Development of a genetic system for Haloferax gibbonsii LR2-5, model host for haloarchaeal viruses

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.

Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae

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.

Genome sequencing and molecular networking analysis of the wild fungus Anthostomella pinea reveal its ability to produce a diverse range of secondary metabolites

BACKGROUND

Filamentous fungi are prolific producers of bioactive molecules and enzymes with important applications in industry. Yet, the vast majority of fungal species remain undiscovered or uncharacterized. Here we focus our attention to a wild fungal isolate that we identified as Anthostomella pinea. The fungus belongs to a complex polyphyletic genus in the family of Xylariaceae, which is known to comprise endophytic and pathogenic fungi that produce a plethora of interesting secondary metabolites. Despite that, Anthostomella is largely understudied and only two species have been fully sequenced and characterized at a genomic level.

RESULTS

In this work, we used long-read sequencing to obtain the complete 53.7 Mb genome sequence including the full mitochondrial DNA. We performed extensive structural and functional annotation of coding sequences, including genes encoding enzymes with potential applications in biotechnology. Among others, we found that the genome of A. pinea encodes 91 biosynthetic gene clusters, more than 600 CAZymes, and 164 P450s. Furthermore, untargeted metabolomics and molecular networking analysis of the cultivation extracts revealed a rich secondary metabolism, and in particular an abundance of sesquiterpenoids and sesquiterpene lactones. We also identified the polyketide antibiotic xanthoepocin, to which we attribute the anti-Gram-positive effect of the extracts that we observed in antibacterial plate assays.

CONCLUSIONS

Taken together, our results provide a first glimpse into the potential of Anthstomella pinea to provide new bioactive molecules and biocatalysts and will facilitate future research into these valuable metabolites.

A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data

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.

From Nontargeted to Targeted Analysis: Feature Selection in the Differentiation of Truffle Species (Tuber spp.) Using 1H NMR Spectroscopy and Support Vector Machine

The price of different truffle types varies according to their culinary value, sometimes by more than a factor of 10. Nonprofessionals can hardly distinguish visually the species within the white or black truffles, making the possibility of food fraud very easy. Therefore, the identification of different truffle species (Tuber spp.) is an analytical task that could be solved in this study. The polar extract from a total of 80 truffle samples was analyzed by 1H NMR spectroscopy in combination with chemometric methods covering five commercially relevant species. All classification models were validated applying a repeated nested cross-validation. In direct comparison, the two very similar looking and closely related black representatives Tuber melanosporum and Tuber indicum could be classified 100% correctly. The most expensive truffle Tuber magnatum could be distinguished 100% from the other relevant white truffle Tuber borchii. In addition, signals for a potential Tuber borchii and a potential Tuber melanosporum marker for targeted approaches could be detected, and the corresponding molecules were identified as betaine and ribonate. A model covering all five truffle species Tuber aestivum, Tuber borchii, Tuber indicum, Tuber magnatum, and Tuber melanosporum was able to correctly discriminate between each of the species.

Opening the Random Forest Black Box of 1H NMR Metabolomics Data by the Exploitation of Surrogate Variables

The untargeted metabolomics analysis of biological samples with nuclear magnetic resonance (NMR) provides highly complex data containing various signals from different molecules. To use these data for classification, e.g., in the context of food authentication, machine learning methods are used. These methods are usually applied as a black box, which means that no information about the complex relationships between the variables and the outcome is obtained. In this study, we show that the random forest-based approach surrogate minimal depth (SMD) can be applied for a comprehensive analysis of class-specific differences by selecting relevant variables and analyzing their mutual impact on the classification model of different truffle species. SMD allows the assignment of variables from the same metabolites as well as the detection of interactions between different metabolites that can be attributed to known biological relationships.

Food Monitoring: Limitations of Accelerated Storage to Predict Molecular Changes in Hazelnuts (Corylus avellana L.) under Realistic Conditions Using UPLC-ESI-IM-QTOF-MS

Accelerated storage is routinely used with pharmaceuticals to predict stability and degradation patterns over time. The aim of this is to assess the shelf life and quality under harsher conditions, providing crucial insights into their long-term stability and potential storage issues. This study explores the potential of transferring this approach to food matrices for shelf-life estimation. Therefore, hazelnuts were stored under accelerated short-term and realistic long-term conditions. Subsequently, they were analyzed with high resolution mass spectrometry, focusing on the lipid profile. LC-MS analysis has shown that many unique processes take place under accelerated conditions that do not occur or occur much more slowly under realistic conditions. This mainly involved the degradation of membrane lipids such as phospholipids, ceramides, and digalactosyldiacylglycerides, while oxidation processes occurred at different rates in both conditions. It can be concluded that a food matrix is far too complex and heterogeneous compared to pharmaceuticals, so that many more processes take place during accelerated storage, which is why the results cannot be used to predict molecular changes in hazelnuts stored under realistic conditions.

Identification of metabolites from complex mixtures by 3D correlation of 1H NMR, MS and LC data using the SCORE-metabolite-ID approach

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 β-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.

Genomic and Metabolomic Analysis of the Endophytic Fungus Fusarium sp. VM-40 Isolated from the Medicinal Plant Vinca minor

The genus Fusarium is well-known to comprise many pathogenic fungi that affect cereal crops worldwide, causing severe damage to agriculture and the economy. In this study, an endophytic fungus designated Fusarium sp. VM-40 was isolated from a healthy specimen of the traditional European medicinal plant Vinca minor. Our morphological characterization and phylogenetic analysis reveal that Fusarium sp. VM-40 is closely related to Fusarium paeoniae, belonging to the F. tricinctum species complex (FTSC), the genomic architecture and secondary metabolite profile of which have not been investigated. Thus, we sequenced the whole genome of Fusarium sp. VM-40 with the new Oxford Nanopore R10.4 flowcells. The assembled genome is 40 Mb in size with a GC content of 47.72%, 15 contigs (≥50,000 bp; N 50~4.3 Mb), and 13,546 protein-coding genes, 691 of which are carbohydrate-active enzyme (CAZyme)-encoding genes. We furthermore predicted a total of 56 biosynthetic gene clusters (BGCs) with antiSMASH, 25 of which showed similarity with known BGCs. In addition, we explored the potential of this fungus to produce secondary metabolites through untargeted metabolomics. Our analyses reveal that this fungus produces structurally diverse secondary metabolites of potential pharmacological relevance (alkaloids, peptides, amides, terpenoids, and quinones). We also employed an epigenetic manipulation method to activate cryptic BGCs, which led to an increased abundance of several known compounds and the identification of several putative new compounds. Taken together, this study provides systematic research on the whole genome sequence, biosynthetic potential, and metabolome of the endophytic fungus Fusarium sp. VM-40.

Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle

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.

Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses

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.

Draft genomes of three closely related low light-adapted Prochlorococcus

OBJECTIVES

The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here.

DATA DESCRIPTION

We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.

Analysis of Hazelnuts (Corylus avellana L.) Stored for Extended Periods by 1H NMR Spectroscopy Monitoring Storage-Induced Changes in the Polar and Nonpolar Metabolome

Storage is a critical step in the post-harvest processing of hazelnuts, as it can lead to mold, rancidity, and off-flavor. However, there is a lack of analytical methods to detect improper or extended storage. To comprehensively investigate the effects of hazelnut storage, samples were stored under five different conditions for up to 18 months. Subsequently, the polar and nonpolar metabolome were analyzed by ¹H NMR spectroscopy and chemometric approaches for classification as well as variable selection. Increases in hexanoic, octanoic, and nonanoic acid, all products of lipid oxidation and responsible for quality defects, were found across all conditions. Furthermore, the concentration of free long-chain fatty acids increased in samples stored at high temperatures. Harsh short-term storage resulted in an increase in fumaric and lactic acid, glucose, fructose, and choline and a decrease in acetic acid.

Updated Virophage Taxonomy and Distinction from Polinton-like Viruses

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.

Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel

The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.

Novel integrative elements and genomic plasticity in ocean ecosystems

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.

AC Kelvin Probe Force Microscopy Enables Charge Mapping in Water

Mapping charged chemical groups at the solid-liquid interface is important in many areas, ranging from colloidal systems to biomolecular interactions. However, classical methods to measure surface charges either lack spatial resolution or─like Kelvin-probe force microscopy (KPFM)─cannot be applied in aqueous solutions because a DC bias voltage is used. Here, we show that using AC Kelvin probe force microscopy (AC-KPFM), in which the DC bias is replaced with an AC voltage of sufficiently high frequency, the surface potential of spatially fixated, charged surface groups can be mapped in aqueous solution. We demonstrate this with micropatterned, functionalized alkanethiol layers which expose ionized amino- and carboxy-groups. These groups are representative of the charged groups of most biomolecules such as proteins. By adjusting the pH of the solution, the charge of the groups was reversibly altered, demonstrating the electrostatic nature of the measured signal. The influence of the electric double layer (EDL) on the measurement is discussed, and we, furthermore, show how charged, micropatterned layers can be used to spatially direct the deposition of nanoparticles of opposite charge.

Impact of Freeze-Drying on the Determination of the Geographical Origin of Almonds (Prunus dulcis Mill.) by Near-Infrared (NIR) Spectroscopy

Near-infrared (NIR) spectroscopy is a proven tool for the determination of food authenticity, mainly because of good classification results and the possibility of industrial use due to its easy and fast application. Since water shows broad absorption bands, the water content of a sample should be as low as possible. Freeze-drying is a commonly used preparatory step for this to reduce the water content in the sample. However, freeze-drying, also known as lyophilization, is very time-consuming impeding the widespread usage of NIR analysis as a rapid method for incoming goods inspections. We used a sample set of 72 almond samples from six economically relevant almond-producing countries to investigate the question of how important lyophilization is to obtain a well-performing classification model. For this approach, the samples were ground and lyophilized for 3 h, 24 h, and 48 h and compared to non-freeze-dried samples. Karl-Fischer titration of non-lyophilized samples showed that water contents ranged from 3.0 to 10.5% and remained constant at 0.36 ± 0.13% after a freeze-drying period of 24 h. The non-freeze-dried samples showed a classification accuracy of 93.9 ± 6.4%, which was in the same range as the samples which were freeze-dried for 3 h (94.2 ± 7.8%), 24 h (92.5 ± 8.7%), and 48 h (95.0 ± 9.0%). Feature selection was performed using the Boruta algorithm, which showed that signals from lipids and proteins are relevant for the origin determination. The presented study showed that samples with low water content, especially nuts, can be analyzed without the time-consuming preparation step of freeze-drying to obtain robust and fast results, which are especially required for incoming goods inspection.

Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean

Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in Synechococcus and low-light adapted Prochlorococcus populations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher new iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower new iron flux). Picocyanobacterial siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, especially at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of marine picocyanobacteria.

Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate

Virophages can parasitize giant DNA viruses and may provide adaptive anti-giant virus defense in unicellular eukaryotes. Under laboratory conditions, the virophage mavirus integrates into the nuclear genome of the marine flagellate Cafeteria burkhardae and reactivates upon superinfection with the giant virus CroV. In natural systems, however, the prevalence and diversity of host-virophage associations has not been systematically explored. Here, we report dozens of integrated virophages in four globally sampled C. burkhardae strains that constitute up to 2% of their host genomes. These endogenous mavirus-like elements (EMALEs) separated into eight types based on GC-content, nucleotide similarity, and coding potential and carried diverse promoter motifs implicating interactions with different giant viruses. Between host strains, some EMALE insertion loci were conserved indicating ancient integration events, whereas the majority of insertion sites were unique to a given host strain suggesting that EMALEs are active and mobile. Furthermore, we uncovered a unique association between EMALEs and a group of tyrosine recombinase retrotransposons, revealing yet another layer of parasitism in this nested microbial system. Our findings show that virophages are widespread and dynamic in wild Cafeteria populations, supporting their potential role in antiviral defense in protists.

Viruses exist in all ecosystems in vast numbers and infect many organisms. Some of them are harmful but others can protect the organisms they infect. For example, a group of viruses called virophages protect microscopic sea creatures called plankton from deadly infections by so-called giant viruses. In fact, virophages need plankton infected with giant viruses to survive because they use enzymes from the giant viruses to turn on their own genes.

A virophage called mavirus integrates its genes into the DNA of a type of plankton called Cafeteria. It lays dormant in the DNA until a giant virus called CroV infects the plankton. This suggests that the mavirus may be a built-in defense against CroV infections and laboratory studies seem to confirm this. But whether wild Cafeteria also use these defenses is unknown.

Hackl et al. show that virophages are common in the DNA of wild Cafeteria and that the two appear to have a mutually beneficial relationship. In the experiments, the researchers sequenced the genomes of four Cafeteria populations from the Atlantic and Pacific Oceans and looked for virophages in their DNA. Each of the four Cafeteria genomes contained dozens of virophages, which suggests that virophages are important to these plankton. This included several relatives of the mavirus and seven new virophages. Virophage genes were often interrupted by so called jumping genes, which may take advantage of the virophages the way the virophages use giant viruses to meet their own needs.

The experiments show that virophages often co-exist with marine plankton from around the world and these relationships are likely beneficial. In fact, the experiments suggest that the virophages may have played an important role in the evolution of these plankton. Further studies may help scientists learn more about virus ecology and how viruses have shaped the evolution of other creatures.

MOSGA: Modular Open-Source Genome Annotator

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.

Cysteine: an overlooked energy and carbon source

Biohybrids composed of microorganisms and nanoparticles have emerged as potential systems for bioenergy and high-value compound production from CO₂ and light energy, yet the cellular and metabolic processes within the biological component of this system are still elusive. Here we dissect the biohybrid composed of the anaerobic acetogenic bacterium Moorella thermoacetica and cadmium sulphide nanoparticles (CdS) in terms of physiology, metabolism, enzymatics and transcriptomic profiling. Our analyses show that while the organism does not grow on l-cysteine, it is metabolized to acetate in the biohybrid system and this metabolism is independent of CdS or light. CdS cells have higher metabolic activity, despite an inhibitory effect of Cd²⁺ on key enzymes, because of an intracellular storage compound linked to arginine metabolism. We identify different routes how cysteine and its oxidized form can be innately metabolized by the model acetogen and what intracellular mechanisms are triggered by cysteine, cadmium or blue light.

Comparison of Regular, Pure Shift, and Fast 2D NMR Experiments for Determination of the Geographical Origin of Walnuts

¹H NMR spectroscopy, in combination with chemometric methods, was used to analyze the methanol/acetonitrile (1:1) extract of walnut (Juglans Regia L.) regarding the geographical origin of 128 authentic samples from different countries (France, Germany, China) and harvest years (2016–2019). Due to the large number of different metabolites within the acetonitrile/methanol extract, the one-dimensional (1D) ¹H NOESY (nuclear Overhauser effect spectroscopy) spectra suffer from strongly overlapping signals. The identification of specific metabolites and statistical analysis are complicated. The use of pure shift ¹H NMR spectra such as PSYCHE (pure shift yielded by chirp excitation) or two-dimensional ASAP-HSQC (acceleration by sharing adjacent polarization-heteronuclear single quantum correlation) spectra for multivariate analysis to determine the geographical origin of foods may be a promising method. Different types of NMR spectra (1D ¹H NOESY, PSYCHE, and ASAP-HSQC) were acquired for each of the 128 walnut samples and the results of the statistical analysis were compared. A support vector machine classifier was applied for differentiation of samples from Germany/China, France/Germany, and France/China. The models obtained by conduction of a repeated nested cross-validation showed accuracies from 58.9% (±1.3%) to 95.9% (±0.8%). The potential of the ¹H-¹³C HSQC as a 2D NMR experiment for metabolomics studies was shown.

Food Profiling: Determination of the Geographical Origin of Walnuts by 1H NMR Spectroscopy Using the Polar Extract

Walnuts, with their health-promoting ingredients, are among the most popular nuts, and practicable methods for determining their geographical origin are needed to tackle food fraud. Authentic walnut samples (235, Juglans Regia L.) from different harvest years (2016-2019) and countries were analyzed by ¹H NMR spectroscopy in combination with chemometric methods to determine their geographical origin. Two sample groups were analyzed at a time with a support vector machine algorithm to obtain two-class classifier models. In total, nine two-class models were built (e.g., Germany/China, France/Germany, and USA/Switzerland), and a repeated nested cross-validation was performed. The models obtained showed high accuracies from 78.0% (±2.3%) to 96.6% (±0.6%). Furthermore, identification of potential chemical markers in the walnut extract was performed.

Determination of the Geographical Origin of Asparagus officinalis L. by 1H NMR Spectroscopy

Food authenticity concerning the geographical origin becomes increasingly important for consumers, food industries, and food authorities. In this study, nontargeted ¹H NMR metabolomics combined with machine learning methodologies was applied to successfully distinguish the geographical origin of 237 samples of white asparagus from Germany, Poland, The Netherlands, Spain, Greece, and Peru. Support vector classification of the geographical origin achieved an accuracy of 91.5% for the entire sample set and 87.8% after undersampling the majority class. Important regions of the spectra could be identified and assigned to potential chemical markers. A subset of samples was compared to isotope-ratio mass spectrometry (IRMS), an established method for the determination of origin of white asparagus in Germany. Here, SVM classification led to accuracies of 79.4% for NMR and 70.9% for IRMS. Finally, the classification of asparagus from different German regions was evaluated, and the influence of year and variety was analyzed.

Detection of Peanut Adulteration in Food Samples by Nuclear Magnetic Resonance Spectroscopy

The addition of cheap and also readily available raw materials, such as peanut powder, to visually and chemically similar matrices is a common problem in the food industry. When peanuts are used as an adulterant, there is an additional risk of potential health hazard to consumers as a result of allergy-induced anaphylaxis. In this study, different series of peanut admixtures to visually similar food products, such as powdered hazelnuts, almonds, and walnuts, were prepared and analyzed by ¹H nuclear magnetic resonance (NMR) spectroscopy. For identification, an isolated signal at 3.05 ppm in the ¹H NMR spectrum of polar peanut extract was used as an indicator of peanut adulteration. The chemical marker was identified as (2S,4R)-N-methyl-4-hydroxy-l-proline by resynthesis of the compound and used as an internal standard. The signal-to-noise ratio and the integral of the signal of the marker can both be used to detect peanut impurities. Overall, an approximate limit of detection of 4% admixtures of peanut in various food products was determined using a 400 MHz spectrometer. With regard to food fraud, we present a viable screening method for detection of economic-relevant peanut adulteration.

Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems.

Expression Profiling and Glycan Engineering of IgG Subclass 1-4 in Nicotiana benthamiana

IgG, the main serum immunoglobulin isotype, exists in four subclasses which selectively appear with distinctive glycosylation profiles. However, very little is known about the biological consequences mainly due to the difficulties in the generation of distinct IgG subtypes with targeted glycosylation. Here, we show a comprehensive expression and glycan modulation profiling of IgG variants in planta that are identical in their antigen binding domain but differ in their subclass appearance. While IgG1, 2, and 4 exhibit similar expression levels and purification yields, IgG3 is generated only at low levels due to the in planta degradation of the heavy chain. All IgG subtypes are produced with four distinct N-glycosylation profiles, differing in sugar residues previously shown to impact IgG activities, i.e., galactosylation, sialylation and core fucosylation. Affinity purified IgG variants are shown to be fully assembled to heterodimers but display different biochemical/physical features. All subtypes are equally well amenable to targeted glycosylation, except sialylated IgG4 which frequently accumulates substantial fractions of unusual oligo-mannosidic structures. IgG variants show significant differences in aggregate formation and endotoxin contamination which are eliminated by additional polishing steps (size exclusion chromatography, endotoxin removal treatments). Collectively we demonstrate the generation of 16 IgG variants at high purity and large glycan homogeneity which constitute an excellent toolbox to further study the biological impact of the two main Fc features, subclass and glycosylation.

Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory

Most plants grow and develop by taking up nutrients from the soil while continuously under threat from foraging animals. Carnivorous plants have turned the tables by capturing and consuming nutrient-rich animal prey, enabling them to thrive in nutrient-poor soil. To better understand the evolution of botanical carnivory, we compared the draft genome of the Venus flytrap (Dionaea muscipula) with that of its aquatic sister, the waterwheel plant Aldrovanda vesiculosa, and the sundew Drosera spatulata. We identified an early whole-genome duplication in the family as source for carnivory-associated genes. Recruitment of genes to the trap from the root especially was a major mechanism in the evolution of carnivory, supported by family-specific duplications. Still, these genomes belong to the gene poorest land plants sequenced thus far, suggesting reduction of selective pressure on different processes, including non-carnivorous nutrient acquisition. Our results show how non-carnivorous plants evolved into the most skillful green hunters on the planet.

Fragment Growing to Design Optimized Inhibitors for Human Blood Group B Galactosyltransferase (GTB)

Human blood group B galactosyltransferase (GTB) catalyzes the galactosylation of the H antigen and is responsible for the formation of the blood group antigen of phenotype B. The ABO blood group system is well studied and routinely serotyped before transfusion and transplantation. Blood type subgroups have been repeatedly linked to an increased occurrence of diseases (e.g., a highly increased incidence rate for pancreatic cancer for individuals with blood group phenotype B). 3-Phenyl-5-(piperazin-1-yl)-1,2,4-thiadiazole 1 has previously been described to inhibit GTB with a K_i value of 800 μm. In this work, we describe a computer-guided fragment-growing approach for the optimization of this fragment that was subsequently realized by synthesizing the most promising ligands. Enlarging the phenyl moiety of fragment 1 to a naphthyl moiety resulted in ligand 3-(naphthalene-1-yl)-5-(piperazin-1-yl)-1,2,4-thiadiazole 2 a, which shows a threefold improvement in binding affinity (K_i =271 μm).

Improving draft genome contiguity with reference-derived in silico mate-pair libraries

Background

Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available.

Findings

In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico.

Conclusions

We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.

1H NMR Spectroscopy for Determination of the Geographical Origin of Hazelnuts

A total of 262 authentic samples was analyzed by ¹H NMR spectroscopy for the geographical discrimination of hazelnuts ( Corylus avellana L.) covering samples from five countries (Germany, France, Georgia, Italy, and Turkey) and the harvest years 2013-2016. This article describes method development starting with an extraction protocol suitable for separation of polar and nonpolar metabolites in addition to reduction of macromolecular components. Using the polar fraction for data analysis, principle component analysis was applied and used to monitor sample preparation and measurement. Several machine learning algorithms were tested to build a classification model. The best results were obtained by a linear discrimination analysis applying a random subspace algorithm. The division of the samples in a trainings set and a test set yielded a cross validation accuracy of 91% for the training set and an accuracy of 96% for the test set. The identification of key features was carried out by Kruskal-Wallis test and t test. A feature assigned to betaine exhibits a significant level for the classification of all five countries and is considered a possible candidate for the development of targeted approaches. Further, the results were compared to a previously published study based on LC-MS analysis of nonpolar metabolites. In summary, this study shows the robustness and high accuracy of a discrimination model based on NMR analysis of polar metabolites.

Marine microbial metagenomes sampled across space and time

Recent advances in understanding the ecology of marine systems have been greatly facilitated by the growing availability of metagenomic data, which provide information on the identity, diversity and functional potential of the microbial community in a particular place and time. Here we present a dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse regions of the Atlantic and Pacific Oceans. One set of metagenomes, collected on GEOTRACES cruises, captures large geographic transects at multiple depths per station. The second set represents two years of time-series data, collected at roughly monthly intervals from 3 depths at two long-term ocean sampling sites, Station ALOHA and BATS. These metagenomes contain genomic information from a diverse range of bacteria, archaea, eukaryotes and viruses. The data's utility is strengthened by the availability of extensive physical, chemical, and biological measurements associated with each sample. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of marine microbial ecosystems.

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis.

Detection of a Toxic Methylated Derivative of Phomopsin A Produced by the Legume-Infesting Fungus Diaporthe toxica

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.

Food Fingerprinting: Metabolomic Approaches for Geographical Origin Discrimination of Hazelnuts (Corylus avellana) by UPLC-QTOF-MS

Ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) was used for geographical origin discrimination of hazelnuts (Corylus avellana L.). Four different LC-MS methods for polar and nonpolar metabolites were evaluated with regard to best discrimination abilities. The most suitable method was used for analysis of 196 authentic samples from harvest years 2014 and 2015 (Germany, France, Italy, Turkey, Georgia), selecting and identifying 20 key metabolites with significant differences in abundancy (5 phosphatidylcholines, 3 phosphatidylethanolamines, 4 diacylglycerols, 7 triacylglycerols, and γ-tocopherol). Classification models using soft independent modeling of class analogy (SIMCA), linear discriminant analysis based on principal component analysis (PCA-LDA), support vector machine classification (SVM), and a customized statistical model based on confidence intervals of selected metabolite levels were created, yielding 99.5% training accuracy at its best by combining SVM and SIMCA. Forty nonauthentic hazelnut samples were subsequently used to estimate as realistically as possible the prediction capacity of the models.

Pharmacokinetic of 3H-deacetylasperulosidic acid in mice

Background: An investigation was conducted to determine the fate of the iridoid derivative deacetylasperulosidic acid (DAA) after oral application to mice.Methods: DAA was extracted from Morinda citrifolia leaf and purified by preparative HPLC. The identity was verified by MS and NMR spectroscopy. A sample of DAA was radioactively labelled with tritium and applied to mice by gavage. The pharmacokinetic of the radioactivity was investigated in blood, organs, urine and feces. Metabolites were isolated in blood and urine by HPLC and identified by LC-MS.  In vitro incubation of DAA with mouse duodenum and liver homogenate and human fecal bacteria was performed and possible metabolites were separated with HPLC.Results: DAA was rapidly absorbed and excreted mainly via the kidneys with a half-life of 30 minutes. Radioactivity was present in all organs with highest concentrations in kidney and liver.  Almost 100% of the radioactivity isolated from urine and organs could be identified as unchanged DAA. Additionally, no metabolism could be observed after in vitro incubation of DAA with mouse small intestine or liver homogenate, however, a total breakdown of the molecule was observed after incubation of DAA with human intestinal bacteria.Conclusions:The absorption and excretion of glycosides such as DAA in mammals without hydrolysis is possibly a defense mechanism of animals against the toxicity of these compounds. Key words: Deacetylasperulosidic acid, DAA, tritium label, pharmacokinetic,iridoid, metabolism

Glycan modulation and sulfoengineering of anti-HIV-1 monoclonal antibody PG9 in plants

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.

proovread: large-scale high-accuracy PacBio correction through iterative short read consensus

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.

A nonionic inhibitor with high specificity for the UDP-Gal donor binding site of human blood group B galactosyltransferase: design, synthesis, and characterization

9-(5-O-α-D-galactopyranosyl)-D-arabinityl-1,3,7-trihydropurine-2,6,8-trione (1) was designed and synthesized as a nonionic inhibitor for the donor binding site of human blood group B galactosyltransferase (GTB). Enzymatic characterization showed 1 to be extremely specific, as the highly homologous human N-acetylgalactosaminyltransferase (GTA) is not inhibited. The binding epitope of 1 demonstrates a high involvement of the arabinityl linker, whereas the galactose residue is only making contact to the protein via its C-2 site, which is very important for the discrimination between galactose and N-acetylgalactosamine, the substrate transferred by GTA. The approach can generate highly specific glycosyltransferase inhibitors.

Blocking Delaunay triangulations

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.