Research Area D - Publications 2019

Journal of Cell Science; 2019; 132: jcs223891; doi: 10.1242/jcs.223891
Journal of Cell Science, online article

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The Fe(II) and 2-oxoglutarate-dependent oxygenase Alkb homologue 1 (Alkbh1) has been shown to act on a wide range of substrates, like DNA, tRNA and histones. Thereby different enzymatic activities have been identified including, among others, demethylation of N3-methylcytosine (m3C) in RNA- and single-stranded DNA oligonucleotides, demethylation of ...

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PNAS, 116 (34) 16866-16871, https://doi.org/10.1073/pnas.1903642116
PNAS, online article

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Lipid droplets (LDs) are ubiquitous organelles comprising a central hub for cellular lipid metabolism and trafficking. This role is tightly associated with their interactions with several cellular organelles. Here, we provide a systematic and quantitative structural description of LDs in their native state in HeLa cells enabled by cellular cryoelectron ...

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Scientific Reports, (2019) 9:10131, https://doi.org/10.1038/s41598-019-46171-2
Scientific Reports, online article

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Assembling composite DNA modules from custom DNA parts has become routine due to recent technological breakthroughs such as Golden Gate modular cloning. Using Golden Gate, one can efficiently assemble custom transcription units and piece units together to generate higher-order assemblies. Although Golden Gate cloning systems have been developed to assemble DNA ...

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Angewandte Chemie International Edition, https://doi.org/10.1002/ange.201904193
Angewandte Chemie International Edition, online article

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Requirements for novel bioconjugation reactions for the synthesis of Antibody‐Drug‐Conjugates (ADCs) are exceptionally high, since conjugation selectivity as well as stability and hydrophobicity of linkers and payloads drastically influence the performance and safety profile of the final product. Herein we describe Cys‐selective ethynylphosphonamidates as new ...

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Leukemia, https://doi.org/10.1038/s41375-019-0497-6
Leukemia, online article

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Acute myeloid leukemia (AML) is an aggressive hematologic neoplasm resulting from the malignant transformation of myeloid progenitors. Despite intensive chemotherapy leading to initial treatment responses, relapse caused by intrinsic or acquired drug resistance represents a major challenge. Here, we report that histone 3 lysine 27 demethylase KDM6A (UTX) is ...

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Nucleic Acids Research, 2019, 1, doi: 10.1093/nar/gkz466
Nucleic Acids Research, online article

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Affinity maturation of the humoral immune response depends on somatic hypermutation (SHM) of immunoglobulin (Ig) genes, which is initiated by targeted lesion introduction by activation-induced deaminase (AID), followed by error-prone DNA repair. Stringent regulation of this process is essential to prevent genetic instability, but no negative feedback control has ...

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Front. Microbiol., 10:1148, doi: 10.3389/fmicb.2019.01148
Front. Microbiol., online article

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Tripeptides with two consecutive prolines are the shortest and most frequent sequences causing ribosome stalling. The bacterial translation elongation factor P (EF-P) relieves this arrest, allowing protein biosynthesis to continue. A seven amino acids long loop between beta-strands β3/β4 is crucial for EF-P function and modified at its tip by lysylation of lysine ...

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EMBO J (2019)38:e101650, https://doi.org/10.15252/embj.2019101650
EMBO, online article

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Small regulatory RNAs (sRNAs) are crucial components of many stress response systems. The envelope stress response (ESR) of Gram‐negative bacteria is a paradigm for sRNA‐mediated stress management and involves, among other factors, the alternative sigma factor E (σE) and one or more sRNAs. In this study, we identified the MicV sRNA as a new member of the σE ...

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Biol. Lett., 15: 20190068., http://dx.doi.org/10.1098/rsbl.2019.0068
Biol. Lett., online article

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The carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) consists of 26 and 52 heptad-repeats in yeast and mammals, respectively. Studies in yeast showed that the strong periodicity of the YSPTSPS heptads is dispensable for cell growth and that di-heptads interspersed by spacers can act as minimal functional units (MFUs) to fulfil ...

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jmb, https://doi.org/10.1016/j.jmb.2019.03.032
jmb, online article

 

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A complex relationship exists between environmental factors, signaling networks and phenotypic individuality in bacteria. In this review, we will focus on the organization, function and control points of multiple-input histidine kinase-based signaling cascades as a source of phenotypic heterogeneity. In particular, we will examine the quorum sensing cascade in ...

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Org. Biomol. Chem., 2019, DOI: 10.1039/c9ob00508k
Org. Biomol. Chem., online article

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We introduce a chemoenzymatic strategy for straightforward in vitro generation of C-terminally linked fusion proteins. Tubulin tyrosine ligase is used for the incorporation of complementary click chemistry handles facilitating subsequent formation of functional bispecific antibody-fragments. This simple strategy may serve as central conjugation hub for a modular ...

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Angewandte Chemie International Edition, https://doi.org/10.1002/anie.201814715
Angewandte Chemie International Edition, online article

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We describe a new technique in protein synthesis that extends the existing repertoire of methods for protein modification: A chemoselective reaction that induces reactivity for a subsequent bioconjugation. Hereby, an azide building block reacts first with an ethynylphosphonite via the Staudinger‐phosphonite reaction (SPhR) to an ethynylphosphonamidate. The ...

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Journal of Bacteriology, Volume 201, Issue 3, e00610-18, https://doi.org/10.1128/JB.00610-18
Journal of Bacteriology, online article

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Escherichia coli and many other bacterial species can enter into a viable but nonculturable (VBNC) state, which is a survival strategy adopted by cells exposed to adverse environmental conditions. Pyruvate is known to be one factor that promotes resuscitation of VBNC cells. Here we studied the role of a pyruvate-sensing network, composed of the histidine ...

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Nucleic Acids Research, 2019, 1, doi: 10.1093/nar/gky1320
Nucleic Acids Research, online article

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Bacteria use quorum sensing to monitor cell density and coordinate group behaviours. In Vibrio cholerae, the causative agent of the diarrheal disease cholera, quorum sensing is connected to virulence gene expression via the two autoinducer molecules, AI-2 and CAI-1. Both autoinducers share one signal transduction pathway to control the production of AphA, a key ...

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COMMUNICATIONS BIOLOGY, (2019) 2:4, https://doi.org/10.1038/s42003-018-0248-7
COMMUNICATIONS BIOLOGY, online article

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All living cells have a large number of proteins that are anchored with one transmembrane helix in the cytoplasmic membrane. Almost nothing is known about their spatiotemporal organization in whole cells. Here we report on the localization and dynamics of one representative, the pH sensor and transcriptional regulator CadC in Escherichia coli. Fluorophore-tagged ...

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