---
_id: '9414'
abstract:
- lang: eng
text: Microtubule plus-end depolymerization rate is a potentially important target
of physiological regulation, but it has been challenging to measure, so its role
in spatial organization is poorly understood. Here we apply a method for tracking
plus ends based on time difference imaging to measure depolymerization rates in
large interphase asters growing in Xenopus egg extract. We observed strong spatial
regulation of depolymerization rates, which were higher in the aster interior
compared with the periphery, and much less regulation of polymerization or catastrophe
rates. We interpret these data in terms of a limiting component model, where aster
growth results in lower levels of soluble tubulin and microtubule-associated proteins
(MAPs) in the interior cytosol compared with that at the periphery. The steady-state
polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the
aster interior. We propose that the limiting component for microtubule assembly
is a MAP that inhibits depolymerization, and that egg asters are tuned to low
microtubule density.
acknowledgement: The authors thank the members of Mitchison, Brugués, and Jay Gatlin
groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG)
for frog maintenance. We thank Nikon for microscopy support at Marine Biological
Laboratory (MBL). K.I. was supported by fellowships from the Honjo International
Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported
by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C.
is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported
by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported
by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research
is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research
is supported by National Institutes of Health Grant no. R35GM131753.
article_processing_charge: No
article_type: original
author:
- first_name: Keisuke
full_name: Ishihara, Keisuke
last_name: Ishihara
- first_name: Franziska
full_name: Decker, Franziska
last_name: Decker
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: James F.
full_name: Pelletier, James F.
last_name: Pelletier
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jan
full_name: Brugués, Jan
last_name: Brugués
- first_name: Timothy J.
full_name: Mitchison, Timothy J.
last_name: Mitchison
citation:
ama: Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879.
doi:10.1091/MBC.E20-11-0723
apa: Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose,
M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. American
Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723
chicago: Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F.
Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation
of Microtubule Depolymerization in Large Asters.” Molecular Biology of the
Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.
ieee: K. Ishihara et al., “Spatial variation of microtubule depolymerization
in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American
Society for Cell Biology, pp. 869–879, 2021.
ista: Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués
J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large
asters. Molecular Biology of the Cell. 32(9), 869–879.
mla: Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization
in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American
Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.
short: K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose,
J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.
date_created: 2021-05-23T22:01:45Z
date_published: 2021-04-19T00:00:00Z
date_updated: 2023-08-08T13:36:02Z
day: '19'
department:
- _id: MaLo
doi: 10.1091/MBC.E20-11-0723
ec_funded: 1
external_id:
isi:
- '000641574700005'
intvolume: ' 32'
isi: 1
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/3.0/
main_file_link:
- open_access: '1'
url: https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723
month: '04'
oa: 1
oa_version: Published Version
page: 869-879
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Molecular Biology of the Cell
publication_identifier:
eissn:
- 1939-4586
issn:
- 1059-1524
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatial variation of microtubule depolymerization in large asters
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA
3.0)
short: CC BY-NC-SA (3.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2021'
...
---
_id: '7572'
abstract:
- lang: eng
text: The polymerization–depolymerization dynamics of cytoskeletal proteins play
essential roles in the self-organization of cytoskeletal structures, in eukaryotic
as well as prokaryotic cells. While advances in fluorescence microscopy and in
vitro reconstitution experiments have helped to study the dynamic properties of
these complex systems, methods that allow to collect and analyze large quantitative
datasets of the underlying polymer dynamics are still missing. Here, we present
a novel image analysis workflow to study polymerization dynamics of active filaments
in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial
tubulin FtsZ as an example, we demonstrate that our method is able to specifically
detect, track and analyze growth and shrinkage of polymers, even in dense networks
of filaments. We believe that this automated method can facilitate the analysis
of a large variety of dynamic cytoskeletal systems, using standard time-lapse
movies obtained from experiments in vitro as well as in the living cell. Moreover,
we provide scripts implementing this method as supplementary material.
alternative_title:
- Methods in Cell Biology
article_processing_charge: No
author:
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: Philipp
full_name: Radler, Philipp
id: 40136C2A-F248-11E8-B48F-1D18A9856A87
last_name: Radler
orcid: '0000-0001-9198-2182 '
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: 'Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis
of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed.
Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006'
apa: Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020).
Computational analysis of filament polymerization dynamics in cytoskeletal networks.
In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier.
https://doi.org/10.1016/bs.mcb.2020.01.006
chicago: Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin
Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal
Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61.
Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006.
ieee: P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational
analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods
in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.
ista: 'Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis
of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell
Biology. Methods in Cell Biology, vol. 158, 145–161.'
mla: Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization
Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by
Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006.
short: P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.),
Methods in Cell Biology, Elsevier, 2020, pp. 145–161.
date_created: 2020-03-08T23:00:47Z
date_published: 2020-02-27T00:00:00Z
date_updated: 2023-10-04T09:50:24Z
day: '27'
department:
- _id: MaLo
doi: 10.1016/bs.mcb.2020.01.006
ec_funded: 1
editor:
- first_name: 'Phong '
full_name: 'Tran, Phong '
last_name: Tran
external_id:
isi:
- '000611826500008'
intvolume: ' 158'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/839571
month: '02'
oa: 1
oa_version: Preprint
page: 145-161
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Methods in Cell Biology
publication_identifier:
issn:
- 0091679X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '8358'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Computational analysis of filament polymerization dynamics in cytoskeletal
networks
type: book_chapter
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 158
year: '2020'
...
---
_id: '7197'
abstract:
- lang: eng
text: During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like
structure at the center of the cell. This Z-ring not only organizes the division
machinery, but treadmilling of FtsZ filaments was also found to play a key role
in distributing proteins at the division site. What regulates the architecture,
dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated
proteins are known to play an important role. Here, using an in vitro reconstitution
approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling
and filament organization into large-scale patterns. Using high-resolution fluorescence
microscopy and quantitative image analysis, we found that ZapA cooperatively increases
the spatial order of the filament network, but binds only transiently to FtsZ
filaments and has no effect on filament length and treadmilling velocity. Together,
our data provides a model for how FtsZ-associated proteins can increase the precision
and stability of the bacterial cell division machinery in a switch-like manner.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
article_number: '5744'
article_processing_charge: No
article_type: original
author:
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: Maria D
full_name: Lopez Pelegrin, Maria D
id: 319AA9CE-F248-11E8-B48F-1D18A9856A87
last_name: Lopez Pelegrin
- first_name: Daniel J. G.
full_name: Pearce, Daniel J. G.
last_name: Pearce
- first_name: Nazmi B
full_name: Budanur, Nazmi B
id: 3EA1010E-F248-11E8-B48F-1D18A9856A87
last_name: Budanur
orcid: 0000-0003-0423-5010
- first_name: Jan
full_name: Brugués, Jan
last_name: Brugués
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
citation:
ama: Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J,
Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks
of FtsZ and its crosslinker ZapA. Nature Communications. 2019;10. doi:10.1038/s41467-019-13702-4
apa: Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur,
N. B., Brugués, J., & Loose, M. (2019). Cooperative ordering of treadmilling
filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13702-4
chicago: Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce,
Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling
Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature
Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13702-4.
ieee: P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur,
J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal
networks of FtsZ and its crosslinker ZapA,” Nature Communications, vol.
10. Springer Nature, 2019.
ista: Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J,
Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal
networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744.
mla: Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments
in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications,
vol. 10, 5744, Springer Nature, 2019, doi:10.1038/s41467-019-13702-4.
short: P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur,
J. Brugués, M. Loose, Nature Communications 10 (2019).
date_created: 2019-12-20T12:22:57Z
date_published: 2019-12-17T00:00:00Z
date_updated: 2023-09-07T13:18:51Z
day: '17'
ddc:
- '570'
department:
- _id: MaLo
- _id: BjHo
doi: 10.1038/s41467-019-13702-4
ec_funded: 1
external_id:
isi:
- '000503009300001'
file:
- access_level: open_access
checksum: a1b44b427ba341383197790d0e8789fa
content_type: application/pdf
creator: dernst
date_created: 2019-12-23T07:34:56Z
date_updated: 2020-07-14T12:47:53Z
file_id: '7208'
file_name: 2019_NatureComm_Caldas.pdf
file_size: 8488733
relation: main_file
file_date_updated: 2020-07-14T12:47:53Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8358'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cooperative ordering of treadmilling filaments in cytoskeletal networks of
FtsZ and its crosslinker ZapA
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10
year: '2019'
...