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1. A novel DPH5-related diphthamide-deficiency syndrome causing embryonic lethality or profound neurodevelopmental disorder.

Author

Shankar, Suma P, Shankar, Suma P, Grimsrud, Kristin, Lanoue, Louise, Egense, Alena, Willis, Brandon, Hörberg, Johanna, AlAbdi, Lama, Mayer, Klaus, Ütkür, Koray, Monaghan, Kristin G, Krier, Joel, Stoler, Joan, Alnemer, Maha, Shankar, Prabhu R, Schaffrath, Raffael, Alkuraya, Fowzan S, Brinkmann, Ulrich, Eriksson, Leif A, Lloyd, Kent, Rauen, Katherine A, Undiagnosed Diseases Network, Shankar, Suma P, Shankar, Suma P, Grimsrud, Kristin, Lanoue, Louise, Egense, Alena, Willis, Brandon, Hörberg, Johanna, AlAbdi, Lama, Mayer, Klaus, Ütkür, Koray, Monaghan, Kristin G, Krier, Joel, Stoler, Joan, Alnemer, Maha, Shankar, Prabhu R, Schaffrath, Raffael, Alkuraya, Fowzan S, Brinkmann, Ulrich, Eriksson, Leif A, Lloyd, Kent, Rauen, Katherine A, and Undiagnosed Diseases Network

Abstract

PurposeDiphthamide is a post-translationally modified histidine essential for messenger RNA translation and ribosomal protein synthesis. We present evidence for DPH5 as a novel cause of embryonic lethality and profound neurodevelopmental delays (NDDs).MethodsMolecular testing was performed using exome or genome sequencing. A targeted Dph5 knockin mouse (C57BL/6Ncrl-Dph5em1Mbp/Mmucd) was created for a DPH5 p.His260Arg homozygous variant identified in 1 family. Adenosine diphosphate-ribosylation assays in DPH5-knockout human and yeast cells and in silico modeling were performed for the identified DPH5 potential pathogenic variants.ResultsDPH5 variants p.His260Arg (homozygous), p.Asn110Ser and p.Arg207Ter (heterozygous), and p.Asn174LysfsTer10 (homozygous) were identified in 3 unrelated families with distinct overlapping craniofacial features, profound NDDs, multisystem abnormalities, and miscarriages. Dph5 p.His260Arg homozygous knockin was embryonically lethal with only 1 subviable mouse exhibiting impaired growth, craniofacial dysmorphology, and multisystem dysfunction recapitulating the human phenotype. Adenosine diphosphate-ribosylation assays showed absent to decreased function in DPH5-knockout human and yeast cells. In silico modeling of the variants showed altered DPH5 structure and disruption of its interaction with eEF2.ConclusionWe provide strong clinical, biochemical, and functional evidence for DPH5 as a novel cause of embryonic lethality or profound NDDs with multisystem involvement and expand diphthamide-deficiency syndromes and ribosomopathies.

Published
2022

2. Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast

Author

Massachusetts Institute of Technology. Department of Biological Engineering, Pollo-Oliveira, Leticia, Klassen, Roland, Davis, Nick, Ciftci, Akif, Bacusmo, Jo Marie, Martinelli, Maria, DeMott, Michael S., Begley, Thomas J., Dedon, Peter C, Schaffrath, Raffael, de Crécy-Lagard, Valérie, Massachusetts Institute of Technology. Department of Biological Engineering, Pollo-Oliveira, Leticia, Klassen, Roland, Davis, Nick, Ciftci, Akif, Bacusmo, Jo Marie, Martinelli, Maria, DeMott, Michael S., Begley, Thomas J., Dedon, Peter C, Schaffrath, Raffael, and de Crécy-Lagard, Valérie

Abstract

Modifications found in the Anticodon Stem Loop (ASL) of tRNAs play important roles in regulating translational speed and accuracy. Threonylcarbamoyl adenosine (t6A37) and 5-methoxycarbonyl methyl-2-thiouridine (mcm5s2U34) are critical ASL modifications that have been linked to several human diseases. The model yeast Saccharomyces cerevisiae is viable despite the absence of both modifications, growth is however greatly impaired. The major observed consequence is a subsequent increase in protein aggregates and aberrant morphology. Proteomic analysis of the t6A-deficient strain (sua5 mutant) revealed a global mistranslation leading to protein aggregation without regard to physicochemical properties or t6A-dependent or biased codon usage in parent genes. However, loss of sua5 led to increased expression of soluble proteins for mitochondrial function, protein quality processing/trafficking, oxidative stress response, and energy homeostasis. These results point to a global function for t6A in protein homeostasis very similar to mcm5/s2U modifications. Keywords: tRNA modification; protein aggregation

Published
2020

3. Guidelines and recommendations on yeast cell death nomenclature

Author

Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andres, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J., Breitenbach, Michael, Burhans, William C., Büttner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina F., Corte-Real, Manuela, Costa, Vitor, Cullin, Christophe, Dawes, Ian, Dengjel, Jorn, Dickman, Martin B., Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Frohlich, Kai-Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W., Grant, Chris M., Greenwood, Michael T., Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Juergen, Herker, Eva, Herrmann, Johannes M., Hofer, Sebastian, Jimenez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P., Ludovico, Paula, Manon, Stephen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn A., Meisinger, Chris, Nielsen, Jens, Nystrom, Thomas, Osiewacz, Heinz D., Outeiro, Tiago F., Park, Hay-Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stephane, Polcic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor F., Sharon, Amir, Sigrist, Stephan J., Sommer-Ruck, Cornelia, Sousa, Maria Joao, Thevelein, Johan M., Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel B., Tuite, Mick, Voegtle, F. -Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Woelfl, Stefan, Zhang, Zhaojie J., Zhao, Richard Y., Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, Madeo, Frank, Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andres, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J., Breitenbach, Michael, Burhans, William C., Büttner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina F., Corte-Real, Manuela, Costa, Vitor, Cullin, Christophe, Dawes, Ian, Dengjel, Jorn, Dickman, Martin B., Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Frohlich, Kai-Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W., Grant, Chris M., Greenwood, Michael T., Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Juergen, Herker, Eva, Herrmann, Johannes M., Hofer, Sebastian, Jimenez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P., Ludovico, Paula, Manon, Stephen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn A., Meisinger, Chris, Nielsen, Jens, Nystrom, Thomas, Osiewacz, Heinz D., Outeiro, Tiago F., Park, Hay-Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stephane, Polcic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor F., Sharon, Amir, Sigrist, Stephan J., Sommer-Ruck, Cornelia, Sousa, Maria Joao, Thevelein, Johan M., Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel B., Tuite, Mick, Voegtle, F. -Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Woelfl, Stefan, Zhang, Zhaojie J., Zhao, Richard Y., Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, and Madeo, Frank

Abstract

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research.

Published
2018
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4. Guidelines and recommendations on yeast cell death nomenclature

Author

Carmona-Gutierrez, D, Bauer, M, Zimmermann, A, Aguilera, A, Austriaco, N, Ayscough, K, Balzan, R, Bar-Nun, S, Barrientos, A, Belenky, P, Blondel, M, Braun, R, Breitenbach, M, Burhans, W, Buettner, S, Cavalieri, D, Chang, M, Cooper, K, Côrte-Real, M, Costa, V, Cullin, C, Dawes, I, Dengjel, J, Dickman, M, Eisenberg, T, Fahrenkrog, B, Fasel, N, Froehlich, K, Gargouri, A, Giannattasio, S, Goffrini, P, Gourlay, C, Grant, C, Greenwood, M, Guaragnella, N, Heger, T, Heinisch, J, Herker, E, Herrmann, J, Hofer, S, Jiménez-Ruiz, A, Jungwirth, H, Kainz, K, Kontoyiannis, D, Ludovico, P, Manon, S, Martegani, E, Mazzoni, C, Megeney, L, Meisinger, C, Nielsen, J, Nystroem, T, Osiewacz, H, Outeiro, T, Park, H, Pendl, T, Petranovic, D, Picot, S, Polčic, P, Powers, T, Ramsdale, M, Rinnerthaler, M, Rockenfeller, P, Ruckenstuhl, C, Schaffrath, R, Segovia, M, Severin, F, Sharon, A, Sigrist, S, Sommer-Ruck, C, Sousa, M, Thevelein, J, Thevissen, K, Titorenko, V, Toledano, M, Tuite, M, Voegtle, F, Westermann, B, Winderickx, J, Wissing, S, Woelfl, S, Zhang, Z, Zhao, R, Zhou, B, Galluzzi, L, Kroemer, G, Madeo, F, Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andrés, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J., Breitenbach, Michael, Burhans, William C., Buettner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina F., Côrte-Real, Manuela, Costa, Vítor, Cullin, Christophe, Dawes, Ian, Dengjel, Jörn, Dickman, Martin B., Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Froehlich, Kai-Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W., Grant, Chris M., Greenwood, Michael T., Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Juergen, Herker, Eva, Herrmann, Johannes M., Hofer, Sebastian, Jiménez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P., Ludovico, Paula, Manon, Stéphen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn A., Meisinger, Chris, Nielsen, Jens, Nystroem, Thomas, Osiewacz, Heinz D., Outeiro, Tiago F., Park, Hay-Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stephane, Polčic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor F., Sharon, Amir, Sigrist, Stephan J., Sommer-Ruck, Cornelia, Sousa, Maria João, Thevelein, Johan M., Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel B., Tuite, Mick, Voegtle, F. -Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Woelfl, Stefan, Zhang, Zhaojie J., Zhao, Richard Y., Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, Madeo, Frank, Carmona-Gutierrez, D, Bauer, M, Zimmermann, A, Aguilera, A, Austriaco, N, Ayscough, K, Balzan, R, Bar-Nun, S, Barrientos, A, Belenky, P, Blondel, M, Braun, R, Breitenbach, M, Burhans, W, Buettner, S, Cavalieri, D, Chang, M, Cooper, K, Côrte-Real, M, Costa, V, Cullin, C, Dawes, I, Dengjel, J, Dickman, M, Eisenberg, T, Fahrenkrog, B, Fasel, N, Froehlich, K, Gargouri, A, Giannattasio, S, Goffrini, P, Gourlay, C, Grant, C, Greenwood, M, Guaragnella, N, Heger, T, Heinisch, J, Herker, E, Herrmann, J, Hofer, S, Jiménez-Ruiz, A, Jungwirth, H, Kainz, K, Kontoyiannis, D, Ludovico, P, Manon, S, Martegani, E, Mazzoni, C, Megeney, L, Meisinger, C, Nielsen, J, Nystroem, T, Osiewacz, H, Outeiro, T, Park, H, Pendl, T, Petranovic, D, Picot, S, Polčic, P, Powers, T, Ramsdale, M, Rinnerthaler, M, Rockenfeller, P, Ruckenstuhl, C, Schaffrath, R, Segovia, M, Severin, F, Sharon, A, Sigrist, S, Sommer-Ruck, C, Sousa, M, Thevelein, J, Thevissen, K, Titorenko, V, Toledano, M, Tuite, M, Voegtle, F, Westermann, B, Winderickx, J, Wissing, S, Woelfl, S, Zhang, Z, Zhao, R, Zhou, B, Galluzzi, L, Kroemer, G, Madeo, F, Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andrés, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J., Breitenbach, Michael, Burhans, William C., Buettner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina F., Côrte-Real, Manuela, Costa, Vítor, Cullin, Christophe, Dawes, Ian, Dengjel, Jörn, Dickman, Martin B., Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Froehlich, Kai-Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W., Grant, Chris M., Greenwood, Michael T., Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Juergen, Herker, Eva, Herrmann, Johannes M., Hofer, Sebastian, Jiménez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P., Ludovico, Paula, Manon, Stéphen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn A., Meisinger, Chris, Nielsen, Jens, Nystroem, Thomas, Osiewacz, Heinz D., Outeiro, Tiago F., Park, Hay-Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stephane, Polčic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor F., Sharon, Amir, Sigrist, Stephan J., Sommer-Ruck, Cornelia, Sousa, Maria João, Thevelein, Johan M., Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel B., Tuite, Mick, Voegtle, F. -Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Woelfl, Stefan, Zhang, Zhaojie J., Zhao, Richard Y., Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, and Madeo, Frank

Abstract

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research.

Published
2018

5. Positioning Europe for the EPITRANSCRIPTOMICS challenge

Author

Jantsch, Michael F., Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Luc, Fuks, Francois, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, Cecile, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Kholodnyuk, Irina Holodnuka, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Banković, Jasna, Banović Đeri, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schaefer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijević, Gordana, Cardona, Fernando, Davalos, Alberto, Ballana, Ester, O'Carroll, Donal, Ule, Jernej, Fray, Rupert, Jantsch, Michael F., Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Luc, Fuks, Francois, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, Cecile, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Kholodnyuk, Irina Holodnuka, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Banković, Jasna, Banović Đeri, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schaefer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijević, Gordana, Cardona, Fernando, Davalos, Alberto, Ballana, Ester, O'Carroll, Donal, Ule, Jernej, and Fray, Rupert

Abstract

The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the similar to 150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.

Published
2018

6. Guidelines and recommendations on yeast cell death nomenclature

Author

Carmona-Gutierrez, D, Bauer, M, Zimmermann, A, Aguilera, A, Austriaco, N, Ayscough, K, Balzan, R, Bar-Nun, S, Barrientos, A, Belenky, P, Blondel, M, Braun, R, Breitenbach, M, Burhans, W, Buettner, S, Cavalieri, D, Chang, M, Cooper, K, Côrte-Real, M, Costa, V, Cullin, C, Dawes, I, Dengjel, J, Dickman, M, Eisenberg, T, Fahrenkrog, B, Fasel, N, Froehlich, K, Gargouri, A, Giannattasio, S, Goffrini, P, Gourlay, C, Grant, C, Greenwood, M, Guaragnella, N, Heger, T, Heinisch, J, Herker, E, Herrmann, J, Hofer, S, Jiménez-Ruiz, A, Jungwirth, H, Kainz, K, Kontoyiannis, D, Ludovico, P, Manon, S, Martegani, E, Mazzoni, C, Megeney, L, Meisinger, C, Nielsen, J, Nystroem, T, Osiewacz, H, Outeiro, T, Park, H, Pendl, T, Petranovic, D, Picot, S, Polčic, P, Powers, T, Ramsdale, M, Rinnerthaler, M, Rockenfeller, P, Ruckenstuhl, C, Schaffrath, R, Segovia, M, Severin, F, Sharon, A, Sigrist, S, Sommer-Ruck, C, Sousa, M, Thevelein, J, Thevissen, K, Titorenko, V, Toledano, M, Tuite, M, Voegtle, F, Westermann, B, Winderickx, J, Wissing, S, Woelfl, S, Zhang, Z, Zhao, R, Zhou, B, Galluzzi, L, Kroemer, G, Madeo, F, Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andrés, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J., Breitenbach, Michael, Burhans, William C., Buettner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina F., Côrte-Real, Manuela, Costa, Vítor, Cullin, Christophe, Dawes, Ian, Dengjel, Jörn, Dickman, Martin B., Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Froehlich, Kai-Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W., Grant, Chris M., Greenwood, Michael T., Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Juergen, Herker, Eva, Herrmann, Johannes M., Hofer, Sebastian, Jiménez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P., Ludovico, Paula, Manon, Stéphen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn A., Meisinger, Chris, Nielsen, Jens, Nystroem, Thomas, Osiewacz, Heinz D., Outeiro, Tiago F., Park, Hay-Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stephane, Polčic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor F., Sharon, Amir, Sigrist, Stephan J., Sommer-Ruck, Cornelia, Sousa, Maria João, Thevelein, Johan M., Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel B., Tuite, Mick, Voegtle, F. -Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Woelfl, Stefan, Zhang, Zhaojie J., Zhao, Richard Y., Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, Madeo, Frank, Carmona-Gutierrez, D, Bauer, M, Zimmermann, A, Aguilera, A, Austriaco, N, Ayscough, K, Balzan, R, Bar-Nun, S, Barrientos, A, Belenky, P, Blondel, M, Braun, R, Breitenbach, M, Burhans, W, Buettner, S, Cavalieri, D, Chang, M, Cooper, K, Côrte-Real, M, Costa, V, Cullin, C, Dawes, I, Dengjel, J, Dickman, M, Eisenberg, T, Fahrenkrog, B, Fasel, N, Froehlich, K, Gargouri, A, Giannattasio, S, Goffrini, P, Gourlay, C, Grant, C, Greenwood, M, Guaragnella, N, Heger, T, Heinisch, J, Herker, E, Herrmann, J, Hofer, S, Jiménez-Ruiz, A, Jungwirth, H, Kainz, K, Kontoyiannis, D, Ludovico, P, Manon, S, Martegani, E, Mazzoni, C, Megeney, L, Meisinger, C, Nielsen, J, Nystroem, T, Osiewacz, H, Outeiro, T, Park, H, Pendl, T, Petranovic, D, Picot, S, Polčic, P, Powers, T, Ramsdale, M, Rinnerthaler, M, Rockenfeller, P, Ruckenstuhl, C, Schaffrath, R, Segovia, M, Severin, F, Sharon, A, Sigrist, S, Sommer-Ruck, C, Sousa, M, Thevelein, J, Thevissen, K, Titorenko, V, Toledano, M, Tuite, M, Voegtle, F, Westermann, B, Winderickx, J, Wissing, S, Woelfl, S, Zhang, Z, Zhao, R, Zhou, B, Galluzzi, L, Kroemer, G, Madeo, F, Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andrés, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J., Breitenbach, Michael, Burhans, William C., Buettner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina F., Côrte-Real, Manuela, Costa, Vítor, Cullin, Christophe, Dawes, Ian, Dengjel, Jörn, Dickman, Martin B., Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Froehlich, Kai-Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W., Grant, Chris M., Greenwood, Michael T., Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Juergen, Herker, Eva, Herrmann, Johannes M., Hofer, Sebastian, Jiménez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P., Ludovico, Paula, Manon, Stéphen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn A., Meisinger, Chris, Nielsen, Jens, Nystroem, Thomas, Osiewacz, Heinz D., Outeiro, Tiago F., Park, Hay-Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stephane, Polčic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor F., Sharon, Amir, Sigrist, Stephan J., Sommer-Ruck, Cornelia, Sousa, Maria João, Thevelein, Johan M., Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel B., Tuite, Mick, Voegtle, F. -Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Woelfl, Stefan, Zhang, Zhaojie J., Zhao, Richard Y., Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, and Madeo, Frank

Abstract

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research.

Published
2018

7. Positioning Europe for the EPITRANSCRIPTOMICS challenge

Author

Jantsch, Michael F, Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Luc, Fuks, Francois, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, Cecile, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Holodnuka Kholodnyuk, Irina, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Bankovic, Jasna, Banovic, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schäfer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijevic, Gordana, Cardona, Fernando, Davalos, Alberto, Ballana, Ester, O Carroll, Donal, Ule, Jernej, Fray, Rupert, Jantsch, Michael F, Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Luc, Fuks, Francois, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, Cecile, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Holodnuka Kholodnyuk, Irina, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Bankovic, Jasna, Banovic, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schäfer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijevic, Gordana, Cardona, Fernando, Davalos, Alberto, Ballana, Ester, O Carroll, Donal, Ule, Jernej, and Fray, Rupert

Abstract

The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20 years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the ~150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.

Published
2018

8. Guidelines and recommendations on yeast cell death nomenclature

Author

Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andrés, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J., Breitenbach, Michael, Burhans, William C., Büttner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina F., Côrte-Real, Manuela, Costa, Vítor, Cullin, Christophe, Dawes, Ian, Dengjel, Jörn, Dickman, Martin B., Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Fröhlich, Kai Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W., Grant, Chris M., Greenwood, Michael T., Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Jürgen, Herker, Eva, Herrmann, Johannes M., Hofer, Sebastian, Jiménez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P., Ludovico, Paula, Manon, Stéphen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn A., Meisinger, Chris, Nielsen, Jens, Nystrøm, Thomas, Osiewacz, Heinz D., Outeiro, Tiago F., Park, Hay Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stephane, Polčic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor F., Sharon, Amir, Sigrist, Stephan J., Sommer-Ruck, Cornelia, Sousa, Maria João, Thevelein, Johan M., Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel B., Tuite, Mick, Vögtle, F. Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Wölfl, Stefan, Zhang, Zhaojie J., Zhao, Richard Y., Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, Madeo, Frank, Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andrés, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J., Breitenbach, Michael, Burhans, William C., Büttner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina F., Côrte-Real, Manuela, Costa, Vítor, Cullin, Christophe, Dawes, Ian, Dengjel, Jörn, Dickman, Martin B., Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Fröhlich, Kai Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W., Grant, Chris M., Greenwood, Michael T., Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Jürgen, Herker, Eva, Herrmann, Johannes M., Hofer, Sebastian, Jiménez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P., Ludovico, Paula, Manon, Stéphen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn A., Meisinger, Chris, Nielsen, Jens, Nystrøm, Thomas, Osiewacz, Heinz D., Outeiro, Tiago F., Park, Hay Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stephane, Polčic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor F., Sharon, Amir, Sigrist, Stephan J., Sommer-Ruck, Cornelia, Sousa, Maria João, Thevelein, Johan M., Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel B., Tuite, Mick, Vögtle, F. Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Wölfl, Stefan, Zhang, Zhaojie J., Zhao, Richard Y., Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, and Madeo, Frank

Abstract

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research.

Published
2018

9. Positioning Europe for the EPITRANSCRIPTOMICS challenge

Author

Jantsch, Michael F, Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Luc, Fuks, Francois, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, Cecile, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Holodnuka Kholodnyuk, Irina, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Bankovic, Jasna, Banovic, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schäfer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijevic, Gordana, Cardona, Fernando, Davalos, Alberto, Ballana, Ester, O Carroll, Donal, Ule, Jernej, Fray, Rupert, Jantsch, Michael F, Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Luc, Fuks, Francois, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, Cecile, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Holodnuka Kholodnyuk, Irina, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Bankovic, Jasna, Banovic, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schäfer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijevic, Gordana, Cardona, Fernando, Davalos, Alberto, Ballana, Ester, O Carroll, Donal, Ule, Jernej, and Fray, Rupert

Abstract

The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20 years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the ~150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.

Published
2018

10. Guidelines and recommendations on yeast cell death nomenclature.

Author

Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andrés, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J, Breitenbach, Michael, Burhans, William WC, Büttner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina KF, Côrte-Real, Manuela, Costa, Vítor, Cullin, Christophe, Dawes, Ian, Dengjel, Jörn, Dickman, Martin MB, Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Fröhlich, Kai-Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W, Grant, Chris M, Greenwood, Michael MT, Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Jürgen, Herker, Eva, Herrmann, Johannes M, Hofer, Sebastian, Jiménez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P, Ludovico, Paula, Manon, Stéphen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn LA, Meisinger, Christa, Nielsen, Jens, Nyström, Thomas, Osiewacz, Heinz HD, Outeiro, Tiago TF, Park, Hay-Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stéphane, Polčic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor FF, Sharon, Amir, Sigrist, Stephan J, Sommer-Ruck, Cornelia, Sousa, Maria João, Thevelein, Johan JM, Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel MB, Tuite, Mick, Vögtle, F-Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Wölfl, Stefan, Zhang, Zhaojie J, Zhao, Richard Y, Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, Madeo, Frank, Carmona-Gutierrez, Didac, Bauer, Maria Anna, Zimmermann, Andreas, Aguilera, Andrés, Austriaco, Nicanor, Ayscough, Kathryn, Balzan, Rena, Bar-Nun, Shoshana, Barrientos, Antonio, Belenky, Peter, Blondel, Marc, Braun, Ralf J, Breitenbach, Michael, Burhans, William WC, Büttner, Sabrina, Cavalieri, Duccio, Chang, Michael, Cooper, Katrina KF, Côrte-Real, Manuela, Costa, Vítor, Cullin, Christophe, Dawes, Ian, Dengjel, Jörn, Dickman, Martin MB, Eisenberg, Tobias, Fahrenkrog, Birthe, Fasel, Nicolas, Fröhlich, Kai-Uwe, Gargouri, Ali, Giannattasio, Sergio, Goffrini, Paola, Gourlay, Campbell W, Grant, Chris M, Greenwood, Michael MT, Guaragnella, Nicoletta, Heger, Thomas, Heinisch, Jürgen, Herker, Eva, Herrmann, Johannes M, Hofer, Sebastian, Jiménez-Ruiz, Antonio, Jungwirth, Helmut, Kainz, Katharina, Kontoyiannis, Dimitrios P, Ludovico, Paula, Manon, Stéphen, Martegani, Enzo, Mazzoni, Cristina, Megeney, Lynn LA, Meisinger, Christa, Nielsen, Jens, Nyström, Thomas, Osiewacz, Heinz HD, Outeiro, Tiago TF, Park, Hay-Oak, Pendl, Tobias, Petranovic, Dina, Picot, Stéphane, Polčic, Peter, Powers, Ted, Ramsdale, Mark, Rinnerthaler, Mark, Rockenfeller, Patrick, Ruckenstuhl, Christoph, Schaffrath, Raffael, Segovia, Maria, Severin, Fedor FF, Sharon, Amir, Sigrist, Stephan J, Sommer-Ruck, Cornelia, Sousa, Maria João, Thevelein, Johan JM, Thevissen, Karin, Titorenko, Vladimir, Toledano, Michel MB, Tuite, Mick, Vögtle, F-Nora, Westermann, Benedikt, Winderickx, Joris, Wissing, Silke, Wölfl, Stefan, Zhang, Zhaojie J, Zhao, Richard Y, Zhou, Bing, Galluzzi, Lorenzo, Kroemer, Guido, and Madeo, Frank

Abstract

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cel-lular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the defi-nition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differ-ential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death rou-tines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the au-thors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the pro-gress of this vibrant field of research., SCOPUS: re.j, info:eu-repo/semantics/published

Published
2018

11. Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Author

Jantsch, Michael MF, Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Lucas, Fuks, François, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, C, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Holodnuka Kholodnyuk, Irina, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz Marek, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Bankovic, Jasna, Banovic, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schäfer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijevic, Gordana, Cardona, F., Davalos, Alberto, Ballana, Ester, O Carroll, Donal, Ule, Jernej, Fray, Rupert, Jantsch, Michael MF, Quattrone, Alessandro, O'Connell, Mary, Helm, Mark, Frye, Michaela, Macias-Gonzales, Manuel, Ohman, Marie, Ameres, Stefan, Willems, Lucas, Fuks, François, Oulas, Anastasis, Vanacova, Stepanka, Nielsen, Henrik, Bousquet-Antonelli, C, Motorin, Yuri, Roignant, Jean-Yves, Balatsos, Nikolaos, Dinnyes, Andras, Baranov, Pavel, Kelly, Vincent, Lamm, Ayelet, Rechavi, Gideon, Pelizzola, Mattia, Liepins, Janis, Holodnuka Kholodnyuk, Irina, Zammit, Vanessa, Ayers, Duncan, Drablos, Finn, Dahl, John Arne, Bujnicki, Janusz Marek, Jeronimo, Carmen, Almeida, Raquel, Neagu, Monica, Costache, Marieta, Bankovic, Jasna, Banovic, Bojana, Kyselovic, Jan, Valor, Luis Miguel, Selbert, Stefan, Pir, Pinar, Demircan, Turan, Cowling, Victoria, Schäfer, Matthias, Rossmanith, Walter, Lafontaine, Denis, David, Alexandre, Carre, Clement, Lyko, Frank, Schaffrath, Raffael, Schwartz, Schraga, Verdel, Andre, Klungland, Arne, Purta, Elzbieta, Timotijevic, Gordana, Cardona, F., Davalos, Alberto, Ballana, Ester, O Carroll, Donal, Ule, Jernej, and Fray, Rupert

Abstract

The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20 years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the ~150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics., SCOPUS: no.j, info:eu-repo/semantics/published

Published
2018

12. Elongator function in tRNA wobble uridine modification is conserved between yeast and plants

Author

Mehlgarten, Constance, Jablonowski, Daniel, Wrackmeyer, Uta, Tschitschmann, Susan, Sondermann, David, Jäger, Gunilla, Gong, Zhizhong, Byström, Anders S, Schaffrath, Raffael, Breunig, Karin D, Mehlgarten, Constance, Jablonowski, Daniel, Wrackmeyer, Uta, Tschitschmann, Susan, Sondermann, David, Jäger, Gunilla, Gong, Zhizhong, Byström, Anders S, Schaffrath, Raffael, and Breunig, Karin D

Abstract

Based on studies in yeast and mammalian cells the Elongator complex has been implicated in functions as diverse as histone acetylation, polarized protein trafficking and tRNA modification. Here we show that Arabidopsis mutants lacking the Elongator subunit AtELP3/ELO3 have a defect in tRNA wobble uridine modification. Moreover, we demonstrate that yeast elp3 and elp1 mutants expressing the respective Arabidopsis Elongator homologues AtELP3/ELO3 and AtELP1/ELO2 assemble integer Elongator complexes indicating a high degree of structural conservation. Surprisingly, in vivo complementation studies based on Elongator-dependent tRNA nonsense suppression and zymocin tRNase toxin assays indicated that while AtELP1 rescued defects of a yeast elp1 mutant, the most conserved Elongator gene AtELP3, failed to complement an elp3 mutant. This lack of complementation is due to incompatibility with yeast ELP1 as coexpression of both plant genes in an elp1 elp3 yeast mutant restored Elongator’s tRNA modification function in vivo. Similarly, AtELP1, not ScELP1 also supported partial complementation by yeast-plant Elp3 hybrids suggesting that AtElp1 has less stringent sequence requirements for Elp3 than ScElp1. We conclude that yeast and plant Elongator share tRNA modification roles and propose that this function might be conserved in Elongator from all eukaryotic kingdoms of life.

Published
2010
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13. tRNA and protein methylase complexes mediate zymocin toxicity in yeast

Author

Studte, Patrick, Zink, Sabrina, Jablonowski, Daniel, Bar, Christian, von der Haar, Tobias, Tuite, Mick F., Schaffrath, Raffael, Studte, Patrick, Zink, Sabrina, Jablonowski, Daniel, Bar, Christian, von der Haar, Tobias, Tuite, Mick F., and Schaffrath, Raffael

Abstract

Modification of Saccharomyces cerevisiae tRNA anticodons at the wobble uridine (U34) position is required for tRNA cleavage by the zymocin tRNase killer toxin from Kluyveromyces lactis. Hence, U34 modification defects including lack of the U34 tRNA methyltransferase Trm9 protect against tRNA cleavage and zymocin. Using zymocin as a tool, we have identified toxin-resistant mutations in TRM9 that are likely to affect the U34 methylation reaction. Most strikingly, C-terminal truncations in Trm9 abolish interaction with Trm112, a protein shown to individually purify with Lys9 and two more methylases, Trm11 and Mtq2. Downregulation of a GAL1-TRM112 allele protects against zymocin whereas LYS9, TRM11 and MTQ2 are dosage suppressors of zymocin. Based on immune precipitation studies, the latter scenario correlates with competition for Trm112 and in excess, some of these Trm112 partners interfere with formation of the toxin-relevant Trm9.Trm112 complex. In contrast to trm11 Delta or lys9 Delta cells, trm112 Delta and mtq2 Delta null mutants are zymocin resistant. In line with the identified role that methylation of Sup45 by Mtq2 has for translation termination by the release factor dimer Sup45.Sup35, we observe that SUP45 overexpression and sup45 mutants suppress zymocin. Intriguingly, this suppression correlates with upregulated levels of tRNA species targeted by zymocin's tRNase activity.

Published
2008

14. tRNA and protein methylase complexes mediate zymocin toxicity in yeast

Author

Studte, Patrick, Zink, Sabrina, Jablonowski, Daniel, Bar, Christian, von der Haar, Tobias, Tuite, Mick F., Schaffrath, Raffael, Studte, Patrick, Zink, Sabrina, Jablonowski, Daniel, Bar, Christian, von der Haar, Tobias, Tuite, Mick F., and Schaffrath, Raffael

Abstract

Modification of Saccharomyces cerevisiae tRNA anticodons at the wobble uridine (U34) position is required for tRNA cleavage by the zymocin tRNase killer toxin from Kluyveromyces lactis. Hence, U34 modification defects including lack of the U34 tRNA methyltransferase Trm9 protect against tRNA cleavage and zymocin. Using zymocin as a tool, we have identified toxin-resistant mutations in TRM9 that are likely to affect the U34 methylation reaction. Most strikingly, C-terminal truncations in Trm9 abolish interaction with Trm112, a protein shown to individually purify with Lys9 and two more methylases, Trm11 and Mtq2. Downregulation of a GAL1-TRM112 allele protects against zymocin whereas LYS9, TRM11 and MTQ2 are dosage suppressors of zymocin. Based on immune precipitation studies, the latter scenario correlates with competition for Trm112 and in excess, some of these Trm112 partners interfere with formation of the toxin-relevant Trm9.Trm112 complex. In contrast to trm11 Delta or lys9 Delta cells, trm112 Delta and mtq2 Delta null mutants are zymocin resistant. In line with the identified role that methylation of Sup45 by Mtq2 has for translation termination by the release factor dimer Sup45.Sup35, we observe that SUP45 overexpression and sup45 mutants suppress zymocin. Intriguingly, this suppression correlates with upregulated levels of tRNA species targeted by zymocin's tRNase activity.

Published
2008

15. tRNA and protein methylase complexes mediate zymocin toxicity in yeast

Author

Studte, Patrick, Zink, Sabrina, Jablonowski, Daniel, Bar, Christian, von der Haar, Tobias, Tuite, Mick F., Schaffrath, Raffael, Studte, Patrick, Zink, Sabrina, Jablonowski, Daniel, Bar, Christian, von der Haar, Tobias, Tuite, Mick F., and Schaffrath, Raffael

Abstract

Modification of Saccharomyces cerevisiae tRNA anticodons at the wobble uridine (U34) position is required for tRNA cleavage by the zymocin tRNase killer toxin from Kluyveromyces lactis. Hence, U34 modification defects including lack of the U34 tRNA methyltransferase Trm9 protect against tRNA cleavage and zymocin. Using zymocin as a tool, we have identified toxin-resistant mutations in TRM9 that are likely to affect the U34 methylation reaction. Most strikingly, C-terminal truncations in Trm9 abolish interaction with Trm112, a protein shown to individually purify with Lys9 and two more methylases, Trm11 and Mtq2. Downregulation of a GAL1-TRM112 allele protects against zymocin whereas LYS9, TRM11 and MTQ2 are dosage suppressors of zymocin. Based on immune precipitation studies, the latter scenario correlates with competition for Trm112 and in excess, some of these Trm112 partners interfere with formation of the toxin-relevant Trm9.Trm112 complex. In contrast to trm11 Delta or lys9 Delta cells, trm112 Delta and mtq2 Delta null mutants are zymocin resistant. In line with the identified role that methylation of Sup45 by Mtq2 has for translation termination by the release factor dimer Sup45.Sup35, we observe that SUP45 overexpression and sup45 mutants suppress zymocin. Intriguingly, this suppression correlates with upregulated levels of tRNA species targeted by zymocin's tRNase activity.

Published
2008

16. tRNA and protein methylase complexes mediate zymocin toxicity in yeast

Author

Studte, Patrick, Zink, Sabrina, Jablonowski, Daniel, Bar, Christian, von der Haar, Tobias, Tuite, Mick F., Schaffrath, Raffael, Studte, Patrick, Zink, Sabrina, Jablonowski, Daniel, Bar, Christian, von der Haar, Tobias, Tuite, Mick F., and Schaffrath, Raffael

Abstract

Modification of Saccharomyces cerevisiae tRNA anticodons at the wobble uridine (U34) position is required for tRNA cleavage by the zymocin tRNase killer toxin from Kluyveromyces lactis. Hence, U34 modification defects including lack of the U34 tRNA methyltransferase Trm9 protect against tRNA cleavage and zymocin. Using zymocin as a tool, we have identified toxin-resistant mutations in TRM9 that are likely to affect the U34 methylation reaction. Most strikingly, C-terminal truncations in Trm9 abolish interaction with Trm112, a protein shown to individually purify with Lys9 and two more methylases, Trm11 and Mtq2. Downregulation of a GAL1-TRM112 allele protects against zymocin whereas LYS9, TRM11 and MTQ2 are dosage suppressors of zymocin. Based on immune precipitation studies, the latter scenario correlates with competition for Trm112 and in excess, some of these Trm112 partners interfere with formation of the toxin-relevant Trm9.Trm112 complex. In contrast to trm11 Delta or lys9 Delta cells, trm112 Delta and mtq2 Delta null mutants are zymocin resistant. In line with the identified role that methylation of Sup45 by Mtq2 has for translation termination by the release factor dimer Sup45.Sup35, we observe that SUP45 overexpression and sup45 mutants suppress zymocin. Intriguingly, this suppression correlates with upregulated levels of tRNA species targeted by zymocin's tRNase activity.

Published
2008

17. Molecular analysis of the LTR retrotransposon Ylt1 from the genome of dimorphic fungus Yarrowia lipolytica

Author

Barth, Gerold, Hyman, Anthony, Schaffrath, Raffael, Kovalchuk, Andriy, Barth, Gerold, Hyman, Anthony, Schaffrath, Raffael, and Kovalchuk, Andriy

Abstract

The retrotransposon Ylt1 was described previously from the genome of the dimorphic fungus Yarrowia lipolytica. Remarkably, Ylt1 is currently the largest LTR retrotransposon reported from fungal genomes. However, little was known about its biology and its interactions with host genome. So, the aim of this work was the characterization of properties of Ylt1.Analysis of proteins encoded by Ylt1 (Gag protein and integrase) was carried out during this work. To enable their detection, both proteins were tagged with HA epitopes. The sizes of Gag protein and putative precursors of Gag protein and integrase were estimated, and a model for the proteolytic processing of the polyprotein of Ylt1 was proposed. It was shown that Gag protein of Ylt1 is about 2-fold larger than Gag proteins of other studied yeast retrotransposons. An analysis of Ylt1 expression was also performed. Production of the Ylt1 Gag protein under different conditions was analyzed by Western blotting. Expression of Ylt1 occurred on all tested carbon sources. The amount of Ylt1 decreased rapidly upon transition to stationary growth phase, in the presence of copper sulfate and under heat shock conditions. It is suggested that Ylt1 is expressed in actively growing cells, whereas stress conditions have a negative impact on its expression. Such expression pattern was not previously reported for other yeast retrotransposons. Activity of Ylt1 in vivo was characterized using an Ylt1 elements tagged with SUC2 gene of Saccharomyces cerevisiae. Mobilization of the marked Ylt1 element and its transposition from autonomous plasmid into host genome was observed in performed experiments. Obtained results strongly support the idea that Ylt1 is transpositionally active. Formation of tandem repeats by newly inserted Ylt1 elements was observed in several cases. It is suggested that integrase function was affected in this case, and that the integration was mediated by homologous recombination instead. Analysis of the Ylt1 insert

Published
2005

18. Molecular analysis of the LTR retrotransposon Ylt1 from the genome of dimorphic fungus Yarrowia lipolytica

Author

Barth, Gerold, Hyman, Anthony, Schaffrath, Raffael, Kovalchuk, Andriy, Barth, Gerold, Hyman, Anthony, Schaffrath, Raffael, and Kovalchuk, Andriy

Abstract

The retrotransposon Ylt1 was described previously from the genome of the dimorphic fungus Yarrowia lipolytica. Remarkably, Ylt1 is currently the largest LTR retrotransposon reported from fungal genomes. However, little was known about its biology and its interactions with host genome. So, the aim of this work was the characterization of properties of Ylt1.Analysis of proteins encoded by Ylt1 (Gag protein and integrase) was carried out during this work. To enable their detection, both proteins were tagged with HA epitopes. The sizes of Gag protein and putative precursors of Gag protein and integrase were estimated, and a model for the proteolytic processing of the polyprotein of Ylt1 was proposed. It was shown that Gag protein of Ylt1 is about 2-fold larger than Gag proteins of other studied yeast retrotransposons. An analysis of Ylt1 expression was also performed. Production of the Ylt1 Gag protein under different conditions was analyzed by Western blotting. Expression of Ylt1 occurred on all tested carbon sources. The amount of Ylt1 decreased rapidly upon transition to stationary growth phase, in the presence of copper sulfate and under heat shock conditions. It is suggested that Ylt1 is expressed in actively growing cells, whereas stress conditions have a negative impact on its expression. Such expression pattern was not previously reported for other yeast retrotransposons. Activity of Ylt1 in vivo was characterized using an Ylt1 elements tagged with SUC2 gene of Saccharomyces cerevisiae. Mobilization of the marked Ylt1 element and its transposition from autonomous plasmid into host genome was observed in performed experiments. Obtained results strongly support the idea that Ylt1 is transpositionally active. Formation of tandem repeats by newly inserted Ylt1 elements was observed in several cases. It is suggested that integrase function was affected in this case, and that the integration was mediated by homologous recombination instead. Analysis of the Ylt1 insert

Published
2005

19. Molecular analysis of the LTR retrotransposon Ylt1 from the genome of dimorphic fungus Yarrowia lipolytica

Author

Barth, Gerold, Hyman, Anthony, Schaffrath, Raffael, Kovalchuk, Andriy, Barth, Gerold, Hyman, Anthony, Schaffrath, Raffael, and Kovalchuk, Andriy

Abstract

The retrotransposon Ylt1 was described previously from the genome of the dimorphic fungus Yarrowia lipolytica. Remarkably, Ylt1 is currently the largest LTR retrotransposon reported from fungal genomes. However, little was known about its biology and its interactions with host genome. So, the aim of this work was the characterization of properties of Ylt1.Analysis of proteins encoded by Ylt1 (Gag protein and integrase) was carried out during this work. To enable their detection, both proteins were tagged with HA epitopes. The sizes of Gag protein and putative precursors of Gag protein and integrase were estimated, and a model for the proteolytic processing of the polyprotein of Ylt1 was proposed. It was shown that Gag protein of Ylt1 is about 2-fold larger than Gag proteins of other studied yeast retrotransposons. An analysis of Ylt1 expression was also performed. Production of the Ylt1 Gag protein under different conditions was analyzed by Western blotting. Expression of Ylt1 occurred on all tested carbon sources. The amount of Ylt1 decreased rapidly upon transition to stationary growth phase, in the presence of copper sulfate and under heat shock conditions. It is suggested that Ylt1 is expressed in actively growing cells, whereas stress conditions have a negative impact on its expression. Such expression pattern was not previously reported for other yeast retrotransposons. Activity of Ylt1 in vivo was characterized using an Ylt1 elements tagged with SUC2 gene of Saccharomyces cerevisiae. Mobilization of the marked Ylt1 element and its transposition from autonomous plasmid into host genome was observed in performed experiments. Obtained results strongly support the idea that Ylt1 is transpositionally active. Formation of tandem repeats by newly inserted Ylt1 elements was observed in several cases. It is suggested that integrase function was affected in this case, and that the integration was mediated by homologous recombination instead. Analysis of the Ylt1 insert

Published
2005

20. Molecular analysis of the LTR retrotransposon Ylt1 from the genome of dimorphic fungus Yarrowia lipolytica

Author

Barth, Gerold, Hyman, Anthony, Schaffrath, Raffael, Kovalchuk, Andriy, Barth, Gerold, Hyman, Anthony, Schaffrath, Raffael, and Kovalchuk, Andriy

Abstract

The retrotransposon Ylt1 was described previously from the genome of the dimorphic fungus Yarrowia lipolytica. Remarkably, Ylt1 is currently the largest LTR retrotransposon reported from fungal genomes. However, little was known about its biology and its interactions with host genome. So, the aim of this work was the characterization of properties of Ylt1.Analysis of proteins encoded by Ylt1 (Gag protein and integrase) was carried out during this work. To enable their detection, both proteins were tagged with HA epitopes. The sizes of Gag protein and putative precursors of Gag protein and integrase were estimated, and a model for the proteolytic processing of the polyprotein of Ylt1 was proposed. It was shown that Gag protein of Ylt1 is about 2-fold larger than Gag proteins of other studied yeast retrotransposons. An analysis of Ylt1 expression was also performed. Production of the Ylt1 Gag protein under different conditions was analyzed by Western blotting. Expression of Ylt1 occurred on all tested carbon sources. The amount of Ylt1 decreased rapidly upon transition to stationary growth phase, in the presence of copper sulfate and under heat shock conditions. It is suggested that Ylt1 is expressed in actively growing cells, whereas stress conditions have a negative impact on its expression. Such expression pattern was not previously reported for other yeast retrotransposons. Activity of Ylt1 in vivo was characterized using an Ylt1 elements tagged with SUC2 gene of Saccharomyces cerevisiae. Mobilization of the marked Ylt1 element and its transposition from autonomous plasmid into host genome was observed in performed experiments. Obtained results strongly support the idea that Ylt1 is transpositionally active. Formation of tandem repeats by newly inserted Ylt1 elements was observed in several cases. It is suggested that integrase function was affected in this case, and that the integration was mediated by homologous recombination instead. Analysis of the Ylt1 insert

Published
2005

21. A novel sit4 phosphatase complex is involved in the response to ceramide stress in yeast

Author

Woodacre, Alexandra, Lone, Museer A., Jablonowski, Daniel, Schneiter, Roger, Giorgini, Flaviano, Schaffrath, Raffael, Woodacre, Alexandra, Lone, Museer A., Jablonowski, Daniel, Schneiter, Roger, Giorgini, Flaviano, and Schaffrath, Raffael

Abstract

Ceramide is a building block for complex sphingolipids in the plasma membrane, but it also plays a significant role in secondary signalling pathways regulating cell proliferation and apoptosis in response to stress. Ceramide activated protein phosphatase activity has been previously observed in association with the Sit4 protein phosphatase. Here we find that sit4Δ mutants have decreased ceramide levels and display resistance to exogenous ceramides and phytosphingosine. Mutants lacking SIT4 or KTI12 display a shift towards nonhydroxylated forms of long chain bases and sphingolipids, suggesting regulation of hydroxylase (SUR2) or ceramide synthase by Sit4p. We have identified novel subunits of the Sit4 complex and have also shown that known Sit4 regulatory subunits—SAP proteins—are not involved in the ceramide response. This is the first observation of separation of function between Sit4 and SAP proteins. We also find that the Sit4p target Elongator is not involved in the ceramide response but that cells deficient in Kti12p—an accessory protein with an undefined regulatory role—have similar ceramide phenotypes to sit4Δ mutants. Therefore, Kti12p may play a similar secondary role in the ceramide response. This evidence points to a novel Sit4-dependent regulatory mechanism in response to ceramide stress.

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