[{"abstract":[{"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.","lang":"eng"}],"_id":"9414","date_published":"2021-04-19T00:00:00Z","article_processing_charge":"No","issue":"9","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)","short":"CC BY-NC-SA (3.0)"},"volume":32,"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","oa":1,"main_file_link":[{"url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723","open_access":"1"}],"article_type":"original","year":"2021","oa_version":"Published Version","scopus_import":"1","external_id":{"isi":["000641574700005"]},"date_updated":"2023-08-08T13:36:02Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["1059-1524"],"eissn":["1939-4586"]},"month":"04","date_created":"2021-05-23T22:01:45Z","page":"869-879","publication":"Molecular Biology of the Cell","department":[{"_id":"MaLo"}],"quality_controlled":"1","intvolume":"        32","status":"public","publisher":"American Society for Cell Biology","isi":1,"day":"19","type":"journal_article","author":[{"first_name":"Keisuke","full_name":"Ishihara, Keisuke","last_name":"Ishihara"},{"first_name":"Franziska","full_name":"Decker, Franziska","last_name":"Decker"},{"last_name":"Dos Santos Caldas","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James F.","full_name":"Pelletier, James F.","last_name":"Pelletier"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin"},{"full_name":"Brugués, Jan","first_name":"Jan","last_name":"Brugués"},{"first_name":"Timothy J.","full_name":"Mitchison, Timothy J.","last_name":"Mitchison"}],"citation":{"mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>.","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.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2021. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>.","ieee":"K. Ishihara <i>et al.</i>, “Spatial variation of microtubule depolymerization in large asters,” <i>Molecular Biology of the Cell</i>, 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.","ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. 2021;32(9):869-879. doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., &#38; Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>","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."},"ec_funded":1,"title":"Spatial variation of microtubule depolymerization in large asters","language":[{"iso":"eng"}],"doi":"10.1091/MBC.E20-11-0723","project":[{"call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"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."},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8358"}]},"project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"language":[{"iso":"eng"}],"doi":"10.1016/bs.mcb.2020.01.006","ec_funded":1,"citation":{"mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” <i>Methods in Cell Biology</i>, edited by Phong  Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>.","ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in <i>Methods in Cell Biology</i>, 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.","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In <i>Methods in Cell Biology</i>, edited by Phong  Tran, 158:145–61. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>.","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., &#38; Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), <i>Methods in Cell Biology</i> (Vol. 158, pp. 145–161). Elsevier. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. <i>Methods in Cell Biology</i>. Vol 158. Elsevier; 2020:145-161. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>","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."},"title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","day":"27","alternative_title":["Methods in Cell Biology"],"type":"book_chapter","author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","first_name":"Paulo R","last_name":"Dos Santos Caldas"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","first_name":"Philipp","last_name":"Radler"},{"first_name":"Christoph M","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Loose, Martin","last_name":"Loose"}],"publisher":"Elsevier","isi":1,"department":[{"_id":"MaLo"}],"quality_controlled":"1","publication":"Methods in Cell Biology","intvolume":"       158","status":"public","page":"145-161","month":"02","date_created":"2020-03-08T23:00:47Z","date_updated":"2023-10-04T09:50:24Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000611826500008"]},"publication_identifier":{"issn":["0091679X"]},"editor":[{"last_name":"Tran","first_name":"Phong ","full_name":"Tran, Phong "}],"oa_version":"Preprint","year":"2020","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"oa":1,"volume":158,"article_processing_charge":"No","_id":"7572","abstract":[{"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.","lang":"eng"}],"date_published":"2020-02-27T00:00:00Z"},{"date_created":"2019-12-20T12:22:57Z","month":"12","isi":1,"publisher":"Springer Nature","intvolume":"        10","status":"public","publication":"Nature Communications","department":[{"_id":"MaLo"},{"_id":"BjHo"}],"quality_controlled":"1","title":"Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA","citation":{"mla":"Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>, vol. 10, 5744, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>.","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.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>.","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,” <i>Nature Communications</i>, 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.","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. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>","apa":"Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., &#38; Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>","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)."},"ec_funded":1,"author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas"},{"id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D","full_name":"Lopez Pelegrin, Maria D","last_name":"Lopez Pelegrin"},{"last_name":"Pearce","full_name":"Pearce, Daniel J. G.","first_name":"Daniel J. G."},{"last_name":"Budanur","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brugués","full_name":"Brugués, Jan","first_name":"Jan"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin","first_name":"Martin"}],"type":"journal_article","day":"17","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"id":"8358","relation":"dissertation_contains","status":"public"}]},"doi":"10.1038/s41467-019-13702-4","ddc":["570"],"language":[{"iso":"eng"}],"article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"_id":"7197","date_published":"2019-12-17T00:00:00Z","article_number":"5744","file":[{"content_type":"application/pdf","file_id":"7208","relation":"main_file","date_created":"2019-12-23T07:34:56Z","file_name":"2019_NatureComm_Caldas.pdf","file_size":8488733,"creator":"dernst","date_updated":"2020-07-14T12:47:53Z","access_level":"open_access","checksum":"a1b44b427ba341383197790d0e8789fa"}],"oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":10,"file_date_updated":"2020-07-14T12:47:53Z","oa_version":"Published Version","has_accepted_license":"1","year":"2019","article_type":"original","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"issn":["2041-1723"]},"external_id":{"isi":["000503009300001"]},"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T13:18:51Z"}]