---
APC_amount: 12348 EUR
OA_place: publisher
OA_type: hybrid
_id: '18778'
abstract:
- lang: eng
text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
repress transcription remains unclear. Here we present cryogenic-electron microscopy
structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
and RNA bind to Pol II during transcription elongation. Further, we show how distinct
domains of the general transcription factor TFIIF control repressive activity.
Together, we reveal how a noncoding RNA can regulate mammalian gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
- _id: PreCl
acknowledgement: We thank the members of the Bernecky laboratory for helpful discussions
and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding
assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU
data collection. We thank D. Slade (Max Perutz Laboratories and Medical University
of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank
N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of
Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank
C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The
funders had no role in study design, data collection and analysis, decision to publish
or preparation of the manuscript. This research was further supported by the Scientific
Service Units of ISTA through resources provided by the Laboratory Support Facility,
Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian
transcriptional repression by noncoding RNA. Nature Structural & Molecular
Biology. 2025;32:607-612. doi:10.1038/s41594-024-01448-7
apa: Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., & Bernecky, C. (2025).
Mechanism of mammalian transcriptional repression by noncoding RNA. Nature
Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01448-7
chicago: Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie
Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.”
Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01448-7.
ieee: K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism
of mammalian transcriptional repression by noncoding RNA,” Nature Structural
& Molecular Biology, vol. 32. Springer Nature, pp. 607–612, 2025.
ista: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of
mammalian transcriptional repression by noncoding RNA. Nature Structural &
Molecular Biology. 32, 607–612.
mla: Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression
by Noncoding RNA.” Nature Structural & Molecular Biology, vol. 32,
Springer Nature, 2025, pp. 607–12, doi:10.1038/s41594-024-01448-7.
short: K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural
& Molecular Biology 32 (2025) 607–612.
corr_author: '1'
date_created: 2025-01-08T11:20:20Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-11-20T10:28:36Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1038/s41594-024-01448-7
external_id:
isi:
- '001390268000001'
pmid:
- '39762629'
file:
- access_level: open_access
checksum: 2919b30b271f395888e880076a680d73
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T08:17:27Z
date_updated: 2025-04-16T08:17:27Z
file_id: '19573'
file_name: 2025_NatureStrucMolBiol_Tluckova.pdf
file_size: 9306639
relation: main_file
success: 1
file_date_updated: 2025-04-16T08:17:27Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
page: 607-612
pmid: 1
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
grant_number: P34185
name: Regulation of mammalian transcription by noncoding RNA
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14644'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2025'
...
---
OA_type: closed access
_id: '19465'
article_number: '415'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Bernecky C. Understanding the machinery that reads the genome. Nature Reviews
Molecular Cell Biology. 2025;26. doi:10.1038/s41580-025-00844-1
apa: Bernecky, C. (2025). Understanding the machinery that reads the genome. Nature
Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-025-00844-1
chicago: Bernecky, Carrie. “Understanding the Machinery That Reads the Genome.”
Nature Reviews Molecular Cell Biology. Springer Nature, 2025. https://doi.org/10.1038/s41580-025-00844-1.
ieee: C. Bernecky, “Understanding the machinery that reads the genome,” Nature
Reviews Molecular Cell Biology, vol. 26. Springer Nature, 2025.
ista: Bernecky C. 2025. Understanding the machinery that reads the genome. Nature
Reviews Molecular Cell Biology. 26, 415.
mla: Bernecky, Carrie. “Understanding the Machinery That Reads the Genome.” Nature
Reviews Molecular Cell Biology, vol. 26, 415, Springer Nature, 2025, doi:10.1038/s41580-025-00844-1.
short: C. Bernecky, Nature Reviews Molecular Cell Biology 26 (2025).
corr_author: '1'
date_created: 2025-03-31T10:07:22Z
date_published: 2025-06-01T00:00:00Z
date_updated: 2025-09-30T11:20:36Z
day: '01'
department:
- _id: CaBe
doi: 10.1038/s41580-025-00844-1
external_id:
isi:
- '001455740100001'
pmid:
- '40155512'
intvolume: ' 26'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
pmid: 1
publication: Nature Reviews Molecular Cell Biology
publication_identifier:
eissn:
- 1471-0080
issn:
- 1471-0072
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Understanding the machinery that reads the genome
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 26
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20077'
abstract:
- lang: eng
text: Hyaluronic acid (HA) is a key extracellular matrix component of vertebrates,
where it mediates cell adhesion, immune regulation, and tissue remodeling through
its interaction with specific receptors. Although HA has been detected in a few
invertebrate species, the lack of fundamental components of the molecular HA pathway
poses relevant objections about its functional role in these species. Mining genomic
and transcriptomic data, we considered the conservation of the gene locus encoding
for the extracellular link protein (XLINK) in marine mussels as well as its expression
patterns. Structural and phylogenetic analyses were undertaken to evaluate possible
similarities with vertebrate orthologs and to infer the origin of this gene in
invertebrates. Biochemical analysis was used to quantify HA in tissues of Mytilus
galloprovincialis. As a result, we confirm that the mussel can produce HA (up
to 1.02 ng/mg in mantle) and that its genome encodes two XLINK gene loci. These
loci are conserved in Mytilidae species and show a complex evolutionary path.
Mussel XLINK genes appeared to be expressed during developmental stages in three
mussel species, ranking in the top 100 expressed genes in M. trossulus at 17 h
post-fertilization. In conclusion, the presence of HA and an active gene with
the potential to bind HA suggests that mussels have the potential to synthesize
and use HA and are among the few invertebrates encoding this gene.
acknowledgement: 'This research was funded by the Italian Ministry of University and
Research (MIUR), grant ID: P2022JEEMT (Developing a tool for the study of haplotype
diversity in Mytilus galloprovincialis (HAMIGA)).'
article_number: '930'
article_processing_charge: Yes
article_type: original
author:
- first_name: Umberto
full_name: Rosani, Umberto
last_name: Rosani
- first_name: Nehir
full_name: Altan, Nehir
last_name: Altan
- first_name: Paola
full_name: Venier, Paola
last_name: Venier
- first_name: Enrico
full_name: Bortoletto, Enrico
last_name: Bortoletto
- first_name: Nicola
full_name: Volpi, Nicola
last_name: Volpi
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. Ancestral origin
and functional expression of a hyaluronic acid pathway complement in mussels.
Biology. 2025;14(8). doi:10.3390/biology14080930
apa: Rosani, U., Altan, N., Venier, P., Bortoletto, E., Volpi, N., & Bernecky,
C. (2025). Ancestral origin and functional expression of a hyaluronic acid pathway
complement in mussels. Biology. MDPI. https://doi.org/10.3390/biology14080930
chicago: Rosani, Umberto, Nehir Altan, Paola Venier, Enrico Bortoletto, Nicola Volpi,
and Carrie Bernecky. “Ancestral Origin and Functional Expression of a Hyaluronic
Acid Pathway Complement in Mussels.” Biology. MDPI, 2025. https://doi.org/10.3390/biology14080930.
ieee: U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, and C. Bernecky,
“Ancestral origin and functional expression of a hyaluronic acid pathway complement
in mussels,” Biology, vol. 14, no. 8. MDPI, 2025.
ista: Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. 2025. Ancestral
origin and functional expression of a hyaluronic acid pathway complement in mussels.
Biology. 14(8), 930.
mla: Rosani, Umberto, et al. “Ancestral Origin and Functional Expression of a Hyaluronic
Acid Pathway Complement in Mussels.” Biology, vol. 14, no. 8, 930, MDPI,
2025, doi:10.3390/biology14080930.
short: U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, C. Bernecky, Biology
14 (2025).
date_created: 2025-07-25T08:28:26Z
date_published: 2025-07-24T00:00:00Z
date_updated: 2025-09-30T14:10:07Z
day: '24'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.3390/biology14080930
external_id:
isi:
- '001557922100001'
file:
- access_level: open_access
checksum: f5e059e66803fa54249c1db029aef0f6
content_type: application/pdf
creator: dernst
date_created: 2025-07-31T09:11:09Z
date_updated: 2025-07-31T09:11:09Z
file_id: '20097'
file_name: 2025_Biology_Rosani.pdf
file_size: 1885781
relation: main_file
success: 1
file_date_updated: 2025-07-31T09:11:09Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '8'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Biology
publication_identifier:
issn:
- 2079-7737
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Ancestral origin and functional expression of a hyaluronic acid pathway complement
in mussels
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 14
year: '2025'
...
---
_id: '20804'
abstract:
- lang: eng
text: RNA polymerase II (Pol II) must be assembled in the cytoplasm before it enters
the nucleus, where it transcribes protein-coding genes. Although transcription
by Pol II is intensively studied, how this central multi-subunit enzyme is made
and the role of dedicated factors remains unclear. Here, we report the integrative
structural analysis of a native human Pol II from the cytoplasm captured near
the end of biogenesis. The complex contained Gdown1 and three biogenesis factors
– RPAP2 and the critical small GTPases GPN1 and GPN3. Cryo-EM analysis of the
complex revealed how Gdown1 and RPAP2 associate with Pol II and prevent the premature
association of transcription factors. Further biochemical and cryo-EM analysis
revealed how RPAP2 recruits GPN1–GPN3 to the complex, and how the assembly of
the RPAP2–GPN1–GPN3 complex is controlled by GTP hydrolysis. The combined results
uncover a network of interactions that chaperone cytoplasmic Pol II to prevent
aberrant interactions, reveal a GTP-controlled switch during the final stages
of Pol II biogenesis, and suggest a general mechanism for the action of GPN-loop
GTPase family of enzymes.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
- _id: PreCl
acknowledgement: We thank A. Salmazo for assistance with Pol II purification. We thank
staff at the VBCF Proteomics facility for immunoprecipitation-mass spectrometry
analysis, and J.A. Stopp for assistance with IP-MS data visualization. This research
was further supported by the Scientific Service Units (SSUs) of IST Austria through
resources provided by the Lab Support Facility (LSF), Electron Microscopy (EMF),
Scientific Computing (SciComp), and the Preclinical Facility (PCF).
article_processing_charge: No
author:
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: Benjamin
full_name: Neuditschko, Benjamin
last_name: Neuditschko
- first_name: Ulla
full_name: Schellhaas, Ulla
last_name: Schellhaas
- first_name: Clemens
full_name: Plaschka, Clemens
last_name: Plaschka
- first_name: Franz
full_name: Herzog, Franz
last_name: Herzog
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure
of cytoplasmic RNA polymerase II. 2025. doi:10.64898/2025.12.10.692585
apa: Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., &
Bernecky, C. (2025). Structure of cytoplasmic RNA polymerase II. bioRxiv. https://doi.org/10.64898/2025.12.10.692585
chicago: Hlavata, Annamaria, Benjamin Neuditschko, Ulla Schellhaas, Clemens Plaschka,
Franz Herzog, and Carrie Bernecky. “Structure of Cytoplasmic RNA Polymerase II.”
bioRxiv, 2025. https://doi.org/10.64898/2025.12.10.692585.
ieee: A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, and C.
Bernecky, “Structure of cytoplasmic RNA polymerase II.” bioRxiv, 2025.
ista: Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C.
2025. Structure of cytoplasmic RNA polymerase II. 10.64898/2025.12.10.692585.
mla: Hlavata, Annamaria, et al. Structure of Cytoplasmic RNA Polymerase II.
bioRxiv, 2025, doi:10.64898/2025.12.10.692585.
short: A. Hlavata, B. Neuditschko, U. Schellhaas, C. Plaschka, F. Herzog, C. Bernecky,
(2025).
corr_author: '1'
date_created: 2025-12-11T13:33:27Z
date_published: 2025-12-10T00:00:00Z
date_updated: 2025-12-15T09:48:22Z
day: '10'
department:
- _id: CaBe
doi: 10.64898/2025.12.10.692585
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.64898/2025.12.10.692585
month: '12'
oa: 1
oa_version: None
publication_status: published
publisher: bioRxiv
status: public
title: Structure of cytoplasmic RNA polymerase II
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
OA_place: publisher
_id: '19431'
abstract:
- lang: eng
text: "Gene expression is crucial for cell differentiation, development and survival
of\r\norganisms. It consists of several steps, starting with transcription that
is mediated by\r\nRNA polymerases. These are protein machineries transcribing
and producing different\r\ntypes of RNAs. Although, the individual steps of transcription
by RNA polymerase II\r\n(Pol II) as well as the structure of Pol II has been extensively
studied, surprisingly,\r\nthere is still little known about its regulation and
assembly in cytoplasm. Among the\r\nproteins that are important in biogenesis
of Pol II are RNA polymerase II associating\r\nproteins (RPAP) and small GPN-loop
GTPases (GPN). Both of these protein groups\r\nwere shown to take essential part
in assembly of Pol II.\r\nThe aim of this project was to deepen our knowledge
in regulation of Pol II in\r\nthe cytoplasm as well as the proteins involved in
this process. Techniques of structural\r\nbiology, biochemistry and cell biology
were employed to study and characterize cytoplasmic Pol II and its interacting
partners.\r\nThis study shows for the first time the structure of cytoplasmic
Pol II at high\r\nresolution. The structure also reveals proteins interacting
with Pol II in cytoplasm,\r\nnamely GDOWN1, RPAP2. Comparing the structure of
cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp
region that is not in closed state.\r\nFurthermore, GDOWN1 and RPAP2 make steric
clashes with various transcription\r\nfactors bound to Pol II during different
stages of transcription. Even though GPN1 and\r\nGPN3 proteins were not resolved
in the cytoplasmic Pol II structure, they are part of\r\nthe complex and their
interaction with Pol II was confirmed in vitro. RPAP2 stabilizes\r\nthese proteins
on Pol II and several experiments suggest that they interact with the\r\nclamp
region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or\r\npartially
open state. Based on these results I propose a novel model of regulation of\r\nPol
II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm\r\nand
doing so they can prevent pre-mature binding of DNA or RNA and different transcription
factors to Pol II in cytoplasm or before engaging in transcription nucleus.\r\nThis
research contributes to the current knowledge of molecular mechanisms\r\nof Pol
II regulation in cytoplasm."
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
acknowledgement: 'I would also like to acknowledge the ISTA Facilities: Lab Support
Facility, Protein Services and Electron Microscopy Facility (EMF) and Scientific
Computing. EMF for their support during data collections and troubleshooting, especially
Valentin. Scientific Computing for solving quickly any issues related with cluster.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
citation:
ama: Hlavata A. Regulation of Cytoplasmic RNA Polymerase II. 2025. doi:10.15479/10.15479/AT-ISTA-19431
apa: Hlavata, A. (2025). Regulation of Cytoplasmic RNA Polymerase II. Institute
of Science and Technology Austria. https://doi.org/10.15479/10.15479/AT-ISTA-19431
chicago: Hlavata, Annamaria. “Regulation of Cytoplasmic RNA Polymerase II.” Institute
of Science and Technology Austria, 2025. https://doi.org/10.15479/10.15479/AT-ISTA-19431.
ieee: A. Hlavata, “Regulation of Cytoplasmic RNA Polymerase II,” Institute of Science
and Technology Austria, 2025.
ista: Hlavata A. 2025. Regulation of Cytoplasmic RNA Polymerase II. Institute of
Science and Technology Austria.
mla: Hlavata, Annamaria. Regulation of Cytoplasmic RNA Polymerase II. Institute
of Science and Technology Austria, 2025, doi:10.15479/10.15479/AT-ISTA-19431.
short: A. Hlavata, Regulation of Cytoplasmic RNA Polymerase II, Institute of Science
and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-03-20T12:52:47Z
date_published: 2025-03-20T00:00:00Z
date_updated: 2026-04-07T11:46:32Z
day: '20'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaBe
doi: 10.15479/10.15479/AT-ISTA-19431
file:
- access_level: closed
checksum: b7ddf424ffe95f8c767c53c8bb62d4f3
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: ahlavata
date_created: 2025-03-24T12:48:36Z
date_updated: 2026-03-20T23:30:04Z
embargo_to: open_access
file_id: '19448'
file_name: PhD_Thesis_Hlavata_final_submission.docx
file_size: 23506747
relation: source_file
- access_level: open_access
checksum: 6c5a59c9bac467c3d0b3ffb8ea6d9fd4
content_type: application/pdf
creator: ahlavata
date_created: 2025-03-24T12:51:10Z
date_updated: 2026-03-20T23:30:04Z
embargo: 2026-03-20
file_id: '19449'
file_name: PhD_Thesis_Hlavata_final_submission_update.pdf
file_size: 9478591
relation: main_file
file_date_updated: 2026-03-20T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '83'
publication_identifier:
eissn:
- 2663-337X
isbn:
- 978-3-99078-055-8
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
title: Regulation of Cytoplasmic RNA Polymerase II
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '15330'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth
and development by controlling plasma membrane protein composition and cargo uptake.
CME relies on the precise recruitment of regulators for vesicle maturation and
release. Homologues of components of mammalian vesicle scission are strong candidates
to be part of the scission machinery in plants, but the precise roles of these
proteins in this process are not fully understood. Here, we characterised the
roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein
2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin,
in the CME by combining high-resolution imaging of endocytic events in vivo and
characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive
similarly late during CME and physically interact, genetic analysis of the sh3p123
triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants
suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis.
These observations imply that despite the presence of many well-conserved endocytic
components, plants have acquired a distinct mechanism for CME.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: "Nataliia Gnyliukh was partially funded by the European Union’s Horizon
2020 research and\r\ninnovation program (2018-2020) under the Marie Sklodowska-Curie
Grant (agreement no.\r\n665385). Taif University Researchers Supporting Project:
TURSP-HC2022/02. and Austrian\r\nScience Fund (FWF): I 6123-B.We thank Prof. Eileen
Lafer and Liping Wang for their suggestions regarding the optimisation of protein
expression and purification. We thank Prof. Sebastian Y. Bednarek for the useful
comments and constructive criticism of the project. We thank Maciek Adamowski for
providing genetic material. This research was supported by the Scientific Service
Units (SSU) of IST-Austria through resources provided by the Electron microscopy
(EMF), Lab Support Facility (LSF) (particularly Dorota Jaworska) and the Bioimaging
Facility (BIF)."
article_number: jcs.261720
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: MK
full_name: Nagel, MK
last_name: Nagel
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: David
full_name: Babic, David
id: db566d23-f6e0-11ea-865d-e6f270e968e7
last_name: Babic
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: SS
full_name: Alotaibi, SS
last_name: Alotaibi
- first_name: E
full_name: Isono, E
last_name: Isono
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Gnyliukh N, Johnson AJ, Nagel M, et al. Role of dynamin-related proteins 2
and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal
of Cell Science. 2024;137(8). doi:10.1242/jcs.261720
apa: Gnyliukh, N., Johnson, A. J., Nagel, M., Monzer, A., Babic, D., Hlavata, A.,
… Friml, J. (2024). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated
endocytosis in Arabidopsis thaliana. Journal of Cell Science. The Company
of Biologists. https://doi.org/10.1242/jcs.261720
chicago: Gnyliukh, Nataliia, Alexander J Johnson, MK Nagel, Aline Monzer, David
Babic, Annamaria Hlavata, SS Alotaibi, E Isono, Martin Loose, and Jiří Friml.
“Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis
in Arabidopsis Thaliana.” Journal of Cell Science. The Company of Biologists,
2024. https://doi.org/10.1242/jcs.261720.
ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in
clathrin-mediated endocytosis in Arabidopsis thaliana,” Journal of Cell Science,
vol. 137, no. 8. The Company of Biologists, 2024.
ista: Gnyliukh N, Johnson AJ, Nagel M, Monzer A, Babic D, Hlavata A, Alotaibi S,
Isono E, Loose M, Friml J. 2024. Role of dynamin-related proteins 2 and SH3P2
in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science.
137(8), jcs. 261720.
mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in
Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” Journal of Cell Science,
vol. 137, no. 8, jcs. 261720, The Company of Biologists, 2024, doi:10.1242/jcs.261720.
short: N. Gnyliukh, A.J. Johnson, M. Nagel, A. Monzer, D. Babic, A. Hlavata, S.
Alotaibi, E. Isono, M. Loose, J. Friml, Journal of Cell Science 137 (2024).
corr_author: '1'
date_created: 2024-04-19T09:54:59Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-09-04T13:49:45Z
day: '01'
ddc:
- '570'
department:
- _id: MaLo
- _id: JiFr
- _id: CaBe
doi: 10.1242/jcs.261720
ec_funded: 1
external_id:
isi:
- '001266917100005'
pmid:
- '38506228'
file:
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checksum: 6dc023f0cc7052ad3cf0a42589d2e30f
content_type: application/pdf
creator: dernst
date_created: 2025-01-09T08:41:16Z
date_updated: 2025-01-09T08:41:16Z
file_id: '18792'
file_name: 2024_JourCellScience_Gnyliukh.pdf
file_size: 25845948
relation: main_file
success: 1
file_date_updated: 2025-01-09T08:41:16Z
has_accepted_license: '1'
intvolume: ' 137'
isi: 1
issue: '8'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: bd76d395-d553-11ed-ba76-f678c14f9033
grant_number: I06123
name: Peptide receptors for auxin canalization in Arabidopsis
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
record:
- id: '14591'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in Arabidopsis thaliana
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 137
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18553'
abstract:
- lang: eng
text: Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates
DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II).
TC-NER is initiated by the recognition of lesion-stalled RNA Pol II by CSB, which
recruits the CRL4CSA ubiquitin ligase and UVSSA. RNA Pol II ubiquitylation at
RPB1-K1268 by CRL4CSA serves as a critical TC-NER checkpoint, governing RNA Pol
II stability and initiating DNA damage excision by TFIIH recruitment. However,
the precise regulatory mechanisms of CRL4CSA activity and TFIIH recruitment remain
elusive. Here, we reveal human serine/threonine-protein kinase 19 (STK19) as a
TC-NER factor, which is essential for correct DNA damage removal and subsequent
transcription restart. Cryogenic electron microscopy (cryo-EM) studies demonstrate
that STK19 is an integral part of the RNA Pol II-TC-NER complex, bridging CSA,
UVSSA, RNA Pol II, and downstream DNA. STK19 stimulates TC-NER complex stability
and CRL4CSA activity, resulting in efficient RNA Pol II ubiquitylation and correct
UVSSA and TFIIH binding. These findings underscore the crucial role of STK19 as
a core TC-NER component.
acknowledged_ssus:
- _id: LifeSc
- _id: PreCl
acknowledgement: We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell
line. This research was further supported by the Scientific Service Units (SSU)
of IST Austria through resources provided by the Lab Support Facility (LSF) and
the Preclinical Facility (PCF). This work is part of the Oncode Institute, which
is partly financed by the Dutch Cancer Society. Research at the Netherlands Cancer
Institute is supported by institutional grants of the Dutch Cancer Society and the
Dutch Ministry of Health, Welfare and Sport. This study was supported by a VICI
(VI.C.182.025) and a TOP Grant (714.017.003) of the Netherlands Organization for
Scientific Research.
article_processing_charge: No
article_type: original
author:
- first_name: Anisha R.
full_name: Ramadhin, Anisha R.
last_name: Ramadhin
- first_name: Shun-Hsiao
full_name: Lee, Shun-Hsiao
last_name: Lee
- first_name: Di
full_name: Zhou, Di
last_name: Zhou
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Camila
full_name: Gonzalo-Hansen, Camila
last_name: Gonzalo-Hansen
- first_name: Marjolein
full_name: van Sluis, Marjolein
last_name: van Sluis
- first_name: Cindy M.A.
full_name: Blom, Cindy M.A.
last_name: Blom
- first_name: Roel C.
full_name: Janssens, Roel C.
last_name: Janssens
- first_name: Anja
full_name: Raams, Anja
last_name: Raams
- first_name: Dick
full_name: Dekkers, Dick
last_name: Dekkers
- first_name: Karel
full_name: Bezstarosti, Karel
last_name: Bezstarosti
- first_name: Dea
full_name: Slade, Dea
last_name: Slade
- first_name: Wim
full_name: Vermeulen, Wim
last_name: Vermeulen
- first_name: Alex
full_name: Pines, Alex
last_name: Pines
- first_name: Jeroen A.A.
full_name: Demmers, Jeroen A.A.
last_name: Demmers
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Titia K.
full_name: Sixma, Titia K.
last_name: Sixma
- first_name: Jurgen A.
full_name: Marteijn, Jurgen A.
last_name: Marteijn
citation:
ama: Ramadhin AR, Lee S-H, Zhou D, et al. STK19 drives transcription-coupled repair
by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH
recruitment. Molecular Cell. 2024;84(24):4740-4757.e12. doi:10.1016/j.molcel.2024.10.030
apa: Ramadhin, A. R., Lee, S.-H., Zhou, D., Testa Salmazo, A. P., Gonzalo-Hansen,
C., van Sluis, M., … Marteijn, J. A. (2024). STK19 drives transcription-coupled
repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and
TFIIH recruitment. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2024.10.030
chicago: Ramadhin, Anisha R., Shun-Hsiao Lee, Di Zhou, Anita P Testa Salmazo, Camila
Gonzalo-Hansen, Marjolein van Sluis, Cindy M.A. Blom, et al. “STK19 Drives Transcription-Coupled
Repair by Stimulating Repair Complex Stability, RNA Pol II Ubiquitylation, and
TFIIH Recruitment.” Molecular Cell. Elsevier, 2024. https://doi.org/10.1016/j.molcel.2024.10.030.
ieee: A. R. Ramadhin et al., “STK19 drives transcription-coupled repair by
stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment,”
Molecular Cell, vol. 84, no. 24. Elsevier, p. 4740–4757.e12, 2024.
ista: Ramadhin AR, Lee S-H, Zhou D, Testa Salmazo AP, Gonzalo-Hansen C, van Sluis
M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen
W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. 2024. STK19 drives
transcription-coupled repair by stimulating repair complex stability, RNA Pol
II ubiquitylation, and TFIIH recruitment. Molecular Cell. 84(24), 4740–4757.e12.
mla: Ramadhin, Anisha R., et al. “STK19 Drives Transcription-Coupled Repair by Stimulating
Repair Complex Stability, RNA Pol II Ubiquitylation, and TFIIH Recruitment.” Molecular
Cell, vol. 84, no. 24, Elsevier, 2024, p. 4740–4757.e12, doi:10.1016/j.molcel.2024.10.030.
short: A.R. Ramadhin, S.-H. Lee, D. Zhou, A.P. Testa Salmazo, C. Gonzalo-Hansen,
M. van Sluis, C.M.A. Blom, R.C. Janssens, A. Raams, D. Dekkers, K. Bezstarosti,
D. Slade, W. Vermeulen, A. Pines, J.A.A. Demmers, C. Bernecky, T.K. Sixma, J.A.
Marteijn, Molecular Cell 84 (2024) 4740–4757.e12.
date_created: 2024-11-15T12:12:54Z
date_published: 2024-12-19T00:00:00Z
date_updated: 2025-09-08T14:42:50Z
day: '19'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1016/j.molcel.2024.10.030
external_id:
isi:
- '001395711300001'
pmid:
- '39547223'
file:
- access_level: open_access
checksum: e051e2766b2d424983778f742cb7c5ed
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T11:17:35Z
date_updated: 2025-01-13T11:17:35Z
file_id: '18844'
file_name: 2024_MolecularCell_Ramadhin.pdf
file_size: 25071994
relation: main_file
success: 1
file_date_updated: 2025-01-13T11:17:35Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 4740-4757.e12
pmid: 1
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: STK19 drives transcription-coupled repair by stimulating repair complex stability,
RNA Pol II ubiquitylation, and TFIIH recruitment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 84
year: '2024'
...
---
OA_type: closed access
_id: '18945'
abstract:
- lang: eng
text: Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase
1 (CK1) are linked to various disease-relevant pathways. However, the lack of
tool compounds for these kinases has significantly hampered our understanding
of their cellular functions and therapeutic potential. Here, we describe the structure-based
development of potent inhibitors of VRK1, a kinase highly expressed in various
tumor types and crucial for cell proliferation and genome integrity. Kinome-wide
profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate
that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion.
Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these
kinases may play overlapping roles in cell proliferation and genome instability.
Together, our findings highlight the potential of VRK1 inhibition in treating
p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies
that target DNA stability or cell division.
acknowledgement: "R.M.C. and K.B.M. are grateful for support by FAPESP (Fundação de
Amparo à Pesquisa do Estado de São Paulo) (grants 2013/50724–5 and 2014/50897–0),
Embrapii (Empresa Brasileira de Pesquisa e Inovação Industrial), CNPq (Conselho
Nacional de Desenvolvimento Científico e Tecnológico) (grant 465651/2014–3) and
Aché Laboratórios Farmacêuticos. R.M.C. and O.G. are also grateful for support by
the Structural Genomics Consortium, a registered charity (1097737) that receives
funds from AbbVie, Bayer AG, Boehringer Ingelheim, Canada Foundation for Innovation,
Eshelman Institute for Innovation, Genentech, Genome Canada through the Ontario
Genomics Institute (OGI-196), EU/EFPIA/OICR/McGill/KTH/Diamond, Innovative Medicines
Initiative 2 Joint Undertaking (EUbOPEN Grant 875510), Janssen, Merck KGaA, Merck
& Co., Pfizer, Takeda, and Wellcome. B.L. and M.H. are grateful for support from
the Swedish Research Council, Swedish Cancer Society, Karolinska Institutet and
The Mark Foundation for Cancer Research. R.A.M.S. (2016/25320–6 and 2018/23322–7),
A.S.S. (2019/14275–8), S.N.S.V (2018/09475–5), V.M.A. (2022/00743–2) and M.R.C.
(2021/04853–4) were recipients of fellowships from the Fundação de Amparo à Pesquisa
do Estado de São Paulo, FAPESP. C.V.R. (88887.146077/2017–00), J.E.T. (88887.373547/2019–00)
and P.Z.R (88887.136432/2017–00) were the recipient of fellowships from the Coordenação
de Aperfeiçoamento de Pessoal de Nível Superior, CAPES.\r\nWe thank all members
of CQMED-UNICAMP for their help and support. We thank the staff of the Life Sciences
Core Facility (LaCTAD) at UNICAMP for the Genomics and Mass Spectrometry analysis.
We thank the NMR facility at UNICAMP Chemistry Institute for its assistance. We
thank the staff at the Northeastern Collaborative Access Team beamlines, which are
funded by the National Institute of General Medical Sciences from the National Institutes
of Health (P41 GM103403). The Pilatus 6M detector on the 24-ID-C beamline is funded
by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced
Photon Source; a U.S. Department of Energy (DOE) Office of Science User Facility
operated for the DOE Office of Science by Argonne National Laboratory under Contract
No. DE-AC02-06CH11357. We thank Diamond Light Source for access to beamline I24.
The authors thank Tammy Havener (SGC-UNC), Abid Hussain Sayyid (KI), and Yiqiu Yang
(KI) for valuable discussions and technical support."
article_processing_charge: No
article_type: original
author:
- first_name: Fernando H.
full_name: de Souza Gama, Fernando H.
last_name: de Souza Gama
- first_name: Luiz A.
full_name: Dutra, Luiz A.
last_name: Dutra
- first_name: Michael
full_name: Hawgood, Michael
last_name: Hawgood
- first_name: Caio Vinícius
full_name: dos Reis, Caio Vinícius
last_name: dos Reis
- first_name: Ricardo A. M.
full_name: Serafim, Ricardo A. M.
last_name: Serafim
- first_name: Marcos A.
full_name: Ferreira, Marcos A.
last_name: Ferreira
- first_name: Bruno V. M.
full_name: Teodoro, Bruno V. M.
last_name: Teodoro
- first_name: Jéssica Emi
full_name: Takarada, Jéssica Emi
last_name: Takarada
- first_name: André S.
full_name: Santiago, André S.
last_name: Santiago
- first_name: Dimitrios-Ilias
full_name: Balourdas, Dimitrios-Ilias
last_name: Balourdas
- first_name: Ann-Sofie
full_name: Nilsson, Ann-Sofie
last_name: Nilsson
- first_name: Bruno
full_name: Urien, Bruno
last_name: Urien
- first_name: Vitor M.
full_name: Almeida, Vitor M.
last_name: Almeida
- first_name: Carina
full_name: Gileadi, Carina
last_name: Gileadi
- first_name: Priscila Z.
full_name: Ramos, Priscila Z.
last_name: Ramos
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Stanley N. S.
full_name: Vasconcelos, Stanley N. S.
last_name: Vasconcelos
- first_name: Micael R.
full_name: Cunha, Micael R.
last_name: Cunha
- first_name: Susanne
full_name: Mueller, Susanne
last_name: Mueller
- first_name: Stefan
full_name: Knapp, Stefan
last_name: Knapp
- first_name: Katlin B.
full_name: Massirer, Katlin B.
last_name: Massirer
- first_name: Jonathan M.
full_name: Elkins, Jonathan M.
last_name: Elkins
- first_name: Opher
full_name: Gileadi, Opher
last_name: Gileadi
- first_name: Alessandra
full_name: Mascarello, Alessandra
last_name: Mascarello
- first_name: Bennie B. L. G.
full_name: Lemmens, Bennie B. L. G.
last_name: Lemmens
- first_name: Cristiano R. W.
full_name: Guimarães, Cristiano R. W.
last_name: Guimarães
- first_name: Hatylas
full_name: Azevedo, Hatylas
last_name: Azevedo
- first_name: Rafael M.
full_name: Couñago, Rafael M.
last_name: Couñago
citation:
ama: de Souza Gama FH, Dutra LA, Hawgood M, et al. Novel dihydropteridinone derivatives
as potent inhibitors of the understudied human kinases vaccinia-related kinase
1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 2024;67(11):8609-8629.
doi:10.1021/acs.jmedchem.3c02250
apa: de Souza Gama, F. H., Dutra, L. A., Hawgood, M., dos Reis, C. V., Serafim,
R. A. M., Ferreira, M. A., … Couñago, R. M. (2024). Novel dihydropteridinone derivatives
as potent inhibitors of the understudied human kinases vaccinia-related kinase
1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. American Chemical
Society. https://doi.org/10.1021/acs.jmedchem.3c02250
chicago: Souza Gama, Fernando H. de, Luiz A. Dutra, Michael Hawgood, Caio Vinícius
dos Reis, Ricardo A. M. Serafim, Marcos A. Ferreira, Bruno V. M. Teodoro, et al.
“Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied
Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” Journal of
Medicinal Chemistry. American Chemical Society, 2024. https://doi.org/10.1021/acs.jmedchem.3c02250.
ieee: F. H. de Souza Gama et al., “Novel dihydropteridinone derivatives as
potent inhibitors of the understudied human kinases vaccinia-related kinase 1
and casein kinase 1δ/ε,” Journal of Medicinal Chemistry, vol. 67, no. 11.
American Chemical Society, pp. 8609–8629, 2024.
ista: de Souza Gama FH, Dutra LA, Hawgood M, dos Reis CV, Serafim RAM, Ferreira
MA, Teodoro BVM, Takarada JE, Santiago AS, Balourdas D-I, Nilsson A-S, Urien B,
Almeida VM, Gileadi C, Ramos PZ, Testa Salmazo AP, Vasconcelos SNS, Cunha MR,
Mueller S, Knapp S, Massirer KB, Elkins JM, Gileadi O, Mascarello A, Lemmens BBLG,
Guimarães CRW, Azevedo H, Couñago RM. 2024. Novel dihydropteridinone derivatives
as potent inhibitors of the understudied human kinases vaccinia-related kinase
1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 67(11), 8609–8629.
mla: de Souza Gama, Fernando H., et al. “Novel Dihydropteridinone Derivatives as
Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1
and Casein Kinase 1δ/ε.” Journal of Medicinal Chemistry, vol. 67, no. 11,
American Chemical Society, 2024, pp. 8609–29, doi:10.1021/acs.jmedchem.3c02250.
short: F.H. de Souza Gama, L.A. Dutra, M. Hawgood, C.V. dos Reis, R.A.M. Serafim,
M.A. Ferreira, B.V.M. Teodoro, J.E. Takarada, A.S. Santiago, D.-I. Balourdas,
A.-S. Nilsson, B. Urien, V.M. Almeida, C. Gileadi, P.Z. Ramos, A.P. Testa Salmazo,
S.N.S. Vasconcelos, M.R. Cunha, S. Mueller, S. Knapp, K.B. Massirer, J.M. Elkins,
O. Gileadi, A. Mascarello, B.B.L.G. Lemmens, C.R.W. Guimarães, H. Azevedo, R.M.
Couñago, Journal of Medicinal Chemistry 67 (2024) 8609–8629.
date_created: 2025-01-29T09:14:19Z
date_published: 2024-05-23T00:00:00Z
date_updated: 2025-01-29T09:19:15Z
day: '23'
department:
- _id: CaBe
doi: 10.1021/acs.jmedchem.3c02250
external_id:
pmid:
- '38780468'
intvolume: ' 67'
issue: '11'
language:
- iso: eng
month: '05'
oa_version: None
page: 8609-8629
pmid: 1
publication: Journal of Medicinal Chemistry
publication_identifier:
eissn:
- 1520-4804
issn:
- 0022-2623
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Novel dihydropteridinone derivatives as potent inhibitors of the understudied
human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2024'
...
---
OA_place: publisher
_id: '18477'
abstract:
- lang: eng
text: "ADAR1 is broadly expressed across various tissues and is vital in regulating
pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded
RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing
autoimmunity and maintaining\r\nimmune tolerance. This editing process has been
detected at millions of sites across the\r\nhuman genome. However, the mechanism
underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear,
with much of the current knowledge derived from\r\ncomparisons to its more extensively
studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates
and applying a combination of biochemical techniques and structural\r\nstudies
using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity
characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1
was successfully optimized, resulting in the\r\nfirst report in the literature
to achieve high protein purity and activity. This advancement\r\nenabled the investigation
of complex formation between ADAR1 and various RNA substrates,\r\nleading to the
identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite
comprehensive optimization of the cryo-EM conditions, the resulting data lacked
the\r\ndesired quality, highlighting the need for similar rigorous optimization
of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex.
The study was complemented by\r\nAlphaFold predictions, which provided some insights
into this mechanism.\r\nMoreover, during this project I established a collaboration
with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs
were identified in bivalve species, and it\r\nwas further demonstrated that ADAR
and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections
with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant
losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared
in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable
of detecting modified nucleotides without the need for reverse transcription.
The\r\ncollaborators initiated optimization of this nanopore-based approach. However,
current\r\ntechnological limitations still constrain the reliable detection of
modified nucleotides.\r\nThe project also examined the impact of RNA editing on
RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that
triggers an interferon response. A primary target\r\nof ADAR1's editing activity
is RNA derived from repetitive elements present in the genome,\r\nparticularly
Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences
are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu
RNAs, as well as the role of A-to-I editing in influencing this binding, are still
not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was
successfully established. This was\r\nachieved through the testing of different
RNA variants and the evaluation of filament\r\nformation using binding techniques
and electron microscopy imaging. This groundwork has\r\nset the conditions for
further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting
on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch
that has provided new insights into MDA5's interaction with dsRNA, it is essential
to\r\nrevise the experimental setup to integrate these findings before moving
forward with the\r\nCryoEM sample analysis."
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
citation:
ama: Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024.
doi:10.15479/at:ista:18477
apa: Kaczmarek, B. M. (2024). Biochemical and structural insights into ADAR1
RNA editing. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18477
chicago: Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA
Editing.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18477.
ieee: B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,”
Institute of Science and Technology Austria, 2024.
ista: Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing.
Institute of Science and Technology Austria.
mla: Kaczmarek, Beata M. Biochemical and Structural Insights into ADAR1 RNA Editing.
Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18477.
short: B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing,
Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-10-27T07:35:13Z
date_published: 2024-10-29T00:00:00Z
date_updated: 2026-04-07T13:23:59Z
day: '29'
ddc:
- '572'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaBe
doi: 10.15479/at:ista:18477
file:
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creator: bkaczmar
date_created: 2024-10-29T11:56:36Z
date_updated: 2025-10-29T23:30:02Z
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file_size: 23136626
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date_created: 2024-10-29T11:56:44Z
date_updated: 2025-10-29T23:30:02Z
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file_date_updated: 2025-10-29T23:30:02Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
isbn:
- 978-3-99078-045-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
title: Biochemical and structural insights into ADAR1 RNA editing
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: repository
_id: '14591'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth
and development by controlling plasma membrane protein composition and cargo uptake.
CME relies on the precise recruitment of regulators for vesicle maturation and
release. Homologues of components of mammalian vesicle scission are strong candidates
to be part of the scissin machinery in plants, but the precise roles of these
proteins in this process is not fully understood. Here, we characterised the roles
of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein
2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin,
in the CME by combining high-resolution imaging of endocytic events in vivo and
characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive
similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3
triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants
suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis.
These observations imply that despite the presence of many well-conserved endocytic
components, plants have acquired a distinct mechanism for CME. One Sentence Summary
In contrast to predictions based on mammalian systems, plant Dynamin-related proteins
2 are recruited to the site of Clathrin-mediated endocytosis independently of
BAR-SH3 proteins.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
article_processing_charge: No
author:
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Marie-Kristin
full_name: Nagel, Marie-Kristin
last_name: Nagel
- first_name: Aline
full_name: Monzer, Aline
id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
last_name: Monzer
- first_name: Annamaria
full_name: Hlavata, Annamaria
id: 36062FEC-F248-11E8-B48F-1D18A9856A87
last_name: Hlavata
- first_name: Erika
full_name: Isono, Erika
last_name: Isono
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins
2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523
apa: Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono,
E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated
endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523
chicago: Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer,
Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related
Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv,
n.d. https://doi.org/10.1101/2023.10.09.561523.
ieee: N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in
clathrin-mediated endocytosis in plants,” bioRxiv. .
ista: Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M,
Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in plants. bioRxiv, 10.1101/2023.10.09.561523.
mla: Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in
Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.
short: N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono,
M. Loose, J. Friml, BioRxiv (n.d.).
corr_author: '1'
date_created: 2023-11-22T10:17:49Z
date_published: 2023-10-10T00:00:00Z
date_updated: 2026-07-04T22:30:56Z
day: '10'
department:
- _id: JiFr
- _id: MaLo
- _id: CaBe
doi: 10.1101/2023.10.09.561523
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.10.09.561523
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '15330'
relation: later_version
status: public
- id: '14510'
relation: dissertation_contains
status: public
status: public
title: Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis
in plants
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12051'
abstract:
- lang: eng
text: Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is
a major determinant of cellular growth, and dysregulation is observed in many
cancer types. Here, we present the purification of human Pol I from cells carrying
a genomic GFP fusion on the largest subunit allowing the structural and functional
analysis of the enzyme across species. In contrast to yeast, human Pol I carries
a single-subunit stalk, and in vitro transcription indicates a reduced proofreading
activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native
state rationalizes the effects of disease-associated mutations and uncovers an
additional domain that is built into the sequence of Pol I subunit RPA1. This
“dock II” domain resembles a truncated HMG box incapable of DNA binding which
may serve as a downstream transcription factor–binding platform in metazoans.
Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase
2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing
factor UBF. These adaptations of the metazoan Pol I transcription system may allow
efficient release of positive DNA supercoils accumulating downstream of the transcription
bubble.
acknowledgement: "The authors especially thank Philip Gunkel for his contribution.
We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn
Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert
Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert
Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the
Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the
Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence
microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant
no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research
Center 960 (TP-A8 to C Engel)."
article_number: e202201568
article_processing_charge: No
article_type: original
author:
- first_name: Julia L
full_name: Daiß, Julia L
last_name: Daiß
- first_name: Michael
full_name: Pilsl, Michael
last_name: Pilsl
- first_name: Kristina
full_name: Straub, Kristina
last_name: Straub
- first_name: Andrea
full_name: Bleckmann, Andrea
last_name: Bleckmann
- first_name: Mona
full_name: Höcherl, Mona
last_name: Höcherl
- first_name: Florian B
full_name: Heiss, Florian B
last_name: Heiss
- first_name: Guillermo
full_name: Abascal-Palacios, Guillermo
last_name: Abascal-Palacios
- first_name: Ewan P
full_name: Ramsay, Ewan P
last_name: Ramsay
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Jean-Clement
full_name: Mars, Jean-Clement
last_name: Mars
- first_name: Torben
full_name: Fürtges, Torben
last_name: Fürtges
- first_name: Astrid
full_name: Bruckmann, Astrid
last_name: Bruckmann
- first_name: Till
full_name: Rudack, Till
last_name: Rudack
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Valérie
full_name: Lamour, Valérie
last_name: Lamour
- first_name: Konstantin
full_name: Panov, Konstantin
last_name: Panov
- first_name: Alessandro
full_name: Vannini, Alessandro
last_name: Vannini
- first_name: Tom
full_name: Moss, Tom
last_name: Moss
- first_name: Christoph
full_name: Engel, Christoph
last_name: Engel
citation:
ama: Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals
an HMG-like docking domain specific to metazoans. Life Science Alliance.
2022;5(11). doi:10.26508/lsa.202201568
apa: Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B.,
… Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking
domain specific to metazoans. Life Science Alliance. Life Science Alliance.
https://doi.org/10.26508/lsa.202201568
chicago: Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl,
Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase
I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” Life
Science Alliance. Life Science Alliance, 2022. https://doi.org/10.26508/lsa.202201568.
ieee: J. L. Daiß et al., “The human RNA polymerase I structure reveals an
HMG-like docking domain specific to metazoans,” Life Science Alliance,
vol. 5, no. 11. Life Science Alliance, 2022.
ista: Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios
G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky
C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase
I structure reveals an HMG-like docking domain specific to metazoans. Life Science
Alliance. 5(11), e202201568.
mla: Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like
Docking Domain Specific to Metazoans.” Life Science Alliance, vol. 5, no.
11, e202201568, Life Science Alliance, 2022, doi:10.26508/lsa.202201568.
short: J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G.
Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann,
T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life
Science Alliance 5 (2022).
date_created: 2022-09-06T18:45:23Z
date_published: 2022-09-01T00:00:00Z
date_updated: 2024-10-21T06:01:48Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.26508/lsa.202201568
external_id:
isi:
- '000972702600001'
file:
- access_level: open_access
checksum: 4201d876a3e5e8b65e319d03300014ad
content_type: application/pdf
creator: dernst
date_created: 2022-09-08T06:41:14Z
date_updated: 2022-09-08T06:41:14Z
file_id: '12062'
file_name: 2022_LifeScienceAlliance_Daiss.pdf
file_size: 3183129
relation: main_file
success: 1
file_date_updated: 2022-09-08T06:41:14Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '11'
keyword:
- Health
- Toxicology and Mutagenesis
- Plant Science
- Biochemistry
- Genetics and Molecular Biology (miscellaneous)
- Ecology
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Life Science Alliance
publication_identifier:
issn:
- 2575-1077
publication_status: published
publisher: Life Science Alliance
quality_controlled: '1'
scopus_import: '1'
status: public
title: The human RNA polymerase I structure reveals an HMG-like docking domain specific
to metazoans
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2022'
...
---
_id: '12143'
abstract:
- lang: eng
text: MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced
by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating
miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown.
We show that the adaptation entails a unique structural role of Dicer’s DExD/H
helicase domain. Although mice tolerate loss of its putative ATPase function,
the complete absence of the domain is lethal because it assures high-fidelity
miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed
that the DExD/H domain has a helicase-unrelated structural function. It locks
Dicer in a closed state, which facilitates miRNA precursor selection. Transition
to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2.
Absence of the DExD/H domain or its mutations unlocks the closed state, reduces
substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally
contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning
of miRNA and RNAi pathways.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: We thank Kristian Vlahovicek (University of Zagreb) for support of
bioinformatics analyses and Vladimir Benes (EMBL Sequencing Facility) and Genomics
and Bioinformatics Core Facility at the Institute of Molecular Genetics for help
with RNA sequencing. The main funding was provided by the Czech Science Foundation
(EXPRO grant 20-03950X to P.S. and 22-19896S to R. Stefl). Early stages of the work
were supported by European Research Council grants under the European Union’s Horizon
2020 Research and Innovation Programme (grants 647403 to P.S. and 649030 to R. Stefl).
V.B., D.F.J., and F.H. were in part supported by PhD student fellowships from the
Charles University; this work will be in part fulfilling requirements for a PhD
degree as “school work.” Funding of D.Z. included the OP RDE project “Internal Grant
Agency of Masaryk University” no. CZ.02.2.69/0.0/0.0/19_073/0016943. The Ministry
of Education, Youth, and Sports of the Czech Republic (MEYS CR) provided institutional
support for CEITEC 2020 project LQ1601. For technical support, we acknowledge EMBL
Monterotondo’s genome engineering and transgenic core facilities, the Czech Centre
for Phenogenomics at the Institute of Molecular Genetics (supported by RVO 68378050
from the Czech Academy of Sciences and LM2018126 and CZ.02.1.01/0.0/0.0/18_046/0015861
CCP Infrastructure Upgrade II from MEYS CR), the Cryo-EM and Proteomics Core Facilities
(CEITEC, Masaryk University) supported by the CIISB research infrastructure (LM2018127
from MEYS CR), and support from the Scientific Service Units of ISTA through resources
from the Electron Microscopy Facility. Computational resources included e-Infrastruktura
CZ (LM2018140) and ELIXIR-CZ (LM2018131) projects by MEYS CR and the Croatian National
Centres of Research Excellence in Personalized Healthcare (#KK.01.1.1.01.0010) and
Data Science and Advanced Cooperative Systems (#KK.01.1.1.01.0009) projects funded
by the European Structural and Investment Funds grants.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Zapletal, David
last_name: Zapletal
- first_name: Eliska
full_name: Taborska, Eliska
last_name: Taborska
- first_name: Josef
full_name: Pasulka, Josef
last_name: Pasulka
- first_name: Radek
full_name: Malik, Radek
last_name: Malik
- first_name: Karel
full_name: Kubicek, Karel
last_name: Kubicek
- first_name: Martina
full_name: Zanova, Martina
last_name: Zanova
- first_name: Christian
full_name: Much, Christian
last_name: Much
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Valeria
full_name: Buccheri, Valeria
last_name: Buccheri
- first_name: Filip
full_name: Horvat, Filip
last_name: Horvat
- first_name: Irena
full_name: Jenickova, Irena
last_name: Jenickova
- first_name: Michaela
full_name: Prochazkova, Michaela
last_name: Prochazkova
- first_name: Jan
full_name: Prochazka, Jan
last_name: Prochazka
- first_name: Matyas
full_name: Pinkas, Matyas
last_name: Pinkas
- first_name: Jiri
full_name: Novacek, Jiri
last_name: Novacek
- first_name: Diego F.
full_name: Joseph, Diego F.
last_name: Joseph
- first_name: Radislav
full_name: Sedlacek, Radislav
last_name: Sedlacek
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Dónal
full_name: O’Carroll, Dónal
last_name: O’Carroll
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- first_name: Petr
full_name: Svoboda, Petr
last_name: Svoboda
citation:
ama: Zapletal D, Taborska E, Pasulka J, et al. Structural and functional basis of
mammalian microRNA biogenesis by Dicer. Molecular Cell. 2022;82(21):4064-4079.e13.
doi:10.1016/j.molcel.2022.10.010
apa: Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M.,
… Svoboda, P. (2022). Structural and functional basis of mammalian microRNA biogenesis
by Dicer. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2022.10.010
chicago: Zapletal, David, Eliska Taborska, Josef Pasulka, Radek Malik, Karel Kubicek,
Martina Zanova, Christian Much, et al. “Structural and Functional Basis of Mammalian
MicroRNA Biogenesis by Dicer.” Molecular Cell. Elsevier, 2022. https://doi.org/10.1016/j.molcel.2022.10.010.
ieee: D. Zapletal et al., “Structural and functional basis of mammalian microRNA
biogenesis by Dicer,” Molecular Cell, vol. 82, no. 21. Elsevier, p. 4064–4079.e13,
2022.
ista: Zapletal D, Taborska E, Pasulka J, Malik R, Kubicek K, Zanova M, Much C, Sebesta
M, Buccheri V, Horvat F, Jenickova I, Prochazkova M, Prochazka J, Pinkas M, Novacek
J, Joseph DF, Sedlacek R, Bernecky C, O’Carroll D, Stefl R, Svoboda P. 2022. Structural
and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell.
82(21), 4064–4079.e13.
mla: Zapletal, David, et al. “Structural and Functional Basis of Mammalian MicroRNA
Biogenesis by Dicer.” Molecular Cell, vol. 82, no. 21, Elsevier, 2022,
p. 4064–4079.e13, doi:10.1016/j.molcel.2022.10.010.
short: D. Zapletal, E. Taborska, J. Pasulka, R. Malik, K. Kubicek, M. Zanova, C.
Much, M. Sebesta, V. Buccheri, F. Horvat, I. Jenickova, M. Prochazkova, J. Prochazka,
M. Pinkas, J. Novacek, D.F. Joseph, R. Sedlacek, C. Bernecky, D. O’Carroll, R.
Stefl, P. Svoboda, Molecular Cell 82 (2022) 4064–4079.e13.
date_created: 2023-01-12T12:05:36Z
date_published: 2022-11-03T00:00:00Z
date_updated: 2023-08-04T08:57:17Z
day: '03'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1016/j.molcel.2022.10.010
external_id:
isi:
- '000898565300011'
pmid:
- '36332606'
file:
- access_level: open_access
checksum: 999e443b54e4fdaa2542ca5a97619731
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T09:29:02Z
date_updated: 2023-01-24T09:29:02Z
file_id: '12354'
file_name: 2022_MolecularCell_Zapletal.pdf
file_size: 7368534
relation: main_file
success: 1
file_date_updated: 2023-01-24T09:29:02Z
has_accepted_license: '1'
intvolume: ' 82'
isi: 1
issue: '21'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 4064-4079.e13
pmid: 1
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural and functional basis of mammalian microRNA biogenesis by Dicer
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 82
year: '2022'
...
---
_id: '10163'
abstract:
- lang: eng
text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol
II) is a regulatory hub for transcription and RNA processing. Here, we identify
PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability
that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a
CTD reader domain that preferentially binds two phosphorylated Serine-2 marks
in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated
Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length
of genes. PHF3 knock-out or SPOC deletion in human cells results in increased
Pol II stalling, reduced elongation rate and an increase in mRNA stability, with
marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed
in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation.
Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation
by bridging transcription with mRNA decay.
acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz
Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help
with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase;
Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for
design of the arrest assay sequences; Petra van der Lelij for help with generating
mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan
Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing
reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski
for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility
for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing;
Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich
Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for
sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne
Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis;
staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support;
Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for
critical comments on the manuscript; Life Science Editors for editing assistance.
M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K.
is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S.
is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian
Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology
Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S
and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic
(CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (Grant agreement
no. 649030); this publication reflects only the author’s view and the Research Executive
Agency is not responsible for any use that may be made of the information it contains.
M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research
is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276,
P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative
‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural
Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action
BM1405 Non-globular proteins - from sequence to structure, function and application
in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF
LS17-008), and by the University of Vienna. This project was funded by the MFPL
start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the
Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”)
to D.S.'
article_number: '6078'
article_processing_charge: No
article_type: original
author:
- first_name: Lisa-Marie
full_name: Appel, Lisa-Marie
last_name: Appel
- first_name: Vedran
full_name: Franke, Vedran
last_name: Franke
- first_name: Melania
full_name: Bruno, Melania
last_name: Bruno
- first_name: Irina
full_name: Grishkovskaya, Irina
last_name: Grishkovskaya
- first_name: Aiste
full_name: Kasiliauskaite, Aiste
last_name: Kasiliauskaite
- first_name: Tanja
full_name: Kaufmann, Tanja
last_name: Kaufmann
- first_name: Ursula E.
full_name: Schoeberl, Ursula E.
last_name: Schoeberl
- first_name: Martin G.
full_name: Puchinger, Martin G.
last_name: Puchinger
- first_name: Sebastian
full_name: Kostrhon, Sebastian
last_name: Kostrhon
- first_name: Carmen
full_name: Ebenwaldner, Carmen
last_name: Ebenwaldner
- first_name: Marek
full_name: Sebesta, Marek
last_name: Sebesta
- first_name: Etienne
full_name: Beltzung, Etienne
last_name: Beltzung
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Gen
full_name: Lin, Gen
last_name: Lin
- first_name: Anna
full_name: Vlasova, Anna
last_name: Vlasova
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
- first_name: Rushad
full_name: Pavri, Rushad
last_name: Pavri
- first_name: Alexander
full_name: Stark, Alexander
last_name: Stark
- first_name: Altuna
full_name: Akalin, Altuna
last_name: Akalin
- first_name: Richard
full_name: Stefl, Richard
last_name: Stefl
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
- first_name: Dea
full_name: Slade, Dea
last_name: Slade
citation:
ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1).
doi:10.1038/s41467-021-26360-2
apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A.,
Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-021-26360-2
chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste
Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal
Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications.
Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2.
ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through
the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no.
1. Springer Nature, 2021.
ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann
T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung
E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R,
Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression
through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.
mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through
the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no.
1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2.
short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T.
Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta,
E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A.
Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications
12 (2021).
date_created: 2021-10-20T14:40:32Z
date_published: 2021-10-19T00:00:00Z
date_updated: 2024-10-21T06:02:05Z
day: '19'
ddc:
- '610'
department:
- _id: CaBe
doi: 10.1038/s41467-021-26360-2
external_id:
isi:
- '000709050300001'
file:
- access_level: open_access
checksum: d99fcd51aebde19c21314e3de0148007
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-21T13:51:49Z
date_updated: 2021-10-21T13:51:49Z
file_id: '10169'
file_name: 2021_NatComm_Appel.pdf
file_size: 5111706
relation: main_file
success: 1
file_date_updated: 2021-10-21T13:51:49Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- general physics and astronomy
- general biochemistry
- genetics and molecular biology
- general chemistry
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: 'Preprint '
relation: earlier_version
url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159
scopus_import: '1'
status: public
title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain
SPOC
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '15061'
abstract:
- lang: eng
text: The actin cytoskeleton, a dynamic network of actin filaments and associated
F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins
are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here
we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2
(EhActn2) with features expected for the common ancestor of Entamoeba and higher
eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2
reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain.
Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD
for Ca2+, binding of which can only be regulated in the presence of physiological
concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain
rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain
cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover
that EhActn2 plays an important role in phagocytic cup formation and might constitute
a new drug target for amoebic dysentery.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: "We thank the staff of the macromolecular crystallography (MX) and
SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss
Light Source for excellent support, and the Life Sciences Facility of the Institute
of Science and Technology Austria for usage of the rheometer. We thank Life Sciences
editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the
Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out
at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s
research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423),
Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura
Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative
Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF)
Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content
Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were
supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award
and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R.
ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I
2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological
Macromolecules. M.B. acknowledges the University Grant Commission, India, for a
senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science
Engineering Research Council. "
article_processing_charge: No
article_type: original
author:
- first_name: Nikos
full_name: Pinotsis, Nikos
last_name: Pinotsis
- first_name: Karolina
full_name: Zielinska, Karolina
last_name: Zielinska
- first_name: Mrigya
full_name: Babuta, Mrigya
last_name: Babuta
- first_name: Joan L.
full_name: Arolas, Joan L.
last_name: Arolas
- first_name: Julius
full_name: Kostan, Julius
last_name: Kostan
- first_name: Muhammad Bashir
full_name: Khan, Muhammad Bashir
last_name: Khan
- first_name: Claudia
full_name: Schreiner, Claudia
last_name: Schreiner
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Luciano
full_name: Ciccarelli, Luciano
last_name: Ciccarelli
- first_name: Martin
full_name: Puchinger, Martin
last_name: Puchinger
- first_name: Eirini A.
full_name: Gkougkoulia, Eirini A.
last_name: Gkougkoulia
- first_name: Euripedes de Almeida
full_name: Ribeiro, Euripedes de Almeida
last_name: Ribeiro
- first_name: Thomas C.
full_name: Marlovits, Thomas C.
last_name: Marlovits
- first_name: Alok
full_name: Bhattacharya, Alok
last_name: Bhattacharya
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
citation:
ama: Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility
and function of an α-actinin similar to the ancestral α-actinin. Proceedings
of the National Academy of Sciences of the United States of America. 2020;117(36):22101-22112.
doi:10.1073/pnas.1917269117
apa: Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M.
B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and
function of an α-actinin similar to the ancestral α-actinin. Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.1917269117
chicago: Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius
Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the
Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.”
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.
ieee: N. Pinotsis et al., “Calcium modulates the domain flexibility and function
of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National
Academy of Sciences of the United States of America, vol. 117, no. 36. National
Academy of Sciences, pp. 22101–22112, 2020.
ista: Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner
C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A,
Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain
flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings
of the National Academy of Sciences of the United States of America. 117(36),
22101–22112.
mla: Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function
of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National
Academy of Sciences of the United States of America, vol. 117, no. 36, National
Academy of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.
short: N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan,
C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia,
E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings
of the National Academy of Sciences of the United States of America 117 (2020)
22101–22112.
date_created: 2024-03-04T10:03:52Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2026-06-18T17:45:21Z
day: '08'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1073/pnas.1917269117
external_id:
pmid:
- '32848067'
intvolume: ' 117'
issue: '36'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.191726911
month: '09'
oa: 1
oa_version: Published Version
page: 22101-22112
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Calcium modulates the domain flexibility and function of an α-actinin similar
to the ancestral α-actinin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...
---
_id: '7580'
abstract:
- lang: eng
text: The eukaryotic endomembrane system is controlled by small GTPases of the Rab
family, which are activated at defined times and locations in a switch-like manner.
While this switch is well understood for an individual protein, how regulatory
networks produce intracellular activity patterns is currently not known. Here,
we combine in vitro reconstitution experiments with computational modeling to
study a minimal Rab5 activation network. We find that the molecular interactions
in this system give rise to a positive feedback and bistable collective switching
of Rab5. Furthermore, we find that switching near the critical point is intrinsically
stochastic and provide evidence that controlling the inactive population of Rab5
on the membrane can shape the network response. Notably, we demonstrate that collective
switching can spread on the membrane surface as a traveling wave of Rab5 activation.
Together, our findings reveal how biochemical signaling networks control vesicle
trafficking pathways and how their nonequilibrium properties define the spatiotemporal
organization of the cell.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_processing_charge: No
article_type: original
author:
- first_name: Urban
full_name: Bezeljak, Urban
id: 2A58201A-F248-11E8-B48F-1D18A9856A87
last_name: Bezeljak
orcid: 0000-0003-1365-5631
- first_name: Hrushikesh
full_name: Loya, Hrushikesh
last_name: Loya
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
- first_name: Timothy E.
full_name: Saunders, Timothy E.
last_name: Saunders
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation
and bistability in a Rab GTPase regulatory network. Proceedings of the National
Academy of Sciences of the United States of America. 2020;117(12):6504-6549.
doi:10.1073/pnas.1921027117
apa: Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., & Loose, M.
(2020). Stochastic activation and bistability in a Rab GTPase regulatory network.
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences. https://doi.org/10.1073/pnas.1921027117
chicago: Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders,
and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory
Network.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921027117.
ieee: U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic
activation and bistability in a Rab GTPase regulatory network,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
117, no. 12. National Academy of Sciences, pp. 6504–6549, 2020.
ista: Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation
and bistability in a Rab GTPase regulatory network. Proceedings of the National
Academy of Sciences of the United States of America. 117(12), 6504–6549.
mla: Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase
Regulatory Network.” Proceedings of the National Academy of Sciences of the
United States of America, vol. 117, no. 12, National Academy of Sciences,
2020, pp. 6504–49, doi:10.1073/pnas.1921027117.
short: U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings
of the National Academy of Sciences of the United States of America 117 (2020)
6504–6549.
date_created: 2020-03-12T05:32:26Z
date_published: 2020-03-24T00:00:00Z
date_updated: 2026-04-08T07:24:55Z
day: '24'
department:
- _id: MaLo
- _id: CaBe
doi: 10.1073/pnas.1921027117
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pmid: 1
project:
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grant_number: RGY0083/2016
name: Reconstitution of cell polarity and axis determination in a cell-free system
publication: Proceedings of the National Academy of Sciences of the United States
of America
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url: https://ist.ac.at/en/news/proteins-as-molecular-switches/
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status: public
scopus_import: '1'
status: public
title: Stochastic activation and bistability in a Rab GTPase regulatory network
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...
---
_id: '7487'
abstract:
- lang: eng
text: 'Glutaminase (GA) catalyzes the first step in mitochondrial glutaminolysis
playing a key role in cancer metabolic reprogramming. Humans express two types
of GA isoforms: GLS and GLS2. GLS isozymes have been consistently related to cell
proliferation, but the role of GLS2 in cancer remains poorly understood. GLS2
is repressed in many tumor cells and a better understanding of its function in
tumorigenesis may further the development of new therapeutic approaches. We analyzed
GLS2 expression in HCC, GBM and neuroblastoma cells, as well as in monkey COS-7
cells. We studied GLS2 expression after induction of differentiation with phorbol
ester (PMA) and transduction with the full-length cDNA of GLS2. In parallel, we
investigated cell cycle progression and levels of p53, p21 and c-Myc proteins.
Using the baculovirus system, human GLS2 protein was overexpressed, purified and
analyzed for posttranslational modifications employing a proteomics LC-MS/MS platform.
We have demonstrated a dual targeting of GLS2 in human cancer cells. Immunocytochemistry
and subcellular fractionation gave consistent results demonstrating nuclear and
mitochondrial locations, with the latter being predominant. Nuclear targeting
was confirmed in cancer cells overexpressing c-Myc- and GFP-tagged GLS2 proteins.
We assessed the subnuclear location finding a widespread distribution of GLS2
in the nucleoplasm without clear overlapping with specific nuclear substructures.
GLS2 expression and nuclear accrual notably increased by treatment of SH-SY5Y
cells with PMA and it correlated with cell cycle arrest at G2/M, upregulation
of tumor suppressor p53 and p21 protein. A similar response was obtained by overexpression
of GLS2 in T98G glioma cells, including downregulation of oncogene c-Myc. Furthermore,
human GLS2 was identified as being hypusinated by MS analysis, a posttranslational
modification which may be relevant for its nuclear targeting and/or function.
Our studies provide evidence for a tumor suppressor role of GLS2 in certain types
of cancer. The data imply that GLS2 can be regarded as a highly mobile and multilocalizing
protein translocated to both mitochondria and nuclei. Upregulation of GLS2 in
cancer cells induced an antiproliferative response with cell cycle arrest at the
G2/M phase.'
article_number: '2259'
article_processing_charge: No
article_type: original
author:
- first_name: Amada R.
full_name: López De La Oliva, Amada R.
last_name: López De La Oliva
- first_name: José A.
full_name: Campos-Sandoval, José A.
last_name: Campos-Sandoval
- first_name: María C.
full_name: Gómez-García, María C.
last_name: Gómez-García
- first_name: Carolina
full_name: Cardona, Carolina
last_name: Cardona
- first_name: Mercedes
full_name: Martín-Rufián, Mercedes
last_name: Martín-Rufián
- first_name: Fernando J.
full_name: Sialana, Fernando J.
last_name: Sialana
- first_name: Laura
full_name: Castilla, Laura
last_name: Castilla
- first_name: Narkhyun
full_name: Bae, Narkhyun
id: 3A5F7CD8-F248-11E8-B48F-1D18A9856A87
last_name: Bae
- first_name: Carolina
full_name: Lobo, Carolina
last_name: Lobo
- first_name: Ana
full_name: Peñalver, Ana
last_name: Peñalver
- first_name: Marina
full_name: García-Frutos, Marina
last_name: García-Frutos
- first_name: David
full_name: Carro, David
last_name: Carro
- first_name: Victoria
full_name: Enrique, Victoria
last_name: Enrique
- first_name: José C.
full_name: Paz, José C.
last_name: Paz
- first_name: Raghavendra G.
full_name: Mirmira, Raghavendra G.
last_name: Mirmira
- first_name: Antonia
full_name: Gutiérrez, Antonia
last_name: Gutiérrez
- first_name: Francisco J.
full_name: Alonso, Francisco J.
last_name: Alonso
- first_name: Juan A.
full_name: Segura, Juan A.
last_name: Segura
- first_name: José M.
full_name: Matés, José M.
last_name: Matés
- first_name: Gert
full_name: Lubec, Gert
last_name: Lubec
- first_name: Javier
full_name: Márquez, Javier
last_name: Márquez
citation:
ama: López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, et al. Nuclear translocation
of glutaminase GLS2 in human cancer cells associates with proliferation arrest
and differentiation. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-58264-4
apa: López De La Oliva, A. R., Campos-Sandoval, J. A., Gómez-García, M. C., Cardona,
C., Martín-Rufián, M., Sialana, F. J., … Márquez, J. (2020). Nuclear translocation
of glutaminase GLS2 in human cancer cells associates with proliferation arrest
and differentiation. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-58264-4
chicago: López De La Oliva, Amada R., José A. Campos-Sandoval, María C. Gómez-García,
Carolina Cardona, Mercedes Martín-Rufián, Fernando J. Sialana, Laura Castilla,
et al. “Nuclear Translocation of Glutaminase GLS2 in Human Cancer Cells Associates
with Proliferation Arrest and Differentiation.” Scientific Reports. Springer
Nature, 2020. https://doi.org/10.1038/s41598-020-58264-4.
ieee: A. R. López De La Oliva et al., “Nuclear translocation of glutaminase
GLS2 in human cancer cells associates with proliferation arrest and differentiation,”
Scientific reports, vol. 10, no. 1. Springer Nature, 2020.
ista: López De La Oliva AR, Campos-Sandoval JA, Gómez-García MC, Cardona C, Martín-Rufián
M, Sialana FJ, Castilla L, Bae N, Lobo C, Peñalver A, García-Frutos M, Carro D,
Enrique V, Paz JC, Mirmira RG, Gutiérrez A, Alonso FJ, Segura JA, Matés JM, Lubec
G, Márquez J. 2020. Nuclear translocation of glutaminase GLS2 in human cancer
cells associates with proliferation arrest and differentiation. Scientific reports.
10(1), 2259.
mla: López De La Oliva, Amada R., et al. “Nuclear Translocation of Glutaminase GLS2
in Human Cancer Cells Associates with Proliferation Arrest and Differentiation.”
Scientific Reports, vol. 10, no. 1, 2259, Springer Nature, 2020, doi:10.1038/s41598-020-58264-4.
short: A.R. López De La Oliva, J.A. Campos-Sandoval, M.C. Gómez-García, C. Cardona,
M. Martín-Rufián, F.J. Sialana, L. Castilla, N. Bae, C. Lobo, A. Peñalver, M.
García-Frutos, D. Carro, V. Enrique, J.C. Paz, R.G. Mirmira, A. Gutiérrez, F.J.
Alonso, J.A. Segura, J.M. Matés, G. Lubec, J. Márquez, Scientific Reports 10 (2020).
date_created: 2020-02-16T23:00:49Z
date_published: 2020-02-10T00:00:00Z
date_updated: 2026-04-02T11:51:06Z
day: '10'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1038/s41598-020-58264-4
external_id:
isi:
- '000560694800012'
pmid:
- '32042057'
file:
- access_level: open_access
checksum: c780bd87476a9c9e12668ff66de3dc96
content_type: application/pdf
creator: dernst
date_created: 2020-02-18T07:43:21Z
date_updated: 2020-07-14T12:47:59Z
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file_name: 2020_ScientificReport_Lopez.pdf
file_size: 4703751
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has_accepted_license: '1'
intvolume: ' 10'
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issue: '1'
language:
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month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41598-020-80651-0
scopus_import: '1'
status: public
title: Nuclear translocation of glutaminase GLS2 in human cancer cells associates
with proliferation arrest and differentiation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10
year: '2020'
...