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Article: The ART of RNAylation: covalent RNA-protein linkage in bacteriophage infection.

Korn, Sophie M / Sharma, Sunny / Steckelberg, Anna-Lena

2023 Volume 49, Issue 2, Page(s) 97–98

Abstract: Bacteriophages have been a treasure trove for the discovery of fundamental biological principles and the expansion of our enzymatic toolkit since the dawn of molecular biology. In a recent study by Wolfram-Schauerte et al. these ubiquitous bacteria- ... ...

Abstract	Bacteriophages have been a treasure trove for the discovery of fundamental biological principles and the expansion of our enzymatic toolkit since the dawn of molecular biology. In a recent study by Wolfram-Schauerte et al. these ubiquitous bacteria-infecting viruses reveal yet another new biological concept: post-translational modification through covalent RNA-protein linkages.
MeSH term(s)	Bacteriophages/genetics ; RNA ; Protein Processing, Post-Translational
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2023-11-16
Publishing country	England
Document type	Journal Article
ZDB-ID	194216-5
ISSN	1362-4326 ; 0968-0004 ; 0376-5067
ISSN (online)	1362-4326
ISSN	0968-0004 ; 0376-5067
DOI	10.1016/j.tibs.2023.10.011
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Article ; Online: The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements.

Korn, Sophie Marianne / Dhamotharan, Karthikeyan / Jeffries, Cy M / Schlundt, Andreas

Nature communications

2023 Volume 14, Issue 1, Page(s) 3331

Abstract: The nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA-coating ... ...

Abstract	The nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA-coating versus precise RNA-binding to designated cis-regulatory elements. Numerous studies report the involvement of its disordered segments in non-selective RNA-recognition, but how N organizes the inevitable recognition of specific motifs remains unanswered. We here use NMR spectroscopy to systematically analyze the interactions of N's N-terminal RNA-binding domain (NTD) with individual cis RNA elements clustering in the SARS-CoV-2 regulatory 5'-genomic end. Supported by broad solution-based biophysical data, we unravel the NTD RNA-binding preferences in the natural genome context. We show that the domain's flexible regions read the intrinsic signature of preferred RNA elements for selective and stable complex formation within the large pool of available motifs.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; RNA, Viral/metabolism ; COVID-19 ; Nucleocapsid/metabolism ; Nucleocapsid Proteins/genetics ; Nucleocapsid Proteins/metabolism
Chemical Substances	RNA, Viral ; Nucleocapsid Proteins
Language	English
Publishing date	2023-06-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38882-y
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Article ; Online: The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

Sophie Marianne Korn / Karthikeyan Dhamotharan / Cy M. Jeffries / Andreas Schlundt

Nature Communications, Vol 14, Iss 1, Pp 1-

2023 Volume 17

Abstract: Abstract The nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA- ... ...

Abstract	Abstract The nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA-coating versus precise RNA-binding to designated cis-regulatory elements. Numerous studies report the involvement of its disordered segments in non-selective RNA-recognition, but how N organizes the inevitable recognition of specific motifs remains unanswered. We here use NMR spectroscopy to systematically analyze the interactions of N’s N-terminal RNA-binding domain (NTD) with individual cis RNA elements clustering in the SARS-CoV-2 regulatory 5’-genomic end. Supported by broad solution-based biophysical data, we unravel the NTD RNA-binding preferences in the natural genome context. We show that the domain’s flexible regions read the intrinsic signature of preferred RNA elements for selective and stable complex formation within the large pool of available motifs.
Keywords	Science ; Q
Subject code	612
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Insight into the Structural Basis for Dual Nucleic Acid-Recognition by the Scaffold Attachment Factor B2 Protein.

Korn, Sophie M / Von Ehr, Julian / Dhamotharan, Karthikeyan / Tants, Jan-Niklas / Abele, Rupert / Schlundt, Andreas

International journal of molecular sciences

2023 Volume 24, Issue 4

Abstract: The family of scaffold attachment factor B (SAFB) proteins comprises three members and was first identified as binders of the nuclear matrix/scaffold. Over the past two decades, SAFBs were shown to act in DNA repair, mRNA/(l)ncRNA processing and as part ... ...

Abstract	The family of scaffold attachment factor B (SAFB) proteins comprises three members and was first identified as binders of the nuclear matrix/scaffold. Over the past two decades, SAFBs were shown to act in DNA repair, mRNA/(l)ncRNA processing and as part of protein complexes with chromatin-modifying enzymes. SAFB proteins are approximately 100 kDa-sized dual nucleic acid-binding proteins with dedicated domains in an otherwise largely unstructured context, but whether and how they discriminate DNA and RNA binding has remained enigmatic. We here provide the SAFB2 DNA- and RNA-binding SAP and RRM domains in their functional boundaries and use solution NMR spectroscopy to ascribe DNA- and RNA-binding functions. We give insight into their target nucleic acid preferences and map the interfaces with respective nucleic acids on sparse data-derived SAP and RRM domain structures. Further, we provide evidence that the SAP domain exhibits intra-domain dynamics and a potential tendency to dimerize, which may expand its specifically targeted DNA sequence range. Our data provide a first molecular basis of and a starting point towards deciphering DNA- and RNA-binding functions of SAFB2 on the molecular level and serve a basis for understanding its localization to specific regions of chromatin and its involvement in the processing of specific RNA species.
MeSH term(s)	RNA/metabolism ; RNA, Messenger/metabolism ; Base Sequence ; Magnetic Resonance Spectroscopy ; Chromatin ; Binding Sites
Chemical Substances	RNA (63231-63-0) ; RNA, Messenger ; Chromatin
Language	English
Publishing date	2023-02-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24043286
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Article ; Online: NMR Reveals Specific Tracts within the Intrinsically Disordered Regions of the SARS-CoV-2 Nucleocapsid Protein Involved in RNA Encountering.

Pontoriero, Letizia / Schiavina, Marco / Korn, Sophie M / Schlundt, Andreas / Pierattelli, Roberta / Felli, Isabella C

Biomolecules

2022 Volume 12, Issue 7

Abstract: The SARS-CoV-2 nucleocapsid (N) protein is crucial for the highly organized packaging and transcription of the genomic RNA. Studying atomic details of the role of its intrinsically disordered regions (IDRs) in RNA recognition is challenging due to the ... ...

Abstract	The SARS-CoV-2 nucleocapsid (N) protein is crucial for the highly organized packaging and transcription of the genomic RNA. Studying atomic details of the role of its intrinsically disordered regions (IDRs) in RNA recognition is challenging due to the absence of structure and to the repetitive nature of their primary sequence. IDRs are known to act in concert with the folded domains of N and here we use NMR spectroscopy to identify the priming events of N interacting with a regulatory SARS-CoV-2 RNA element.
MeSH term(s)	COVID-19 ; Humans ; Magnetic Resonance Spectroscopy ; Protein Binding ; RNA, Viral/metabolism ; SARS-CoV-2
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-07-02
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12070929
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Article ; Online: Scotopic and Photopic Conventional Visual Acuity and Hyperacuity - Binocular Summation.

Korn, Sophie / Al-Nosairy, Khaldoon O / Gopiswaminathan, Akshara V / João, Catarina / Scanferla, Lorenzo / Bach, Michael / Hoffmann, Michael B

Translational vision science & technology

2024 Volume 13, Issue 4, Page(s) 25

Abstract: Purpose: The purpose of this study was to determine and compare binocular summation (BiS) of conventional visual acuity (cVA) versus hyperacuity (hVA) for photopic and scotopic luminance conditions as a potential biomarker to assess the outcome of ... ...

Abstract	Purpose: The purpose of this study was to determine and compare binocular summation (BiS) of conventional visual acuity (cVA) versus hyperacuity (hVA) for photopic and scotopic luminance conditions as a potential biomarker to assess the outcome of interventions on binocular function. Methods: Sixteen young adults (age range [years] = 21-31; 8 women; cVA logMAR < 0.0) participated in this study. The Freiburg Visual Acuity Test (FrACT) was used for VA testing and retested on another day. Both cVA and hVA were determined for dark grey optotypes on light grey background. Participants underwent 40 minutes of dark adaptation prior to scotopic VA testing. Binocular and monocular VA testing was performed. The eye with better VA over the 2 days of testing was selected, the BiS was quantified (binocular VA - better monocular VA) and repeated measures ANOVAs were performed. Results: Binocular VA exceeded monocular VA for all luminance conditions, VA-types, and sessions. We report BiS estimates for photopic and scotopic cVA and hVA, (logMAR BiS ± SEM [decimal BiS]): photopic = -0.01 ± 0.01 [1.03] and -0.06 ± 0.03 [1.15]; and scotopic = -0.05 ± 0.01 [1.12] and -0.11 ± 0.04 [1.28], respectively). Improvement for binocular vision estimates ranged from 0.01 to 0.11 logMAR. A repeated-measures ANOVA (RM ANOVA) did not reveal significant effects of LUMINANCE or VA TYPE on BiS, albeit a trend for strongest BiS for scotopic hVA (15% vs. 28%, photopic versus scotopic, respectively) and weakest for photopic cVA (3% vs. 12%, photopic versus scotopic conditions, respectively). Conclusions: Our results indicate that BiS of VA is relevant to scotopic and photopic hVA and cVA. It appears therefore a plausible candidate biomarker to assess the outcome of retinal therapies restoring rod or cone function on binocular vision. Translational relevance: Binocular summation of visual acuity might serve as a clinical biomarker to monitor therapy outcome on binocular rod and cone-mediated vision.
MeSH term(s)	Young Adult ; Humans ; Female ; Adult ; Visual Acuity ; Vision Tests/methods ; Vision, Binocular ; Vision, Ocular ; Biomarkers
Chemical Substances	Biomarkers
Language	English
Publishing date	2024-04-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2674602-5
ISSN	2164-2591 ; 2164-2591
ISSN (online)	2164-2591
ISSN	2164-2591
DOI	10.1167/tvst.13.4.25
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Article ; Online: 1

Wang, Ying / Kirkpatrick, John / Zur Lage, Susanne / Korn, Sophie M / Neißner, Konstantin / Schwalbe, Harald / Schlundt, Andreas / Carlomagno, Teresa

Biomolecular NMR assignments

2021 Volume 15, Issue 2, Page(s) 287–295

Abstract: The current COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become a worldwide health crisis, necessitating coordinated scientific research and urgent identification of new drug targets for treatment of ... ...

Abstract	The current COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become a worldwide health crisis, necessitating coordinated scientific research and urgent identification of new drug targets for treatment of COVID-19 lung disease. The covid19-nmr consortium seeks to support drug development by providing publicly accessible NMR data on the viral RNA elements and proteins. The SARS-CoV-2 genome comprises a single RNA of about 30 kb in length, in which 14 open reading frames (ORFs) have been annotated, and encodes approximately 30 proteins. The first two-thirds of the SARS-CoV-2 genome is made up of two large overlapping open-reading-frames (ORF1a and ORF1b) encoding a replicase polyprotein, which is subsequently cleaved to yield 16 so-called non-structural proteins. The non-structural protein 1 (Nsp1), which is considered to be a major virulence factor, suppresses host immune functions by associating with host ribosomal complexes at the very end of its C-terminus. Furthermore, Nsp1 facilitates initiation of viral RNA translation via an interaction of its N-terminal domain with the 5' untranslated region (UTR) of the viral RNA. Here, we report the near-complete backbone chemical-shift assignments of full-length SARS-CoV-2 Nsp1 (19.8 kDa), which reveal the domain organization, secondary structure and backbone dynamics of Nsp1, and which will be of value to further NMR-based investigations of both the biochemical and physiological functions of Nsp1.
MeSH term(s)	Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Protein Domains ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry
Chemical Substances	Viral Nonstructural Proteins
Language	English
Publishing date	2021-03-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2388861-1
ISSN	1874-270X ; 1874-2718
ISSN (online)	1874-270X
ISSN	1874-2718
DOI	10.1007/s12104-021-10019-6
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Article ; Online: 1H, 13C, and 15N backbone chemical-shift assignments of SARS-CoV-2 non-structural protein 1 (leader protein)

Wang, Ying / Kirkpatrick, John / Zur Lage, Susanne / Korn, Sophie M / Neißner, Konstantin / Schwalbe, Harald / Schlundt, Andreas / Carlomagno, Teresa

Biomolecular NMR assignments ; Netherlands

2021

Abstract	The current COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become a worldwide health crisis, necessitating coordinated scientific research and urgent identification of new drug targets for treatment of COVID-19 lung disease. The covid19-nmr consortium seeks to support drug development by providing publicly accessible NMR data on the viral RNA elements and proteins. The SARS-CoV-2 genome comprises a single RNA of about 30 kb in length, in which 14 open reading frames (ORFs) have been annotated, and encodes approximately 30 proteins. The first two-thirds of the SARS-CoV-2 genome is made up of two large overlapping open-reading-frames (ORF1a and ORF1b) encoding a replicase polyprotein, which is subsequently cleaved to yield 16 so-called non-structural proteins. The non-structural protein 1 (Nsp1), which is considered to be a major virulence factor, suppresses host immune functions by associating with host ribosomal complexes at the very end of its C-terminus. Furthermore, Nsp1 facilitates initiation of viral RNA translation via an interaction of its N-terminal domain with the 5' untranslated region (UTR) of the viral RNA. Here, we report the near-complete backbone chemical-shift assignments of full-length SARS-CoV-2 Nsp1 (19.8 kDa), which reveal the domain organization, secondary structure and backbone dynamics of Nsp1, and which will be of value to further NMR-based investigations of both the biochemical and physiological functions of Nsp1.
Keywords	5′ untranslated region ; NMR spectroscopy ; New drug targets ; Non-structural proteins ; Nsp1 ; SARS-CoV-2
Subject code	572
Language	English
Publishing date	2021-03-26
Publisher	SPringer
Publishing country	de
Document type	Article ; Online
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Article ; Online: Use and Perception of Digital Health Technologies by Surgical Patients in Germany in the Pre-COVID-19 Era: Survey Study.

Korn, Sandra / Böttcher, Maximilian David / Busse, Theresa Sophie / Kernebeck, Sven / Breucha, Michael / Ehlers, Jan / Kahlert, Christoph / Weitz, Jürgen / Bork, Ulrich

JMIR formative research

2022 Volume 6, Issue 5, Page(s) e33985

Abstract: Background: This survey study investigates surgical patients' use and perception of digital health technologies in Germany in the pre-COVID-19 era.: Objective: The objective of this study was to relate surgical patients' characteristics to the use ... ...

Abstract	Background: This survey study investigates surgical patients' use and perception of digital health technologies in Germany in the pre-COVID-19 era. Objective: The objective of this study was to relate surgical patients' characteristics to the use and perception of several digital health technologies. Methods: In this single-center, cross-sectional survey study in the outpatient department of a university hospital in Germany, 406 patients completed a questionnaire with the following three domains: general information and use of the internet, smartphones, and general digital health aspects. Analyses were stratified by age group and highest education level achieved. Results: We found significant age-based differences in most of the evaluated aspects. Younger patients were more open to using new technologies in private and medical settings but had more security concerns. Although searching for information on illnesses on the web was common, the overall acceptance of and trust in web-based consultations were rather low, with <50% of patients in each age group reporting acceptance and trust. More people with academic qualifications than without academic qualifications searched for information on the web before visiting physicians (73/121, 60.3% and 100/240, 41.7%, respectively). Patients with academic degrees were also more engaged in health-related information and communication technology use. Conclusions: These results support the need for eHealth literacy, health literacy, and available digital devices and internet access to support the active, meaningful use of information and communication technologies in health care. Uncertainties and a lack of knowledge exist, especially regarding telemedicine and the use of medical and health apps. This is especially pronounced among older patients and patients with a low education status.
Language	English
Publishing date	2022-05-20
Publishing country	Canada
Document type	Journal Article
ISSN	2561-326X
ISSN (online)	2561-326X
DOI	10.2196/33985
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Article ; Online: 1

Korn, Sophie M / Lambertz, Roderick / Fürtig, Boris / Hengesbach, Martin / Löhr, Frank / Richter, Christian / Schwalbe, Harald / Weigand, Julia E / Wöhnert, Jens / Schlundt, Andreas

Biomolecular NMR assignments

2020 Volume 15, Issue 1, Page(s) 129–135

Abstract: The current outbreak of the highly infectious COVID-19 respiratory disease is caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). To fight the pandemic, the search for promising viral drug targets has become a ... ...

Abstract	The current outbreak of the highly infectious COVID-19 respiratory disease is caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). To fight the pandemic, the search for promising viral drug targets has become a cross-border common goal of the international biomedical research community. Within the international Covid19-NMR consortium, scientists support drug development against SARS-CoV-2 by providing publicly available NMR data on viral proteins and RNAs. The coronavirus nucleocapsid protein (N protein) is an RNA-binding protein involved in viral transcription and replication. Its primary function is the packaging of the viral RNA genome. The highly conserved architecture of the coronavirus N protein consists of an N-terminal RNA-binding domain (NTD), followed by an intrinsically disordered Serine/Arginine (SR)-rich linker and a C-terminal dimerization domain (CTD). Besides its involvement in oligomerization, the CTD of the N protein (N-CTD) is also able to bind to nucleic acids by itself, independent of the NTD. Here, we report the near-complete NMR backbone chemical shift assignments of the SARS-CoV-2 N-CTD to provide the basis for downstream applications, in particular site-resolved drug binding studies.
MeSH term(s)	Carbon Isotopes ; Coronavirus Nucleocapsid Proteins/chemistry ; Crystallography, X-Ray ; Dimerization ; Drug Design ; Hydrogen ; Hydrogen-Ion Concentration ; Magnetic Resonance Spectroscopy ; Nitrogen Isotopes ; Phosphoproteins/chemistry ; Protein Binding ; Protein Domains ; Protein Interaction Mapping ; Protein Structure, Secondary ; SARS-CoV-2/chemistry
Chemical Substances	Carbon Isotopes ; Coronavirus Nucleocapsid Proteins ; Nitrogen Isotopes ; Nitrogen-15 ; Phosphoproteins ; nucleocapsid phosphoprotein, SARS-CoV-2 ; Hydrogen (7YNJ3PO35Z) ; Carbon-13 (FDJ0A8596D)
Language	English
Publishing date	2020-12-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2388861-1
ISSN	1874-270X ; 1874-2718
ISSN (online)	1874-270X
ISSN	1874-2718
DOI	10.1007/s12104-020-09995-y
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