TY  - JOUR
A1  - Whisnant, Adam W.
A1  - Jürges, Christopher S.
A1  - Hennig, Thomas
A1  - Wyler, Emanuel
A1  - Prusty, Bhupesh
A1  - Rutkowski, Andrzej J.
A1  - L'hernault, Anne
A1  - Djakovic, Lara
A1  - Göbel, Margarete
A1  - Döring, Kristina
A1  - Menegatti, Jennifer
A1  - Antrobus, Robin
A1  - Matheson, Nicholas J.
A1  - Künzig, Florian W. H.
A1  - Mastrobuoni, Guido
A1  - Bielow, Chris
A1  - Kempa, Stefan
A1  - Liang, Chunguang
A1  - Dandekar, Thomas
A1  - Zimmer, Ralf
A1  - Landthaler, Markus
A1  - Grässer, Friedrich
A1  - Lehner, Paul J.
A1  - Friedel, Caroline C.
A1  - Erhard, Florian
A1  - Dölken, Lars
T1  - Integrative functional genomics decodes herpes simplex virus 1
JF  - Nature Communications
N2  - The predicted 80 open reading frames (ORFs) of herpes simplex virus 1 (HSV-1) have been intensively studied for decades. Here, we unravel the complete viral transcriptome and translatome during lytic infection with base-pair resolution by computational integration of multi-omics data. We identify a total of 201 transcripts and 284 ORFs including all known and 46 novel large ORFs. This includes a so far unknown ORF in the locus deleted in the FDA-approved oncolytic virus Imlygic. Multiple transcript isoforms expressed from individual gene loci explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncations. We show that NTEs with non-canonical start codons govern the subcellular protein localization and packaging of key viral regulators and structural proteins. We extend the current nomenclature to include all viral gene products and provide a genome browser that visualizes all the obtained data from whole genome to single-nucleotide resolution. Here, using computational integration of multi-omics data, the authors provide a detailed transcriptome and translatome of herpes simplex virus 1 (HSV-1), including previously unidentified ORFs and N-terminal extensions. The study also provides a HSV-1 genome browser and should be a valuable resource for further research.
KW  - infected-cell protein
KW  - messenger RNA
KW  - binding protein
KW  - type 1
KW  - identification
KW  - ICP27
KW  - translation
KW  - expression
KW  - sequence
KW  - domain
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-229884
VL  - 11
ER  - 
TY  - JOUR
A1  - Rutkowski, Andrzej J.
A1  - Erhard, Florian
A1  - L'Hernault, Anne
A1  - Bonfert, Thomas
A1  - Schilhabel, Markus
A1  - Crump, Colin
A1  - Rosenstiel, Philip
A1  - Efstathiou, Stacey
A1  - Zimmer, Ralf
A1  - Friedel, Caroline C.
A1  - Dölken, Lars
T1  - Widespread disruption of host transcription termination in HSV-1 infection
JF  - Nature Communications
N2  - Herpes simplex virus 1 (HSV-1) is an important human pathogen and a paradigm for virus-induced host shut-off. Here we show that global changes in transcription and RNA processing and their impact on translation can be analysed in a single experimental setting by applying 4sU-tagging of newly transcribed RNA and ribosome profiling to lytic HSV-1 infection. Unexpectedly, we find that HSV-1 triggers the disruption of transcription termination of cellular, but not viral, genes. This results in extensive transcription for tens of thousands of nucleotides beyond poly(A) sites and into downstream genes, leading to novel intergenic splicing between exons of neighbouring cellular genes. As a consequence, hundreds of cellular genes seem to be transcriptionally induced but are not translated. In contrast to previous reports, we show that HSV-1 does not inhibit co-transcriptional splicing. Our approach thus substantially advances our understanding of HSV-1 biology and establishes HSV-1 as a model system for studying transcription termination.
KW  - herpes simplex virus
KW  - RNA polymerase II
KW  - gene expression
KW  - alpha-globin
KW  - motif discovery
KW  - regulatory protein ICP27
KW  - poly(A) site usage
KW  - pre-messenger RNA
KW  - splicing inhibition
KW  - type 1 ICP27
Y1  - 2015
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-148643
VL  - 6
IS  - 7126
ER  - 
TY  - JOUR
A1  - vom Dahl, Christian
A1  - Müller, Christoph Emanuel
A1  - Berisha, Xhevat
A1  - Nagel, Georg
A1  - Zimmer, Thomas
T1  - Coupling the cardiac voltage-gated sodium channel to channelrhodopsin-2 generates novel optical switches for action potential studies
JF  - Membranes
N2  - Voltage-gated sodium (Na\(^+\)) channels respond to short membrane depolarization with conformational changes leading to pore opening, Na\(^+\) influx, and action potential (AP) upstroke. In the present study, we coupled channelrhodopsin-2 (ChR2), the key ion channel in optogenetics, directly to the cardiac voltage-gated Na\(^+\) channel (Na\(_v\)1.5). Fusion constructs were expressed in Xenopus laevis oocytes, and electrophysiological recordings were performed by the two-microelectrode technique. Heteromeric channels retained both typical Na\(_v\)1.5 kinetics and light-sensitive ChR2 properties. Switching to the current-clamp mode and applying short blue-light pulses resulted either in subthreshold depolarization or in a rapid change of membrane polarity typically seen in APs of excitable cells. To study the effect of individual K\(^+\) channels on the AP shape, we co-expressed either K\(_v\)1.2 or hERG with one of the Na\(_v\)1.5-ChR2 fusions. As expected, both delayed rectifier K\(^+\) channels shortened AP duration significantly. K\(_v\)1.2 currents remarkably accelerated initial repolarization, whereas hERG channel activity efficiently restored the resting membrane potential. Finally, we investigated the effect of the LQT3 deletion mutant ΔKPQ on the AP shape and noticed an extremely prolonged AP duration that was directly correlated to the size of the non-inactivating Na\(^+\) current fraction. In conclusion, coupling of ChR2 to a voltage-gated Na\(^+\) channel generates optical switches that are useful for studying the effect of individual ion channels on the AP shape. Moreover, our novel optogenetic approach provides the potential for an application in pharmacology and optogenetic tissue-engineering.
KW  - optogenetics
KW  - channelrhodopsin
KW  - voltage-gated Na\(^+\) channel
KW  - action potential
KW  - delayed rectifier potassium channel
KW  - hERG
KW  - long QT syndrome
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-288228
SN  - 2077-0375
VL  - 12
IS  - 10
ER  - 
TY  - JOUR
A1  - Pluta, Natalie
A1  - Hoffjan, Sabine
A1  - Zimmer, Frederic
A1  - Köhler, Cornelia
A1  - Lücke, Thomas
A1  - Mohr, Jennifer
A1  - Vorgerd, Matthias
A1  - Nguyen, Hoa Huu Phuc
A1  - Atlan, David
A1  - Wolf, Beat
A1  - Zaum, Ann-Kathrin
A1  - Rost, Simone
T1  - Homozygous inversion on chromosome 13 involving SGCG detected by short read whole genome sequencing in a patient suffering from limb-girdle muscular dystrophy
JF  - Genes
N2  - New techniques in molecular genetic diagnostics now allow for accurate diagnosis in a large proportion of patients with muscular diseases. Nevertheless, many patients remain unsolved, although the clinical history and/or the muscle biopsy give a clear indication of the involved genes. In many cases, there is a strong suspicion that the cause must lie in unexplored gene areas, such as deep-intronic or other non-coding regions. In order to find these changes, next-generation sequencing (NGS) methods are constantly evolving, making it possible to sequence entire genomes to reveal these previously uninvestigated regions. Here, we present a young woman who was strongly suspected of having a so far genetically unsolved sarcoglycanopathy based on her clinical history and muscle biopsy. Using short read whole genome sequencing (WGS), a homozygous inversion on chromosome 13 involving SGCG and LINC00621 was detected. The breakpoint in intron 2 of SGCG led to the absence of γ-sarcoglycan, resulting in the manifestation of autosomal recessive limb-girdle muscular dystrophy 5 (LGMDR5) in the young woman.
KW  - inversion
KW  - sarcoglycanopathy
KW  - whole genome sequencing (WGS)
KW  - next generation sequencing (NGS)
KW  - LGMDR5
KW  - muscle disease
KW  - genetic diagnostics
Y1  - 2022
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-288122
SN  - 2073-4425
VL  - 13
IS  - 10
ER  - 
TY  - JOUR
A1  - Ghirardo, Andrea
A1  - Nosenko, Tetyana
A1  - Kreuzwieser, Jürgen
A1  - Winkler, J. Barbro
A1  - Kruse, Jörg
A1  - Albert, Andreas
A1  - Merl-Pham, Juliane
A1  - Lux, Thomas
A1  - Ache, Peter
A1  - Zimmer, Ina
A1  - Alfarraj, Saleh
A1  - Mayer, Klaus F. X.
A1  - Hedrich, Rainer
A1  - Rennenberg, Heinz
A1  - Schnitzler, Jörg-Peter
T1  - Protein expression plasticity contributes to heat and drought tolerance of date palm
JF  - Oecologia
N2  - Climate change is increasing the frequency and intensity of warming and drought periods around the globe, currently representing a threat to many plant species. Understanding the resistance and resilience of plants to climate change is, therefore, urgently needed. As date palm (Phoenix dactylifera) evolved adaptation mechanisms to a xeric environment and can tolerate large diurnal and seasonal temperature fluctuations, we studied the protein expression changes in leaves, volatile organic compound emissions, and photosynthesis in response to variable growth temperatures and soil water deprivation. Plants were grown under controlled environmental conditions of simulated Saudi Arabian summer and winter climates challenged with drought stress. We show that date palm is able to counteract the harsh conditions of the Arabian Peninsula by adjusting the abundances of proteins related to the photosynthetic machinery, abiotic stress and secondary metabolism. Under summer climate and water deprivation, these adjustments included efficient protein expression response mediated by heat shock proteins and the antioxidant system to counteract reactive oxygen species formation. Proteins related to secondary metabolism were downregulated, except for the P. dactylifera isoprene synthase (PdIspS), which was strongly upregulated in response to summer climate and drought. This study reports, for the first time, the identification and functional characterization of the gene encoding for PdIspS, allowing future analysis of isoprene functions in date palm under extreme environments. Overall, the current study shows that reprogramming of the leaf protein profiles confers the date palm heat- and drought tolerance. We conclude that the protein plasticity of date palm is an important mechanism of molecular adaptation to environmental fluctuations.
KW  - abiotic stress
KW  - isoprene
KW  - proteomics
KW  - photosynthesis
KW  - Phoenix dactylifera
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-308075
SN  - 0029-8549
SN  - 1432-1939
VL  - 197
IS  - 4
ER  -