Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Drahomíra Faktorová; R. Ellen R. Nisbet; José A. Fernández Robledo; Elena Casacuberta; Lisa Sudek; Andrew E. Allen; Manuel Ares; Cristina Aresté; Cecilia Balestreri; Adrian C. Barbrook; Patrick Beardslee; Sara Bender; David S. Booth; François-Yves Bouget; Chris Bowler; Susana A. Breglia; Colin Brownlee; Gertraud Burger; Heriberto Cerutti; Rachele Cesaroni; Miguel A. Chiurillo; Thomas Clemente; Duncan B. Coles; Jackie L. Collier; Elizabeth C. Cooney; Kathryn Coyne; Roberto Docampo; Christopher L. Dupont; Virginia Edgcomb; Elin Einarsson; Pía A. Elustondo; Fernan Federici; Veronica Freire-Beneitez; Nastasia J. Freyria; Kodai Fukuda; Paulo A. García; Peter R. Girguis; Fatma Gomaa; Sebastian G. Gornik; Jian Guo; Vladimír Hampl; Yutaka Hanawa; Esteban R. Haro-Contreras; Elisabeth Hehenberger; Andrea Highfield; Yoshihisa Hirakawa; Amanda Hopes; Christopher J. Howe; Ian Hu; Jorge Ibañez; Nicholas A. T. Irwin; Yuu Ishii; Natalia Ewa Janowicz; Adam C. Jones; Ambar Kachale; Konomi Fujimura-Kamada; Binnypreet Kaur; Jonathan Z. Kaye; Eleanna Kazana; Patrick J. Keeling; Nicole King; Lawrence A. Klobutcher; Noelia Lander; Imen Lassadi; Zhuhong Li; Senjie Lin; Jean-Claude Lozano; Fulei Luan; Shinichiro Maruyama; Tamara Matute; Cristina Miceli; Jun Minagawa; Mark Moosburner; Sebastián R. Najle; Deepak Nanjappa; Isabel C. Nimmo; Luke Noble; Anna M. G. Novák Vanclová; Mariusz Nowacki; Isaac Nuñez; Arnab Pain; Angela Piersanti; Sandra Pucciarelli; Jan Pyrih; Joshua S. Rest; Mariana Rius; Deborah Robertson; Albane Ruaud; Iñaki Ruiz-Trillo; Monika A. Sigg; Pamela A. Silver; Claudio H. Slamovits; G. Jason Smith; Brittany N. Sprecher; Rowena Stern; Estienne C. Swart; Anastasios D. Tsaousis; Lev Tsypin; Aaron Turkewitz; Jernej Turnšek; Matus Valach; Valérie Vergé; Peter von Dassow; Tobias von der Haar; Ross F. Waller; Lu Wang; Xiaoxue Wen; Glen Wheeler; April Woods; Huan Zhang; Thomas Mock; Alexandra Z. Worden; Julius Lukeš

doi:10.1038/s41592-020-0796-x

Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Drahomíra Faktorová, R. Ellen R. Nisbet, José A. Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel Ares, Cristina Aresté, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, François-Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele CesaroniMiguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pía A. Elustondo, Fernan Federici, Veronica Freire-Beneitez, Nastasia J. Freyria, Kodai Fukuda, Paulo A. García, Peter R. Girguis, Fatma Gomaa, Sebastian G. Gornik, Jian Guo, Vladimír Hampl, Yutaka Hanawa, Esteban R. Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, Amanda Hopes, Christopher J. Howe, Ian Hu, Jorge Ibañez, Nicholas A. T. Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C. Jones, Ambar Kachale, Konomi Fujimura-Kamada, Binnypreet Kaur, Jonathan Z. Kaye, Eleanna Kazana, Patrick J. Keeling, Nicole King, Lawrence A. Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, Mark Moosburner, Sebastián R. Najle, Deepak Nanjappa, Isabel C. Nimmo, Luke Noble, Anna M. G. Novák Vanclová, Mariusz Nowacki, Isaac Nuñez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S. Rest, Mariana Rius, Deborah Robertson, Albane Ruaud, Iñaki Ruiz-Trillo, Monika A. Sigg, Pamela A. Silver, Claudio H. Slamovits, G. Jason Smith, Brittany N. Sprecher, Rowena Stern, Estienne C. Swart, Anastasios D. Tsaousis, Lev Tsypin, Aaron Turkewitz, Jernej Turnšek, Matus Valach, Valérie Vergé, Peter von Dassow, Tobias von der Haar, Ross F. Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z. Worden, Julius Lukeš

Research output: Contribution to journal › Article › peer-review

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Abstract

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

Original language	English (US)
Journal	Nature Methods
DOIs	https://doi.org/10.1038/s41592-020-0796-x
State	Published - Apr 6 2020

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10.1038/s41592-020-0796-x

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Faktorová, D., Nisbet, R. E. R., Fernández Robledo, J. A., Casacuberta, E., Sudek, L., Allen, A. E., Ares, M., Aresté, C., Balestreri, C., Barbrook, A. C., Beardslee, P., Bender, S., Booth, D. S., Bouget, F.-Y., Bowler, C., Breglia, S. A., Brownlee, C., Burger, G., Cerutti, H., ... Lukeš, J. (2020). Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods. https://doi.org/10.1038/s41592-020-0796-x

@article{b4d402dbdaf24b0c87dd59c193843013,

title = "Genetic tool development in marine protists: emerging model organisms for experimental cell biology",

abstract = "Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.",

author = "Drahom{\'i}ra Faktorov{\'a} and Nisbet, {R. Ellen R.} and {Fern{\'a}ndez Robledo}, {Jos{\'e} A.} and Elena Casacuberta and Lisa Sudek and Allen, {Andrew E.} and Manuel Ares and Cristina Arest{\'e} and Cecilia Balestreri and Barbrook, {Adrian C.} and Patrick Beardslee and Sara Bender and Booth, {David S.} and Fran{\c c}ois-Yves Bouget and Chris Bowler and Breglia, {Susana A.} and Colin Brownlee and Gertraud Burger and Heriberto Cerutti and Rachele Cesaroni and Chiurillo, {Miguel A.} and Thomas Clemente and Coles, {Duncan B.} and Collier, {Jackie L.} and Cooney, {Elizabeth C.} and Kathryn Coyne and Roberto Docampo and Dupont, {Christopher L.} and Virginia Edgcomb and Elin Einarsson and Elustondo, {P{\'i}a A.} and Fernan Federici and Veronica Freire-Beneitez and Freyria, {Nastasia J.} and Kodai Fukuda and Garc{\'i}a, {Paulo A.} and Girguis, {Peter R.} and Fatma Gomaa and Gornik, {Sebastian G.} and Jian Guo and Vladim{\'i}r Hampl and Yutaka Hanawa and Haro-Contreras, {Esteban R.} and Elisabeth Hehenberger and Andrea Highfield and Yoshihisa Hirakawa and Amanda Hopes and Howe, {Christopher J.} and Ian Hu and Jorge Iba{\~n}ez and Irwin, {Nicholas A. T.} and Yuu Ishii and Janowicz, {Natalia Ewa} and Jones, {Adam C.} and Ambar Kachale and Konomi Fujimura-Kamada and Binnypreet Kaur and Kaye, {Jonathan Z.} and Eleanna Kazana and Keeling, {Patrick J.} and Nicole King and Klobutcher, {Lawrence A.} and Noelia Lander and Imen Lassadi and Zhuhong Li and Senjie Lin and Jean-Claude Lozano and Fulei Luan and Shinichiro Maruyama and Tamara Matute and Cristina Miceli and Jun Minagawa and Mark Moosburner and Najle, {Sebasti{\'a}n R.} and Deepak Nanjappa and Nimmo, {Isabel C.} and Luke Noble and {Nov{\'a}k Vanclov{\'a}}, {Anna M. G.} and Mariusz Nowacki and Isaac Nu{\~n}ez and Arnab Pain and Angela Piersanti and Sandra Pucciarelli and Jan Pyrih and Rest, {Joshua S.} and Mariana Rius and Deborah Robertson and Albane Ruaud and I{\~n}aki Ruiz-Trillo and Sigg, {Monika A.} and Silver, {Pamela A.} and Slamovits, {Claudio H.} and {Jason Smith}, G. and Sprecher, {Brittany N.} and Rowena Stern and Swart, {Estienne C.} and Tsaousis, {Anastasios D.} and Lev Tsypin and Aaron Turkewitz and Jernej Turn{\v s}ek and Matus Valach and Val{\'e}rie Verg{\'e} and {von Dassow}, Peter and {von der Haar}, Tobias and Waller, {Ross F.} and Lu Wang and Xiaoxue Wen and Glen Wheeler and April Woods and Huan Zhang and Thomas Mock and Worden, {Alexandra Z.} and Julius Luke{\v s}",

note = "KAUST Repository Item: Exported on 2020-04-23 Acknowledgements: We thank M. Salisbury and D. Lacono, C. Poirier, M. Hamilton, C. Eckmann, H. Igel, C. Yung and K. Hoadley for assistance; V.K. Nagarajan, M. Accerbi and P.J. Green who carried out Agrobacterium studies in Heterosigma akashiwo, and N. Kraeva, C. Bianchi and V. Yurchenko for the help with designing the p57-V5+NeoR construct. We are also grateful to the protocols.io team (L. Teytelman and A. Broellochs) for their support. This collaborative effort was supported by the Gordon and Betty Moore Foundation EMS Program of the Marine Microbiology Initiative (grant nos. GBMF4972 and 4972.01 to F.-Y.B.; GBMF4970 and 4970.01 to M.A. and A.Z.W.; GBMF3788 to A.Z.W.; GBMF 4968 and 4968.01 to H.C.; GBMF4984 to V.H.; GBMF4974 and 4974.01 to C. Brownlee; GBMF4964 to Y. Hirakawa; GBMF4961 to T. Mock; GBMF4958 to P.S.; GBMF4957 to A.T.; GBMF4960 to G.J.S.; GBMF4979 to K.C.; GBMF4982 and 4982.01 to J.L.C.; GBMF4964 to P.J.K.; GBMF4981 to P.v.D.; GBMF5006 to A.E.A.; GBMF4986 to C.M.; GBMF4962 to J.A.F.R.; GBMF4980 and 4980.01 to S.L.; GBMF 4977 and 4977.01 to R.F.W.; GBMF4962.01 to C.H.S.; GBMF4985 to J.M.; GBMF4976 and 4976.01 to C.H.; GBMF4963 and 4963.01 to V.E.; GBMF5007 to C.L.D.; GBMF4983 and 4983.01 to J.L.; GBMF4975 and 4975.01 to A.D.T.; GBMF4973 and 4973.01 to I.R.-T. and GBMF4965 to N.K.), by The Leverhulme Trust (RPG-2017-364) to T. Mock and A. Hopes, and by ERD funds (16_019/0000759) from the Czech Ministry of Education to J.L.",

year = "2020",

month = apr,

day = "6",

doi = "10.1038/s41592-020-0796-x",

language = "English (US)",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

}

Faktorová, D, Nisbet, RER, Fernández Robledo, JA, Casacuberta, E, Sudek, L, Allen, AE, Ares, M, Aresté, C, Balestreri, C, Barbrook, AC, Beardslee, P, Bender, S, Booth, DS, Bouget, F-Y, Bowler, C, Breglia, SA, Brownlee, C, Burger, G, Cerutti, H, Cesaroni, R, Chiurillo, MA, Clemente, T, Coles, DB, Collier, JL, Cooney, EC, Coyne, K, Docampo, R, Dupont, CL, Edgcomb, V, Einarsson, E, Elustondo, PA, Federici, F, Freire-Beneitez, V, Freyria, NJ, Fukuda, K, García, PA, Girguis, PR, Gomaa, F, Gornik, SG, Guo, J, Hampl, V, Hanawa, Y, Haro-Contreras, ER, Hehenberger, E, Highfield, A, Hirakawa, Y, Hopes, A, Howe, CJ, Hu, I, Ibañez, J, Irwin, NAT, Ishii, Y, Janowicz, NE, Jones, AC, Kachale, A, Fujimura-Kamada, K, Kaur, B, Kaye, JZ, Kazana, E, Keeling, PJ, King, N, Klobutcher, LA, Lander, N, Lassadi, I, Li, Z, Lin, S, Lozano, J-C, Luan, F, Maruyama, S, Matute, T, Miceli, C, Minagawa, J, Moosburner, M, Najle, SR, Nanjappa, D, Nimmo, IC, Noble, L, Novák Vanclová, AMG, Nowacki, M, Nuñez, I, Pain, A, Piersanti, A, Pucciarelli, S, Pyrih, J, Rest, JS, Rius, M, Robertson, D, Ruaud, A, Ruiz-Trillo, I, Sigg, MA, Silver, PA, Slamovits, CH, Jason Smith, G, Sprecher, BN, Stern, R, Swart, EC, Tsaousis, AD, Tsypin, L, Turkewitz, A, Turnšek, J, Valach, M, Vergé, V, von Dassow, P, von der Haar, T, Waller, RF, Wang, L, Wen, X, Wheeler, G, Woods, A, Zhang, H, Mock, T, Worden, AZ & Lukeš, J 2020, 'Genetic tool development in marine protists: emerging model organisms for experimental cell biology', Nature Methods. https://doi.org/10.1038/s41592-020-0796-x

TY - JOUR

T1 - Genetic tool development in marine protists: emerging model organisms for experimental cell biology

AU - Faktorová, Drahomíra

AU - Nisbet, R. Ellen R.

AU - Fernández Robledo, José A.

AU - Casacuberta, Elena

AU - Sudek, Lisa

AU - Allen, Andrew E.

AU - Ares, Manuel

AU - Aresté, Cristina

AU - Balestreri, Cecilia

AU - Barbrook, Adrian C.

AU - Beardslee, Patrick

AU - Bender, Sara

AU - Booth, David S.

AU - Bouget, François-Yves

AU - Bowler, Chris

AU - Breglia, Susana A.

AU - Brownlee, Colin

AU - Burger, Gertraud

AU - Cerutti, Heriberto

AU - Cesaroni, Rachele

AU - Chiurillo, Miguel A.

AU - Clemente, Thomas

AU - Coles, Duncan B.

AU - Collier, Jackie L.

AU - Cooney, Elizabeth C.

AU - Coyne, Kathryn

AU - Docampo, Roberto

AU - Dupont, Christopher L.

AU - Edgcomb, Virginia

AU - Einarsson, Elin

AU - Elustondo, Pía A.

AU - Federici, Fernan

AU - Freire-Beneitez, Veronica

AU - Freyria, Nastasia J.

AU - Fukuda, Kodai

AU - García, Paulo A.

AU - Girguis, Peter R.

AU - Gomaa, Fatma

AU - Gornik, Sebastian G.

AU - Guo, Jian

AU - Hampl, Vladimír

AU - Hanawa, Yutaka

AU - Haro-Contreras, Esteban R.

AU - Hehenberger, Elisabeth

AU - Highfield, Andrea

AU - Hirakawa, Yoshihisa

AU - Hopes, Amanda

AU - Howe, Christopher J.

AU - Hu, Ian

AU - Ibañez, Jorge

AU - Irwin, Nicholas A. T.

AU - Ishii, Yuu

AU - Janowicz, Natalia Ewa

AU - Jones, Adam C.

AU - Kachale, Ambar

AU - Fujimura-Kamada, Konomi

AU - Kaur, Binnypreet

AU - Kaye, Jonathan Z.

AU - Kazana, Eleanna

AU - Keeling, Patrick J.

AU - King, Nicole

AU - Klobutcher, Lawrence A.

AU - Lander, Noelia

AU - Lassadi, Imen

AU - Li, Zhuhong

AU - Lin, Senjie

AU - Lozano, Jean-Claude

AU - Luan, Fulei

AU - Maruyama, Shinichiro

AU - Matute, Tamara

AU - Miceli, Cristina

AU - Minagawa, Jun

AU - Moosburner, Mark

AU - Najle, Sebastián R.

AU - Nanjappa, Deepak

AU - Nimmo, Isabel C.

AU - Noble, Luke

AU - Novák Vanclová, Anna M. G.

AU - Nowacki, Mariusz

AU - Nuñez, Isaac

AU - Pain, Arnab

AU - Piersanti, Angela

AU - Pucciarelli, Sandra

AU - Pyrih, Jan

AU - Rest, Joshua S.

AU - Rius, Mariana

AU - Robertson, Deborah

AU - Ruaud, Albane

AU - Ruiz-Trillo, Iñaki

AU - Sigg, Monika A.

AU - Silver, Pamela A.

AU - Slamovits, Claudio H.

AU - Jason Smith, G.

AU - Sprecher, Brittany N.

AU - Stern, Rowena

AU - Swart, Estienne C.

AU - Tsaousis, Anastasios D.

AU - Tsypin, Lev

AU - Turkewitz, Aaron

AU - Turnšek, Jernej

AU - Valach, Matus

AU - Vergé, Valérie

AU - von Dassow, Peter

AU - von der Haar, Tobias

AU - Waller, Ross F.

AU - Wang, Lu

AU - Wen, Xiaoxue

AU - Wheeler, Glen

AU - Woods, April

AU - Zhang, Huan

AU - Mock, Thomas

AU - Worden, Alexandra Z.

AU - Lukeš, Julius

N1 - KAUST Repository Item: Exported on 2020-04-23 Acknowledgements: We thank M. Salisbury and D. Lacono, C. Poirier, M. Hamilton, C. Eckmann, H. Igel, C. Yung and K. Hoadley for assistance; V.K. Nagarajan, M. Accerbi and P.J. Green who carried out Agrobacterium studies in Heterosigma akashiwo, and N. Kraeva, C. Bianchi and V. Yurchenko for the help with designing the p57-V5+NeoR construct. We are also grateful to the protocols.io team (L. Teytelman and A. Broellochs) for their support. This collaborative effort was supported by the Gordon and Betty Moore Foundation EMS Program of the Marine Microbiology Initiative (grant nos. GBMF4972 and 4972.01 to F.-Y.B.; GBMF4970 and 4970.01 to M.A. and A.Z.W.; GBMF3788 to A.Z.W.; GBMF 4968 and 4968.01 to H.C.; GBMF4984 to V.H.; GBMF4974 and 4974.01 to C. Brownlee; GBMF4964 to Y. Hirakawa; GBMF4961 to T. Mock; GBMF4958 to P.S.; GBMF4957 to A.T.; GBMF4960 to G.J.S.; GBMF4979 to K.C.; GBMF4982 and 4982.01 to J.L.C.; GBMF4964 to P.J.K.; GBMF4981 to P.v.D.; GBMF5006 to A.E.A.; GBMF4986 to C.M.; GBMF4962 to J.A.F.R.; GBMF4980 and 4980.01 to S.L.; GBMF 4977 and 4977.01 to R.F.W.; GBMF4962.01 to C.H.S.; GBMF4985 to J.M.; GBMF4976 and 4976.01 to C.H.; GBMF4963 and 4963.01 to V.E.; GBMF5007 to C.L.D.; GBMF4983 and 4983.01 to J.L.; GBMF4975 and 4975.01 to A.D.T.; GBMF4973 and 4973.01 to I.R.-T. and GBMF4965 to N.K.), by The Leverhulme Trust (RPG-2017-364) to T. Mock and A. Hopes, and by ERD funds (16_019/0000759) from the Czech Ministry of Education to J.L.

PY - 2020/4/6

Y1 - 2020/4/6

N2 - Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

AB - Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

UR - http://hdl.handle.net/10754/662477

UR - http://www.nature.com/articles/s41592-020-0796-x

U2 - 10.1038/s41592-020-0796-x

DO - 10.1038/s41592-020-0796-x

M3 - Article

C2 - 32251396

SN - 1548-7091

JO - Nature Methods

JF - Nature Methods

ER -

Genetic tool development in marine protists: emerging model organisms for experimental cell biology

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