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Krueger, A.

Publications and source records attributed to Krueger, A..

At least 19 recordsLinked to original sources

Context-dependent siderophore exploitability shapes microbial community structure

1)Siderophores are classically viewed as shared iron-scavenging public goods, yet their ecological roles in multispecies communities remain poorly defined. Here, we establish a synthetic microbial community to dissect how different siderophores, their uptake compatibility and spatial structure shape iron competition. Using Corynebacterium glutamicum as a model, we show that this siderophore non-producer accesses diverse xenosiderophores, including enterobactin secreted by Escherichia coli. However, exploitation was constrained and co-cultures converged to stable compositions. Dose-response experiments combined with mathematical modelling indicated that the producer retains more effective access to enterobactin than the exploiter. Presence of Pseudomonas putida altered this interaction, as it exploited enterobactin while producing pyoverdine, a siderophore inaccessible to the other community members that restricted their iron access. Across different cultivation scales, community dynamics was strongly influenced by spatial organization and initial composition. These findings identify siderophores as context-dependent iron-allocation agents that can promote microbial coexistence or exclusion.

microbiology↗

Rapid Bacterial Identification and Antibiotic Susceptibility Testing through Interferometry-based Surface Topography Measurement

Scientists have long classified organisms based on shared morphological characteristics. However, modern taxonomy, particularly for bacteria, is largely defined at the genetic level. Yet the information encoded in genetics propagates through many levels of biological organization: genes determine patterns of gene expression and protein production which, in turn, influence cellular physiology and behavior which, in turn, influence the collective morphology of growing populations. It is unclear how far up this hierarchy that the lower level taxonomic information remains preserved. Here, we show that bacterial genera can be identified from differences in the three-dimensional topographies of their growing populations. Using coherence-scanning white-light interferometry (WLI), which is capable of nanometer-resolution, we measure bacterial population topographies of 77 different clinical isolates representing four different genera. We then extract ten biophysically relevant features describing their surface structure. Using a simple machine-learning classifier, these topographic features identified bacterial genus with 97% accuracy, demonstrating that genus-level information remains present at the scale of population morphology. We hypothesize that these topographic "fingerprints" arise because differences in the underlying biophysics of bacterial growth propagate upward into measurable differences in population structure. To test this hypothesis, we performed biophysical simulations of bacterial population growth and applied our experimentally trained classifier directly to the resulting simulated topographies. By systematically modifying simulation parameters, we determined which changes were necessary to generate topographies classified as each of the experimentally observed genera. We find that a relatively small number of differences in cellular growth, cell-surface interactions, and initial conditions are sufficient to recreate the genus-associated differences observed experimentally, and we then show that using the topographic features from the simulations we can recover the underlying parameters used to simulate the topographies. Together, these results show that differences in lower-level bacterial behavior can propagate into distinct population-scale morphologies, and that taxonomic information can remain recoverable far above the molecular scale at which bacterial identity is conventionally defined.

biophysics↗

HIF-1α coordinates adrenal steroidogenesis through direct transcriptional control and regulation of miRNA biogenesis

BackgroundAdrenal steroid hormone production is essential for systemic stress adaptation and metabolic homeostasis, and it is tightly regulated by oxygen availability. Previously, we demonstrated that acute hypoxia suppresses adrenal steroidogenesis through HIF-1-dependent induction of microRNAs (miRNAs) that target key steroidogenic enzymes. However, the mechanisms by which HIF-1 controls miRNA expression and activity in this context remain unclear. MethodsTo address this issue, we mapped the genome-wide HIF-1 binding landscape in murine adrenocortical cells using Cleavage Under Targets & Tagmentation (CUT&Tag). We integrated this data with gene expression analyses following pharmacological HIF-1 stabilization, physiological hypoxia, and genetic HIF-1 depletion to distinguish HIF-1-dependent effects from broader hypoxia-driven responses. ResultsWe detected HIF-1 binding at loci encoding steroidogenic enzymes and steroidogenesis-associated miRNAs. Unexpectedly, we also detected binding at genes involved in miRNA biogenesis and function, including components of the nuclear microprocessor complex and the cytoplasmic RNA-induced silencing complex (RISC). Functional analyses revealed that hypoxia broadly represses the expression of miRNA-processing genes through both HIF-1-dependent and -independent mechanisms. Notably, HIF-1 selectively modulated or counteracted this repression in a gene-specific manner, indicating a regulatory role beyond direct transcriptional activation. ConclusionsThese findings reveal an unrecognized layer of hypoxia-driven cell communication, wherein HIF-1 coordinates the transcriptional and post-transcriptional regulation of adrenal steroidogenesis by shaping the miRNA-processing landscape. This work extends our understanding of how oxygen-sensitive signaling pathways integrate gene expression and RNA-based regulatory mechanisms to control endocrine function.

molecular biology↗

DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity

Bacteria deploy diverse antiphage defense systems, including small bioactive molecules providing protection at the multicellular level. DNA-intercalating anthracyclines, such as daunorubicin, exhibit broad antiphage activity, but the underlying mechanism has remained elusive. Here, we systematically screened the Escherichia coli BASEL phage collection to elucidate the mode of action of DNA-intercalating antiphage molecules. We identified taxonomically distinct clusters of susceptible viral groups and show that, in T5-like phages (Markadamsvirinae), daunorubicin blocks infection after first-step transfer (FST). In the presence of daunorubicin, continued expression of pre-early genes leads to abortive infection via mutual destruction, where both phage and host succumb. Analogous abortive-infection phenotypes occur across taxonomically diverse phages exposed to chemically distinct DNA-intercalating molecules. Notably, we show that daunorubicin synergizes with downstream nucleic acid-targeting defenses underscoring context-dependent outcomes. Together, these findings reveal how chemical defense contributes to the multilayered antiviral immunity and highlight the intricate interplay between mechanistic inhibition and infection outcome.

microbiology↗

A novel biosensor for ferrous iron developed via CoBiSe:A computational method for rapid biosensor design

Genetically encoded biosensors enable monitoring of metabolite dynamics in living organisms. We present CoBiSe, a computational approach using Constraint Network Analysis to identify optimal insertion sites for reporter modules in molecular recognition elements (MREs). Applied to the iron-binding protein DtxR from Corynebacterium glutamicum, CoBiSe identified a flexible connective loop (residues 138-150) for inserting the reporter module, resulting in IronSenseR, a novel ratiometric biosensor for ferrous iron (Fe{superscript 2}). IronSenseR demonstrates high specificity for Fe{superscript 2} with dissociation constants of 1.55 {+/-} 0.08 {micro}M (FeSO4) and 2.44 {+/-} 0.28 {micro}M (FeCl2), while showing no binding to Fe3 and other divalent cations. In vivo assessment in Escherichia coli, Pseudomonas putida and Corynebacterium glutamicum confirmed IronSenseRs capability to detect changes in the intracellular iron pool. The creation of IronSenseR underlines that, by reducing search space and eliminating labor-intensive screening, CoBiSe streamlines biosensor development and enables precise creation of next-generation biosensors for diverse metabolites.

bioengineering↗

Septin7 is essential in early hematopoiesis, but redundant at later stages

The unique cytoskeletal protein Septin7 is generally considered to be required for cytokinesis in yeast and mammals. Whole body genetic ablation of Septin7 in mice is embryonic lethal. Septin7-deficient fibroblasts and HeLa cells are defective in cytokinesis and undergo obligate multinucleation. Surprisingly, lymphocyte- and myeloid-specific deletion of Septin7 in mice did not result in any detectable abnormalities in blood lineage development, suggesting that Septin7 is dispensable for steady-state hematopoiesis. In contrast, Septin7-deficient hematopoietic stem cells failed to engraft and establish donor chimerism following transplantation, indicating that Septin7 is essential for hematopoietic stem cell function under stress conditions. To reconcile these contradictory findings, we analyzed the effects of Septin7 deletion in hematopoietic cells from mice with either pan-hematopoietic or lymphoid lineage-specific Septin7 deletion. Our results demonstrate that Cre-induced deletion of the floxed Septin7 allele is inefficient during the early stages of hematopoiesis, suggesting strong selection pressure against Septin7 deficiency at this stage. In contrast, deletion of Septin7 at the common lymphoid progenitor stage, as well as in Hoxb8-immortalized hematopoietic progenitors, is efficient and does not result in any noticeable defects in cell division. Taken together, our findings indicate that Septin7 is essential during early hematopoiesis but becomes dispensable at later stages.

biochemistry↗

Photoaffinity enabled transcriptome-wide identification of splice modulating small molecule-RNA binding events in native cells

Splice modulating small molecules have been developed to promote the U1 snRNP to engage with pre-mRNAs with strong and altered sequence preference. Transcriptomic profiling of bulk RNA from compound treated cells enables detection of RNAs impacted; however, it is difficult to delineate whether transcriptional changes are a consequence of direct compound treatment or trans-acting effects. To identify RNA targets that bind directly with splice modulating compounds, we deployed a photoaffinity labeling (PAL)-based Chem-CLIP approach. Through this workflow, we identify the telomerase lncRNA (TERC) as a previously unknown target of this class of clinically relevant small molecules. Using cellular {Delta} SHAPE-MaP, we orthogonally validate and further define the compound binding site as likely to be the conserved CR4/5 domain. Additionally, a thorough analysis of the PAL-based Chem-CLIP data reveals that considering competed RNAs, irrespective of magnitude of enrichment, adds a rich dimension of hit calling. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/623654v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1ef467eorg.highwire.dtl.DTLVardef@1fd201dorg.highwire.dtl.DTLVardef@1478f83org.highwire.dtl.DTLVardef@11ef59a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

A rational approach for the targeted discovery and characterisation of microbiome-derived therapeutics

The human gut microbiome is intrinsically involved in health and disease, representing a wealth of untapped therapeutic potential. Here, we demonstrate the utility and potential of a metagenome guided, large cohort-based approach for the rational selection of live biotherapeutics from the human gut. We applied this approach to Inflammatory Bowel Disease (IBD), identifying several lead candidates that were significantly depleted in individuals with IBD compared to healthy controls. Their therapeutic potential was assessed in preclinical models of IBD where they improved markers of disease pathology by reducing inflammation and promoting mucosal healing and wound repair. All leads had excellent safety profiles in silico and in vitro, and several additionally presented favourable manufacturing properties, supporting their progression into clinical trials. We believe that this rational approach will be generalisable to any disease state with underlying microbiome aetiology and will expedite the development of novel microbiome-derived therapeutics to improve human health.

microbiology↗

The essential kinase TgGSK regulates centrosome division and endodyogeny in Toxoplasma gondii

Intracellular replication is crucial for the success of apicomplexan parasites, including Toxoplasma gondii. Therefore, essential players in parasite replication present potential targets for drug development. In this study, we have characterized TgGSK, a glycogen synthase kinase homolog that plays an important role in Toxoplasma endodyogeny. We have shown that TgGSK has a dynamic localization that is concurrent with the cell cycle. In non-dividing parasites, this kinase is highly concentrated in the nucleus. However, during division, TgGSK displays a cytosolic localization, with concentration foci at the centrosomes, a key organelle involved in parasite division, and the basal end. Conditional knockdown of TgGSK determined that it is essential for the completion of the lytic cycle and proper parasite division. Parasites lacking endogenous protein levels of TgGSK exhibited defects in division synchronicity and the segregation of the nucleus and apicoplast into forming daughter cells. These phenotypes are associated with defects in centrosome duplication and fission. Global phosphoproteomic analysis determined TgGSK-dependent phosphorylation of RNA-processing, basal end, and centrosome proteins. Consistent with the putative regulation of RNA-processing proteins, global transcriptomic analysis suggests that TgGSK is needed for proper splicing. Finally, we show that TgGSK interacts with GCN5b, a well-characterized acetyltransferase with roles in transcriptional control. Conversely, GCN5b chemical inhibition results in specific degradation of TgGSK. Thus, these studies reveal the involvement of TgGSK in various crucial processes, including endodyogeny and splicing, and identify acetylation as a possible mechanism by which this essential kinase is regulated. AUTHOR SUMMARYToxoplasma gondii infects nearly a third of the worlds human population. While infection is largely asymptomatic in healthy adults, in immunocompromised or immunosuppressed individuals it can lead to brain lesions and even death. Similarly, toxoplasmosis can result in stillbirth, birth defects, and blindness of a developing fetus in the case of a congenital infection. With minimal treatments for Toxoplasmosis available, it is crucial to study parasite-specific processes that could be potential drug targets for the treatment of Toxoplasmosis. In this study, we investigated the protein TgGSK that is essential for parasite survival and proper division. We showed that TgGSK may perform its essential functions through interaction with the centrosome, an organelle that plays a major role in cell division in many organisms. We also show in this study a role for TgGSK in proper processing of messenger RNAs. Taken together, we have performed an in-depth study of the functional role of the essential protein TgGSK in Toxoplasma gondii. Importantly, TgGSK was shown to have more similarity to plant proteins than mammalian proteins which may allow for the possibility of targeting of this protein for therapeutic treatment of toxoplasmosis.

microbiology↗

HIF1α controls steroidogenesis under acute hypoxic stress

BackgroundHypoxia is a critical physiological and pathological condition known to influence various cellular processes, including steroidogenesis. While previous studies, including our own, have highlighted the regulatory effects of Hypoxia-Inducible Factor 1 (HIF1) on steroid production, the specific molecular mechanisms remain poorly understood. This study investigates the role of hypoxia and HIF1 in steroid biosynthesis across multiple experimental models during acute exposure to low oxygen levels. MethodsTo assess the extent to which acute hypoxia modulates steroidogenesis, we employed several approaches, including the Y1 adrenocortical cell line, an ex vivo adrenal gland explant model, and a conditional HIF1-deficient mouse line in the adrenal cortex. We focused on various regulatory patterns that may critically suppress steroidogenesis. ResultsIn Y1 cells and adrenal gland explants, hypoxia induced the upregulation of specific microRNAs, leading to the suppression of mRNA levels of key steroidogenic enzymes and reduced steroid hormone production. The hypoxia/HIF1-dependent induction of these microRNAs and the consequent modulation of steroid production were confirmed in vivo. Notably, using our conditional HIF1-deficient mouse line, we found that the increase in miRNA expression under hypoxic conditions is directly dependent on HIF1. Furthermore, the regulation of steroidogenic enzymes (e.g., StAR and Cyp11a1) and steroid production occurred at the level of protein translation, revealing an unexpected layer of control under hypoxic conditions in vivo. ConclusionsThese findings elucidate the molecular mechanisms underlying acute hypoxia-induced changes in steroid biosynthesis and may also be useful in developing new strategies for various steroid hormone pathologies.

molecular biology↗

Endoglin regulates the integrity of the bone marrow vasculature

Endoglin (Eng) is an accessory receptor for transforming growth factor-{beta} (TGF-{beta}) that is critical for maintaining vascular integrity. Mutations in Eng cause hereditary hemorrhagic telangiectasia (HHT), resulting in arteriovenous malformations (AVMs) and blood abnormalities. Despite the known association between Eng deficiency and AVMs, the underlying mechanisms are unclear. In addition, the role of the bone marrow (BM), a major source of immune and blood cells, in endothelial Eng (EC-Eng) deficiency is unexplored. We show that BM blood vessels conditionally deficient in Eng (cKO) undergo a structured remodeling process over four weeks, with distinct proliferative and resolution phases. These phases involve angiogenic set points, the involvement of integrins, and the modulation of vascular integrity. In addition, we observe changes in hematopoietic stem and progenitor cells (HSPC) and circulating granulocytes, along with reduced red blood cells and platelets due to splenic sequestration. Using a conditional heterozygous EC-Eng deficient mouse model, reflecting the genetics of HHT patients, we identify vascular changes similar to those in the cKO model. Taken together, using multiple in vivo approaches, we suggest that reduced Eng expression in the endothelium drives significant BM vascular remodeling, sharing mechanisms with early vascular processes associated with AVM formation. Explanation of NoveltyOur findings reveal that BM blood vessels deficient in endoglin undergo an orchestrated remodeling process with distinct proliferative and resolution phases over several weeks. We identify specific angiogenic set points and profound alterations in vascular integrity, along with hematopoietic changes starting at the level of hematopoietic stem and progenitor cells. These findings advance our understanding of the role of Eng in vascular remodeling and may provide novel therapeutic targets for HHT. Key PointsO_LIConditional EC-Eng deficiency leads to vascular remodeling in the BM of mice in a temporally orchestrated manner. C_LIO_LIEC-Eng facilitates vascular integrity, hematopoietic homeostasis, and immune cell mobilization. C_LI

molecular biology↗

Single NV in nanodiamond for quantum sensing of protein dynamics in an ABEL trap

Enzymes are cellular protein machines using a variety of conformational changes to power fast biochemical catalysis. Our goal is to exploit the single-spin properties of the luminescent NV (nitrogen-vacancy) center in nanodiamonds to reveal the dynamics of an active enzyme complex at physiological conditions with the highest spatio-temporal resolution. Specifically attached to the membrane enzyme FoF1-ATP synthase, the NV sensor will report the adenosine triphosphate (ATP)-driven full rotation of Fo motor subunits in ten consecutive 36{degrees} steps. Conformational dynamics are monitored using either a double electron-electron resonance scheme or NV- magnetometry with optical readout or using NV- relaxometry with a superparamagnetic nanoparticle as the second marker attached to the same enzyme. First, we show how all photophysical parameters like individual size, charge, brightness, spectral range of fluorescence and fluorescence lifetime can be determined for the NV- center in a single nanodiamond held in aqueous solution by a confocal anti-Brownian electrokinetic trap (ABEL trap). Stable photon count rates of individual nanodiamonds and the absence of blinking allow for observation times of single nanodiamonds in solution exceeding hundreds of seconds. For the proposed quantum sensing of nanometer-sized distance changes within an active enzyme, we show that local magnetic field fluctuations can be detected all-optically by analyzing fluorescence lifetime changes of the NV- center in each nanodiamond in solution.

biophysics↗

The biophysical basis of bacterial colony growth

Bacteria often attach to surfaces and grow densely-packed communities called biofilms. As biofilms grow, they expand across the surface, increasing their surface area and access to nutrients. Thus, the overall growth rate of a biofilm is directly dependent on its "range expansion" rate. One factor that limits the range expansion rate is vertical growth; at the biofilm edge there is a direct trade-off between horizontal and vertical growth--the more a biofilm grows up, the less it can grow out. Thus, the balance of horizontal and vertical growth impacts the range expansion rate and, crucially, the overall biofilm growth rate. However, the biophysical connection between horizontal and vertical growth remains poorly understood, due in large part to difficulty in resolving biofilm shape with sufficient spatial and temporal resolution from small length scales to macroscopic sizes. Here, we experimentally show that the horizontal expansion rate of bacterial colonies is controlled by the contact angle at the biofilm edge. Using white light interferometry, we measure the three-dimensional surface morphology of growing colonies, and find that small colonies are surprisingly well-described as spherical caps. At later times, nutrient diffusion and uptake prevent the tall colony center from growing exponentially. However, the colony edge always has a region short enough to grow exponentially; the size and shape of this region, characterized by its contact angle, along with cellular doubling time, determines the range expansion rate. We found that the geometry of the exponentially growing biofilm edge is well-described as a spherical-cap-napkin-ring, i.e., a spherical cap with a cylindrical hole in its center (where the biofilm is too tall to grow exponentially). We derive an exact expression for the spherical-cap-napkin-ring-based range expansion rate; further, to first order, the expansion rate only depends on the colony contact angle, the thickness of the exponentially growing region, and the cellular doubling time. We experimentally validate both of these expressions. In line with our theoretical predictions, we find that biofilms with long cellular doubling times and small contact angles do in fact grow faster than biofilms with short cellular doubling times and large contact angles. Accordingly, sensitivity analysis shows that biofilm growth rates are more sensitive to their contact angles than to their cellular growth rates. Thus, to understand the fitness of a growing biofilm, one must account for its shape, not just its cellular doubling time.

biophysics↗

A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match

MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs are expected to predominantly occur in the 3 untranslated region and involve perfect base-pairing of the miRNA seed. Here, we generate a high-resolution map of miR-181a/b-1 (miR-181) MREs to define the targeting rules of miR-181 in developing murine T-cells. By combining a multi-omics approach with computational high-resolution analyses, we uncover novel miR-181 targets and demonstrate that miR-181 acts predominantly through RNA destabilization. Importantly, we discover an alternative seed match and identify a distinct set of targets with repeat elements in the coding sequence which are targeted by miR-181 and mediate translational inhibition. In conclusion, deep profiling of MREs in primary cells is critical to expand physiologically relevant targetomes and establish context-dependent miRNA targeting rules. Key Points* Deep profiling identifies novel targets of miR-181 associated with global gene regulation. * miR-181 MREs in repeat elements in the coding sequence act through translational inhibition. * High-resolution analysis reveals an alternative seed match in functional MREs.

immunology↗

High-resolution mapping of cell-cycle dynamics during steady-state T-cell development and regeneration in vivo

Control of cell proliferation is critical for the lymphocyte life cycle. However, little is known on how stage-specific alterations in cell cycle behavior drive proliferation dynamics during T-cell development. Here, we employed in vivo dual-nucleoside pulse labeling combined with determination of DNA replication over time as well as fluorescent ubiquitination-based cell cycle indicator mice to establish a quantitative high-resolution map of cell cycle kinetics of thymocytes. We developed an agent-based mathematical model of T-cell developmental dynamics. To generate the capacity for proliferative bursts, cell cycle acceleration followed a stretch model, characterized by simultaneous and proportional contraction of both G1 and S phase. Analysis of cell cycle phase dynamics during regeneration showed tailored adjustments of cell cycle phase dynamics. Taken together, our results highlight intrathymic cell cycle regulation as an adjustable system to maintain physiologic tissue homeostasis and foster our understanding of dysregulation of the T-cell developmental program.

immunology↗

Structural and biochemical characterisation of the N-Carbamoyl-beta-Alanine Amidohydrolases from Rhizobium radiobacter MDC 8606

N-Carbamoyl-{beta}-Alanine Amidohydrolase (C{beta}AA) constitute one of the most important groups of industrially relevant enzymes used in production of optically pure amino acids and derivatives. In this study, a N-carbamoyl-{beta}-alanine amidohydrolase encoding gene from Rhizobium radiobacter MDC 8606 was cloned and overexpressed in Escherichia coli. The purified recombinant enzyme (RrC{beta}AA) showed a specific activity of 14 U/mg using N-carbamoyl-{beta}-alanine as a substrate with an optimum activity of 55{degrees}C at pH 8.0. In this work, we report also the first prokaryotic N-carbamoyl-{beta}-alanine amidohydrolases structure at a resolution of 2.0 [A]. A discontinuous catalytic domain and a dimerization domain attached through a flexible hinge region at the domain interface has been revealed. We have found that the ligand is interacting with a conserved glutamic acid (Glu131), histidine (H385) and arginine (Arg291) residues. Studies let us to explain the preference on the enzyme for linear carbamoyl substrates as large carbamoyl substrates cannot fit in the active site of the enzyme. This work envisages the use of RrC{beta}AA from the Rhizobium radiobacter MDC 8606 for the industrial production of L--, L-{beta}-, and L-{gamma} - amino acids. The structural analysis provides new insights on enzyme-substrate interaction, which shed light on engineering of N-carbamoyl-{beta}-alanine amidohydrolases for high catalytic activity and broad substrate specificity.

biochemistry↗

Insights from CRISPR/Cas9-mediated gene editing of centromeric histone H3 (CENH3) in carrot (Daucus carota subsp. sativus)

The generation of haploids is one of the most powerful means to accelerate the plant breeding process. In most crop species, an efficient haploid technology is not yet available or only applicable to a limited set of genotypes. Recent results published for Arabidopsis thaliana and major cereal crops like maize and wheat about successful haploid induction by CRISPR/Cas9-mediated editing of the centromeric histone H3 gene (CENH3) suggest that this novel method for the production of haploid plants might also be applicable to vegetable species like carrot. Here, we report and summarize the different experimental and genetic approaches that have been focused in the past few years on CRISPR/Cas9-based editing of the carrot CENH3 gene. We also describe the discovery of a second CENH3 locus in the carrot genome, which complicates the attempts to generate and to analyse putative haploid inducer genotypes. We show that three different CRISPR/Cas9 target constructs, used alone or in combinations, could successfully target carrot CENH3. Promising mutants such as in-frame indel or in-frame deletion mutants have been found, but their successful usage as putative haploid inducer is uncertain yet. Next generation sequencing of amplicons spanning CRISPR target sites and transcript-based amplicon sequencing seemed to be appropriate methods to select promising mutants, to estimate mutation frequencies, and to allow a first prediction which gene was concerned. Another aim of this study was the simultaneous knockout and complementation of the endogenous carrot CENH3 gene by an alien CENH3 gene. Co-transformation of a CRISPR/Cas9-based carrot CENH3 knockout construct together with a CENH3 gene cloned from ginseng (Panax ginseng) was performed by using Rhizobium rhizogenes. It was shown, that ginseng CENH3 protein is accumulated inside the kinetochore region of carrot chromosomes, indicating that PgCENH3 might be a suited candidate for this approach. However, presently it is unclear, if this gene is fully functioning during the meiotic cell divisions and able to complement lethal gametes. Challenges and future prospects to develop a CENH3-based HI system for carrot are discussed.

plant biology↗

Immobilised enzyme cascade for targeted glycosylation

Glycosylation is a critical post-translational modification of proteins, improving properties such as folding, half-life and functionality. However, glycosylation is a non-templated and heterogeneous process because of the promiscuity of the enzymes involved. Here we describe a platform for sequential glycosylation reactions for tailored sugar structures (SUGAR-TARGET) that allows bespoke, controlled N-linked glycosylation in vitro. This novel proof-of-concept system is enabled by immobilised enzymes produced with a "one-step immobilisation/purification" method to express, biotinylate in vivo and immobilise glycosyltransferases. The immobilised enzymes are used in a reaction cascade mimicking a human-like N-linked glycosylation pathway where promiscuity naturally exists. The enzyme cascade is applied to free glycans, and a monomeric Fc domain expressed in glycoengineered Pichia pastoris, yielding near homogeneous glycoforms (>95% conversion). Finally, immobilised {beta}-1,4 galactosyltransferase is used to enhance the galactosylation profile of three different IgGs yielding 80.2 - 96.3 % terminal galactosylation. Enzyme recycling was further demonstrated for 7 cycles, with a combined reaction time greater than 140 hours. The novel SUGAR-TARGET platform is easy to implement, modular and reusable, and therefore can lead to the development of homogeneous glycan structures for functional and clinical evaluation. The use of immobilised enzymes enables the economical modification of cell-based material supporting applications at a large industrial scale.

bioengineering↗