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

Author

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

Subjects
Genetics, Biotechnology, Life Below Water, Biodiversity, DNA, Ecosystem, Environment, Eukaryota, Green Fluorescent Proteins, Marine Biology, Models, Biological, Species Specificity, Transformation, Genetic, Biological Sciences, Technology, Medical and Health Sciences, Developmental 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.

Published
2020

3. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

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

Subjects
Biological Sciences, Technology, Medical and Health Sciences, Developmental Biology
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

4. Cytochrome c 6A of Chloroplasts

Author

Howe, Christopher J., Nimmo, Robert H., Barbrook, Adrian C., Bendall, Derek S., Govindjee, Series editor, Sharkey, Thomas D., Series editor, Cramer, William A., editor, and Kallas, Toivo, editor

Published
2016
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11. Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

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

Subjects
Cell Biology, Biochemistry, Molecular Biology, Biotechnology
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.

Published
2020

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

Author

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

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.

Published
2020

14. Plastid Origins

Author

Howe, Christopher J., primary, Barbrook, Adrian C., additional, and Lockhart, Peter J., additional

Published
1995
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16. Genetic tool development in marine protists: Emerging model organisms for experimental cell biology

Author

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

Published
2019
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17. Genetic transformation of the dinoflagellate chloroplast

Author

Nimmo, Isabel C, primary, Barbrook, Adrian C, additional, Lassadi, Imen, additional, Chen, Jit Ern, additional, Geisler, Katrin, additional, Smith, Alison G, additional, Aranda, Manuel, additional, Purton, Saul, additional, Waller, Ross F, additional, Nisbet, R Ellen R, additional, and Howe, Christopher J, additional

Published
2019
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22. Comparative analysis of dinoflagellate chloroplast genomes reveals rRNA and tRNA genes

Author

Hiller Roger G, Plenderleith Lindsey J, Santucci Nicole, Barbrook Adrian C, and Howe Christopher J

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Peridinin-containing dinoflagellates have a highly reduced chloroplast genome, which is unlike that found in other chloroplast containing organisms. Genome reduction appears to be the result of extensive transfer of genes to the nuclear genome. Unusually the genes believed to be remaining in the chloroplast genome are found on small DNA 'minicircles'. In this study we present a comparison of sets of minicircle sequences from three dinoflagellate species. Results PCR was used to amplify several minicircles from Amphidinium carterae so that a homologous set of gene-containing minicircles was available for Amphidinium carterae and Amphidinium operculatum, two apparently closely related peridinin-containing dinoflagellates. We compared the sequences of these minicircles to determine the content and characteristics of their chloroplast genomes. We also made comparisons with minicircles which had been obtained from Heterocapsa triquetra, another peridinin-containing dinoflagellate. These in silico comparisons have revealed several genetic features which were not apparent in single species analyses. The features include further protein coding genes, unusual rRNA genes, which we show are transcribed, and the first examples of tRNA genes from peridinin-containing dinoflagellate chloroplast genomes. Conclusion Comparative analysis of minicircle sequences has allowed us to identify previously unrecognised features of dinoflagellate chloroplast genomes, including additional protein and RNA genes. The chloroplast rRNA gene sequences are radically different from those in other organisms, and in many ways resemble the rRNA genes found in some highly reduced mitochondrial genomes. The retention of certain tRNA genes in the dinoflagellate chloroplast genome has important implications for models of chloroplast-mitochondrion interaction.

Published
2006
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23. Manuscript evolution

Author

Howe, Christopher J., Barbrook, Adrian C., Spencer, Matthew, Robinson, Peter, Bordalejo, Barbara, and Mooney, Linne R.

Published
2001
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24. Genetic transformation of the dinoflagellate chloroplast

Author

Nimmo, Isabel C., primary, Barbrook, Adrian C., additional, Chen, Jit Ern, additional, Geisler, Katrin, additional, Smith, Alison G., additional, Aranda, Manuel, additional, Saul, Purton, additional, Waller, Ross F., additional, Nisbet, R. Ellen R., additional, and Howe, Christopher J., additional

Published
2018
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36. Manuscript evolution

Author

Howe, Christopher J., primary, Barbrook, Adrian C., additional, Spencer, Matthew, additional, Robinson, Peter, additional, Bordalejo, Barbara, additional, and Mooney, Linne R., additional

Published
2001
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37. How Molecules Evolve in Eubacteria

Author

Lockhart, Peter J., primary, Huson, Daniel, additional, Maier, Uwe, additional, Fraunholz, Martin J., additional, Van de Peer§, Yves, additional, Barbrook, Adrian C., additional, Howe, Christopher J., additional, and Steel, Mike A., additional

Published
2000
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41. Genetic tool development in marine protists: emerging model organisms for experimental cell biology

Author

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

Subjects
Transformation, Genetic, Species Specificity, Green Fluorescent Proteins, Eukaryota, Marine Biology, 14. Life underwater, Biodiversity, DNA, Environment, Models, Biological, Ecosystem
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.

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

Author

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

Subjects
Resource, 631/1647/767/722, 14. Life underwater, 631/337
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.

43. Novel plastid gene minicircles in the dinoflagellate Amphidinium operculatum

Author

Ellen, R., Nisbet, R., Lila Koumandou, V., Barbrook, Adrian C., and Howe, Christopher J.

Subjects
*GENES, *GENETICS, *GENOMES, *RNA
Abstract

Seven new minicircles, forming part of the fragmented plastid genome of the dinoflagellate Amphidinium operculatum, have been identified by PCR. Three minicircles are full-length, one of 2.6 kb encoding the 23S rRNA gene, one of 2.4 kb containing the psaB gene, and a third of 2.5 kb containing the psbD, psbE and psbI genes. This is the first report of a three-gene minicircle. All three genes are conventional in length, with the same codon bias found in other minicircle genes. The psbI gene sequence is very divergent. One empty minicircle, of 1.7 kb, and three ‘microcircles’, between 400 and 600 bp, have also been identified by PCR. They appear to be formed from full-length minicircles by homologous recombination and internal deletion. All three microcircles contain the core region common to minicircles, but are missing a coding region, providing further evidence that the core region is necessary for minicircle replication and maintenance. [Copyright &y& Elsevier]

Published
2004
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44. Polyuridylylation and processing of transcripts from multiple gene minicircles in chloroplasts of the dinoflagellate Amphidinium carterae

Author

Christopher J. Howe, Lindsey J. Plenderleith, Adrian C. Barbrook, Jennifer Burrows, R. Ellen R. Nisbet, Richard G. Dorrell, Barbrook, Adrian C, Dorrell, Richard G, Burrows, Jennifer, Plenderleith, Lindsey J, Nisbet, R Ellen R, and Howe, Christopher J

Subjects
Poly U, Chloroplasts, ved/biology.organism_classification_rank.species, Genes, Protozoan, Plant Science, Biology, Minicircle, Genome, Models, Biological, chloroplast, Transcription (biology), Amphidinium carterae, Genes, Chloroplast, Genetics, RNA Processing, Post-Transcriptional, Gene, minicircles, Messenger RNA, ved/biology, food and beverages, RNA, General Medicine, DNA, Protozoan, polyU, Molecular biology, transcript processing, Rolling circle replication, Dinoflagellida, DNA, Circular, protist, Agronomy and Crop Science, RNA, Protozoan
Abstract

Although transcription and transcript processing in the chloroplasts of plants have been extensively characterised, the RNA metabolism of other chloroplast lineages across the eukaryotes remains poorly understood. In this paper, we use RT-PCR to study transcription and transcript processing in the chloroplasts of Amphidinium carterae, a model peridinin-containing dinoflagellate. These organisms have a highly unusual chloroplast genome, with genes located on multiple small 'minicircle' elements, and a number of idiosyncratic features of RNA metabolism including transcription via a rolling circle mechanism, and 3' terminal polyuridylylation of transcripts. We demonstrate that transcription occurs in A. carterae via a rolling circle mechanism, as previously shown in the dinoflagellate Heterocapsa, and present evidence for the production of both polycistronic and monocistronic transcripts from A. carterae minicircles, including several regions containing ORFs previously not known to be expressed. We demonstrate the presence of both polyuridylylated and non-polyuridylylated transcripts in A. carterae, and show that polycistronic transcripts can be terminally polyuridylylated. We present a model for RNA metabolism in dinoflagellate chloroplasts where long polycistronic precursors are processed to form mature transcripts. Terminal polyuridylylation may mark transcripts with the correct 3' end. Refereed/Peer-reviewed

Published
2012

45. Dinoflagellate chloroplasts--where have all the genes gone?

Author

Koumandou VL, Nisbet RE, Barbrook AC, and Howe CJ

Subjects
Animals, Cell Nucleus metabolism, Conserved Sequence, Dinoflagellida ultrastructure, Genome, Models, Genetic, Plasmids metabolism, Plastids metabolism, Chloroplasts genetics, Dinoflagellida genetics, Dinoflagellida physiology
Published
2004
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46. Evolution of the chloroplast genome.

Author

Howe CJ, Barbrook AC, Koumandou VL, Nisbet RE, Symington HA, and Wightman TF

Subjects
Amino Acid Sequence, Animals, Bacteria genetics, Base Composition, Dinoflagellida genetics, Molecular Sequence Data, DNA, Chloroplast genetics, Evolution, Molecular, Genome, Plastids genetics
Abstract

We discuss the suggestion that differences in the nucleotide composition between plastid and nuclear genomes may provide a selective advantage in the transposition of genes from plastid to nucleus. We show that in the adenine, thymine (AT)-rich genome of Borrelia burgdorferi several genes have an AT-content lower than the average for the genome as a whole. However, genes whose plant homologues have moved from plastid to nucleus are no less AT-rich than genes whose plant homologues have remained in the plastid, indicating that both classes of gene are able to support a high AT-content. We describe the anomalous organization of dinoflagellate plastid genes. These are located on small circles of 2-3 kbp, in contrast to the usual plastid genome organization of a single large circle of 100-200 kbp. Most circles contain a single gene. Some circles contain two genes and some contain none. Dinoflagellate plastids have retained far fewer genes than other plastids. We discuss a similarity between the dinoflagellate minicircles and the bacterial integron system.

Published
2003
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