genética , Liberación del Virus , Replicación Viral
9.
Appl Environ Microbiol ; 86(24)2020 11 24.
Artículo en Inglés | MEDLINE | ID: mdl-33097507

RESUMEN

Stenotrophomonas maltophilia is one of the most frequently isolated multidrug-resistant nosocomial opportunistic pathogens. It contributes to disease progression in cystic fibrosis (CF) patients and is frequently isolated from wounds, infected tissues, and catheter surfaces. On these diverse surfaces S. maltophilia lives in single-species or multispecies biofilms. Since very little is known about common processes in biofilms of different S. maltophilia isolates, we analyzed the biofilm profiles of 300 clinical and environmental isolates from Europe of the recently identified main lineages Sgn3, Sgn4, and Sm2 to Sm18. The analysis of the biofilm architecture of 40 clinical isolates revealed the presence of multicellular structures and high phenotypic variability at a strain-specific level. Further, transcriptome analyses of biofilm cells of seven clinical isolates identified a set of 106 shared strongly expressed genes and 33 strain-specifically expressed genes. Surprisingly, the transcriptome profiles of biofilm versus planktonic cells revealed that just 9.43% ± 1.36% of all genes were differentially regulated. This implies that just a small set of shared and commonly regulated genes is involved in the biofilm lifestyle. Strikingly, iron uptake appears to be a key factor involved in this metabolic shift. Further, metabolic analyses implied that S. maltophilia employs a mostly fermentative growth mode under biofilm conditions. The transcriptome data of this study together with the phenotypic and metabolic analyses represent so far the largest data set on S. maltophilia biofilm versus planktonic cells. This study will lay the foundation for the identification of strategies for fighting S. maltophilia biofilms in clinical and industrial settings.IMPORTANCE Microorganisms living in a biofilm are much more tolerant to antibiotics and antimicrobial substances than planktonic cells are. Thus, the treatment of infections caused by microorganisms living in biofilms is extremely difficult. Nosocomial infections (among others) caused by S. maltophilia, particularly lung infection among CF patients, have increased in prevalence in recent years. The intrinsic multidrug resistance of S. maltophilia and the increased tolerance to antimicrobial agents of its biofilm cells make the treatment of S. maltophilia infection difficult. The significance of our research is based on understanding the common mechanisms involved in biofilm formation of different S. maltophilia isolates, understanding the diversity of biofilm architectures among strains of this species, and identifying the differently regulated processes in biofilm versus planktonic cells. These results will lay the foundation for the treatment of S. maltophilia biofilms.


Asunto(s)
Biopelículas , Genes Bacterianos , Variación Genética , Stenotrophomonas maltophilia/fisiología , Stenotrophomonas maltophilia/patogenicidad , Europa (Continente) , Perfilación de la Expresión Génica , Fenotipo , Proteolisis , Stenotrophomonas maltophilia/genética , Virulencia
10.
J Proteome Res ; 18(6): 2458-2466, 2019 06 07.
Artículo en Inglés | MEDLINE | ID: mdl-31058502

RESUMEN

A recent field of metabolomic applications is the analysis of mixtures, for example, in food science or the early recognition of diseases. Particularly in large-scale studies, the number of intermediate states or mixtures tends to expand significantly and in practice, a manual analysis is extremely difficult if not nearly impossible. In this study, we present a model in which the NMR spectra of mixtures are calculated based on the spectral superposition of corresponding pure samples. Instead of using real spectra, where chemical shifts may be influenced by matrix effects, the linear combination of reduced data (buckets) was applied for the calculation. Starting from a set of 262 hazelnut samples of five Eurasian countries we obtained more than 160 000 NMR spectra with mixed geographic origin. Using these as a basis we calculated assessment curves to estimate to which extent admixtures are recognized within a multivariate classification model. Subsequently the calculated data were compared with the measured spectra of tangible mixtures to validate and assess the suitability of this method. The calculated spectra are very similar to the acquired data, and the resulting deviations are on a similar scale to the errors of current metabolomic measurements. Thus, with a suitable sample basis, various different mixtures can be simulated and limitations of the model can be described. This approach reduces time and resource consumption and allows valid predictions based on calculated NMR spectra. In addition to the first example dealing with the admixtures classification of single commodity foods, this approach may also be applied to simulate metabolic progression in other areas.


Asunto(s)
Corylus/genética , Análisis de los Alimentos , Metabolómica/métodos , Algoritmos , Corylus/clasificación , Corylus/metabolismo , Espectroscopía de Resonancia Magnética
11.
Anal Bioanal Chem ; 411(26): 6857-6866, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31420709

RESUMEN

We show an alternative way to visualize time course NMR data without the application of multivariate data analysis, based on the temporal change of the metabolome of hazelnuts after mold infestation. Fresh hazelnuts were inoculated with eight different natural mold species and the growth was studied over a period of 14 days. The data were plotted in a color-coded scheme showing metabolic changes as a function of chemical shift, which we named signal pattern plot. This plot graphically displays alteration (trend) of a respected signal over time and allows visual interpretation in a simple manner. Changes are compared with a reference sample stored under identical conditions as the infected nuts. The plot allows, at a glance, the recognition of individual landmarks specific to a sample group as well as common features of the spectra. Each sample reveals an individual signal pattern. The plot facilitates the recognition of signals that belong to biological relevant metabolites. Betaine and five signals were identified that specifically changed upon mold infestation. Graphical abstract.


Asunto(s)
Corylus/metabolismo , Corylus/microbiología , Metaboloma , Metabolómica/métodos , Espectroscopía de Protones por Resonancia Magnética/métodos , Aspergillus niger/fisiología , Betaína/análisis , Betaína/metabolismo , Corylus/química , Hongos/fisiología , Interacciones Huésped-Patógeno , Enfermedades de las Plantas/microbiología
12.
Proc Natl Acad Sci U S A ; 112(41): 12675-80, 2015 Oct 13.
Artículo en Inglés | MEDLINE | ID: mdl-26417081

RESUMEN

Broadly neutralizing anti-HIV-1 monoclonal antibodies, such as PG9, and its derivative RSH hold great promise in AIDS therapy and prevention. An important feature related to the exceptional efficacy of PG9 and RSH is the presence of sulfated tyrosine residues in their antigen-binding regions. To maximize antibody functionalities, we have now produced glycan-optimized, fucose-free versions of PG9 and RSH in Nicotiana benthamiana. Both antibodies were efficiently sulfated in planta on coexpression of an engineered human tyrosylprotein sulfotransferase, resulting in antigen-binding and virus neutralization activities equivalent to PG9 synthesized by mammalian cells ((CHO)PG9). Based on the controlled production of both sulfated and nonsulfated variants in plants, we could unequivocally prove that tyrosine sulfation is critical for the potency of PG9 and RSH. Moreover, the fucose-free antibodies generated in N. benthamiana are capable of inducing antibody-dependent cellular cytotoxicity, an activity not observed for (CHO)PG9. Thus, tailoring of the antigen-binding site combined with glycan modulation and sulfoengineering yielded plant-produced anti-HIV-1 antibodies with effector functions superior to PG9 made in CHO cells.


Asunto(s)
Anticuerpos Monoclonales , Anticuerpos Anti-VIH , VIH-1 , Ingeniería Metabólica/métodos , Nicotiana , Animales , Anticuerpos Monoclonales/biosíntesis , Anticuerpos Monoclonales/genética , Células CHO , Cricetinae , Cricetulus , Glicosilación , Anticuerpos Anti-VIH/biosíntesis , Humanos , Polisacáridos/biosíntesis , Polisacáridos/genética , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/genética , Nicotiana/genética , Nicotiana/metabolismo
13.
J Nat Prod ; 80(6): 1930-1934, 2017 06 23.
Artículo en Inglés | MEDLINE | ID: mdl-28613872

RESUMEN

Phomopsin A (PHO-A), produced by the fungus Diaporthe toxica, is a mycotoxin known to be responsible for fatal liver disease of lupin-fed sheep. The full spectrum of the toxic secondary metabolites produced by D. toxica is still unknown. PHO-A and the naturally occurring derivatives B-E have been subject to several studies to reveal their structures as well as chemical and toxicological properties. In this work, a methylated derivative (1) of PHO-A isolated from lupin seeds inoculated with D. toxica is described. It was characterized by high-resolution mass and NMR data and shown to be the N-methylated derivative of PHO-A. 1 is cytotoxic against HepG2 cells.


Asunto(s)
Ascomicetos/química , Fabaceae/microbiología , Micotoxinas/análisis , Animales , Células Hep G2/efectos de los fármacos , Humanos , Estructura Molecular , Micotoxinas/química , Resonancia Magnética Nuclear Biomolecular , Semillas/química , Ovinos
15.
Bioinformatics ; 30(21): 3004-11, 2014 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-25015988

RESUMEN

MOTIVATION: Today, the base code of DNA is mostly determined through sequencing by synthesis as provided by the Illumina sequencers. Although highly accurate, resulting reads are short, making their analyses challenging. Recently, a new technology, single molecule real-time (SMRT) sequencing, was developed that could address these challenges, as it generates reads of several thousand bases. But, their broad application has been hampered by a high error rate. Therefore, hybrid approaches that use high-quality short reads to correct erroneous SMRT long reads have been developed. Still, current implementations have great demands on hardware, work only in well-defined computing infrastructures and reject a substantial amount of reads. This limits their usability considerably, especially in the case of large sequencing projects. RESULTS: Here we present proovread, a hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high-performance computing cluster. On genomic and transcriptomic test cases covering Escherichia coli, Arabidopsis thaliana and human, proovread achieved accuracies up to 99.9% and outperformed the existing hybrid correction programs. Furthermore, proovread-corrected sequences were longer and the throughput was higher. Thus, proovread combines the most accurate correction results with an excellent adaptability to the available hardware. It will therefore increase the applicability and value of SMRT sequencing. AVAILABILITY AND IMPLEMENTATION: proovread is available at the following URL: http://proovread.bioapps.biozentrum.uni-wuerzburg.de.


Asunto(s)
Secuencia de Consenso , Análisis de Secuencia de ADN/métodos , Arabidopsis/genética , Secuencia de Bases , Escherichia coli/genética , Perfilación de la Expresión Génica , Genómica , Humanos , Programas Informáticos
16.
Virus Evol ; 10(1): vead088, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38516656

RESUMEN

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.

17.
FEMS Microbes ; 5: xtae023, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39170752

RESUMEN

In urinary tract infections (UTIs), different bacteria can live in a polymicrobial community consisting of different species. It is unknown how community members affect the conjugation efficiency of uropathogenic Escherichia coli. We investigated the influence of individual species often coisolated from urinary infections (UTI) on the conjugation efficiency of E. coli isolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donor E. coli strain containing the pOXA-48 plasmid and six uropathogenic E. coli isolates, in the presence and absence of five different species commonly coisolated in polymicrobial UTIs to elucidate their effect on the conjugation efficiency of E. coli. We found that the basal conjugation rates of pOXA-48, in the absence of other species, are dependent on the bacterial host genetic background. Additionally, we found that bacterial interactions have an overall positive effect on the conjugation rate of pOXA-48. Particularly, Gram-positive enterococcal species were found to enhance the conjugation rates towards uropathogenic E. coli isolates. We hypothesize that the nature of the coculture and physical interactions are important for these increased conjugation rates in an artificial urine medium environment.

18.
Biochim Biophys Acta ; 1824(3): 443-9, 2012 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-22079737

RESUMEN

(1)H NMR spectroscopy was used to follow the cleavage of sucrose by invertase. The parameters of the enzyme's kinetics, K(m) and V(max), were directly determined from progress curves at only one concentration of the substrate. For comparison with the classical Michaelis-Menten analysis, the reaction progress was also monitored at various initial concentrations of 3.5 to 41.8mM. Using the Lambert W function the parameters K(m) and V(max) were fitted to obtain the experimental progress curve and resulted in K(m)=28mM and V(max)=13µM/s. The result is almost identical to an initial rate analysis that, however, costs much more time and experimental effort. The effect of product inhibition was also investigated. Furthermore, we analyzed a much more complex reaction, the conversion of farnesyl diphosphate into (+)-germacrene D by the enzyme germacrene D synthase, yielding K(m)=379µM and k(cat)=0.04s(-1). The reaction involves an amphiphilic substrate forming micelles and a water insoluble product; using proper controls, the conversion can well be analyzed by the progress curve approach using the Lambert W function.


Asunto(s)
Transferasas Alquil y Aril/química , Proteínas de Plantas/química , Fosfatos de Poliisoprenilo/química , Proteínas de Saccharomyces cerevisiae/química , Sesquiterpenos de Germacrano/química , Sesquiterpenos/química , Sacarosa/química , beta-Fructofuranosidasa/química , Algoritmos , Transferasas Alquil y Aril/aislamiento & purificación , Transferasas Alquil y Aril/metabolismo , Escherichia coli/genética , Cinética , Espectroscopía de Resonancia Magnética , Micelas , Proteínas de Plantas/aislamiento & purificación , Proteínas de Plantas/metabolismo , Fosfatos de Poliisoprenilo/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/enzimología , Proteínas de Saccharomyces cerevisiae/metabolismo , Sesquiterpenos/metabolismo , Sesquiterpenos de Germacrano/metabolismo , Solidago/química , Solidago/enzimología , Especificidad por Sustrato , Sacarosa/metabolismo , beta-Fructofuranosidasa/metabolismo
19.
Comput Geom ; 46(2): 154-159, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23483043

RESUMEN

Given a set B of n black points in general position, we say that a set of white points W blocks B if in the Delaunay triangulation of [Formula: see text] there is no edge connecting two black points. We give the following bounds for the size of the smallest set W blocking B: (i) [Formula: see text] white points are always sufficient to block a set of n black points, (ii) if B is in convex position, [Formula: see text] white points are always sufficient to block it, and (iii) at least [Formula: see text] white points are always necessary to block a set of n black points.

20.
Sci Rep ; 13(1): 15834, 2023 09 22.
Artículo en Inglés | MEDLINE | ID: mdl-37740032

RESUMEN

Not only in metabolomics studies, but also in natural product chemistry, reliable identification of metabolites usually requires laborious steps of isolation and purification and remains a bottleneck in many studies. Direct metabolite identification from a complex mixture without individual isolation is therefore a preferred approach, but due to the large number of metabolites present in natural products, this approach is often hampered by signal overlap in the respective 1H NMR spectra. This paper presents a method for the three-dimensional mathematical correlation of NMR with MS data over the third dimension of the time course of a chromatographic fractionation. The MATLAB application SCORE-metabolite-ID (Semi-automatic COrrelation analysis for REliable metabolite IDentification) provides semi-automatic detection of correlated NMR and MS data, allowing NMR signals to be related to associated mass-to-charge ratios from ESI mass spectra. This approach enables fast and reliable dereplication of known metabolites and facilitates the dynamic analysis for the identification of unknown compounds in any complex mixture. The strategy was validated using an artificial mixture and further tested on a polar extract of a pine nut sample. Straightforward identification of 40 metabolites could be shown, including the identification of ß-D-glucopyranosyl-1-N-indole-3-acetyl-N-L-aspartic acid (1) and Nα-(2-hydroxy-2-carboxymethylsuccinyl)-L-arginine (2), the latter being identified in a food sample for the first time.


Asunto(s)
Productos Biológicos , Imagen por Resonancia Magnética , Espectroscopía de Protones por Resonancia Magnética , Arginina , Fraccionamiento Químico
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