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12 results on '"Savidor A"'

1. Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischemic injury

Author

Shakked, Avraham, Petrover, Zachary, Aharonov, Alla, Ghiringhelli, Matteo, Umansky, Kfir-Baruch, Kain, David, Elkahal, Jacob, Divinsky, Yalin, Nguyen, Phong Dang, Miyara, Shoval, Friedlander, Gilgi, Savidor, Alon, Zhang, Lingling, Perez, Dahlia E, Sarig, Rachel, Lendengolts, Daria, Bueno-Levy, Hanna, Kastan, Nathaniel, Levin, Yishai, Bakkers, Jeroen, Gepstein, Lior, Tzahor, Eldad, Shakked, Avraham, Petrover, Zachary, Aharonov, Alla, Ghiringhelli, Matteo, Umansky, Kfir-Baruch, Kain, David, Elkahal, Jacob, Divinsky, Yalin, Nguyen, Phong Dang, Miyara, Shoval, Friedlander, Gilgi, Savidor, Alon, Zhang, Lingling, Perez, Dahlia E, Sarig, Rachel, Lendengolts, Daria, Bueno-Levy, Hanna, Kastan, Nathaniel, Levin, Yishai, Bakkers, Jeroen, Gepstein, Lior, and Tzahor, Eldad

Abstract

Cardiomyocyte proliferation and dedifferentiation have fueled the field of regenerative cardiology in recent years, whereas the reverse process of redifferentiation remains largely unexplored. Redifferentiation is characterized by the restoration of function lost during dedifferentiation. Previously, we showed that ERBB2-mediated heart regeneration has these two distinct phases: transient dedifferentiation and redifferentiation. Here we survey the temporal transcriptomic and proteomic landscape of dedifferentiation-redifferentiation in adult mouse hearts and reveal that well-characterized dedifferentiation features largely return to normal, although elements of residual dedifferentiation remain, even after the contractile function is restored. These hearts appear rejuvenated and show robust resistance to ischemic injury, even 5 months after redifferentiation initiation. Cardiomyocyte redifferentiation is driven by negative feedback signaling and requires LATS1/2 Hippo pathway activity. Our data reveal the importance of cardiomyocyte redifferentiation in functional restoration during regeneration but also protection against future insult, in what could lead to a potential prophylactic treatment against ischemic heart disease for at-risk patients.

Published
2023

2. BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures

Author

Danino, Yehuda M., Molitor, Lena, Rosenbaum-Cohen, Tamar, Kaiser, Sebastian, Cohen, Yahel, Porat, Ziv, Marmor-Kollet, Hagai, Katina, Corine, Savidor, Alon, Rotkopf, Ron, Ben-Isaac, Eyal, Golani, Ofra, Levin, Yishai, Monchaud, David, Hickson, Ian D., Hornstein, Eran, Danino, Yehuda M., Molitor, Lena, Rosenbaum-Cohen, Tamar, Kaiser, Sebastian, Cohen, Yahel, Porat, Ziv, Marmor-Kollet, Hagai, Katina, Corine, Savidor, Alon, Rotkopf, Ron, Ben-Isaac, Eyal, Golani, Ofra, Levin, Yishai, Monchaud, David, Hickson, Ian D., and Hornstein, Eran

Abstract

Bloom's syndrome (BLM) protein is a known nuclear helicase that is able to unwind DNA secondary structures such as G-quadruplexes (G4s). However, its role in the regulation of cytoplasmic processes that involve RNA G-quadruplexes (rG4s) has not been previously studied. Here, we demonstrate that BLM is recruited to stress granules (SGs), which are cytoplasmic biomolecular condensates composed of RNAs and RNA-binding proteins. BLM is enriched in SGs upon different stress conditions and in an rG4-dependent manner. Also, we show that BLM unwinds rG4s and acts as a negative regulator of SG formation. Altogether, our data expand the cellular activity of BLM and shed light on the function that helicases play in the dynamics of biomolecular condensates.

Published
2023

3. Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischemic injury

Author

Cardiologie onderzoek 2, Onderzoek, Child Health, Circulatory Health, Shakked, Avraham, Petrover, Zachary, Aharonov, Alla, Ghiringhelli, Matteo, Umansky, Kfir Baruch, Kain, David, Elkahal, Jacob, Divinsky, Yalin, Nguyen, Phong Dang, Miyara, Shoval, Friedlander, Gilgi, Savidor, Alon, Zhang, Lingling, Perez, Dahlia E., Sarig, Rachel, Lendengolts, Daria, Bueno-Levy, Hanna, Kastan, Nathaniel, Levin, Yishai, Bakkers, Jeroen, Gepstein, Lior, Tzahor, Eldad, Cardiologie onderzoek 2, Onderzoek, Child Health, Circulatory Health, Shakked, Avraham, Petrover, Zachary, Aharonov, Alla, Ghiringhelli, Matteo, Umansky, Kfir Baruch, Kain, David, Elkahal, Jacob, Divinsky, Yalin, Nguyen, Phong Dang, Miyara, Shoval, Friedlander, Gilgi, Savidor, Alon, Zhang, Lingling, Perez, Dahlia E., Sarig, Rachel, Lendengolts, Daria, Bueno-Levy, Hanna, Kastan, Nathaniel, Levin, Yishai, Bakkers, Jeroen, Gepstein, Lior, and Tzahor, Eldad

Published
2023

4. BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures

Author

Danino, Yehuda M., Molitor, Lena, Rosenbaum-Cohen, Tamar, Kaiser, Sebastian, Cohen, Yahel, Porat, Ziv, Marmor-Kollet, Hagai, Katina, Corine, Savidor, Alon, Rotkopf, Ron, Ben-Isaac, Eyal, Golani, Ofra, Levin, Yishai, Monchaud, David, Hickson, Ian D., Hornstein, Eran, Danino, Yehuda M., Molitor, Lena, Rosenbaum-Cohen, Tamar, Kaiser, Sebastian, Cohen, Yahel, Porat, Ziv, Marmor-Kollet, Hagai, Katina, Corine, Savidor, Alon, Rotkopf, Ron, Ben-Isaac, Eyal, Golani, Ofra, Levin, Yishai, Monchaud, David, Hickson, Ian D., and Hornstein, Eran

Abstract

Bloom's syndrome (BLM) protein is a known nuclear helicase that is able to unwind DNA secondary structures such as G-quadruplexes (G4s). However, its role in the regulation of cytoplasmic processes that involve RNA G-quadruplexes (rG4s) has not been previously studied. Here, we demonstrate that BLM is recruited to stress granules (SGs), which are cytoplasmic biomolecular condensates composed of RNAs and RNA-binding proteins. BLM is enriched in SGs upon different stress conditions and in an rG4-dependent manner. Also, we show that BLM unwinds rG4s and acts as a negative regulator of SG formation. Altogether, our data expand the cellular activity of BLM and shed light on the function that helicases play in the dynamics of biomolecular condensates.

Published
2023

5. Ribonucleotide reductase from Fusarium oxysporum does not Respond to DNA replication stress

Author

Cohen, Rotem, Milo, Shira, Sharma, Sushma, Savidor, Alon, Covo, Shay, Cohen, Rotem, Milo, Shira, Sharma, Sushma, Savidor, Alon, and Covo, Shay

Abstract

Ribonucleotide reductase (RNR) catalyzes the rate limiting step in dNTP biosynthesis and is tightly regulated at the transcription and activity levels. One of the best characterized responses of yeast to DNA damage is up-regulation of RNR transcription and activity and consequently, elevation of the dNTP pools. Hydroxyurea is a universal inhibitor of RNR that causes S phase arrest. It is used in the clinic to treat certain types of cancers. Here we studied the response of the fungal plant pathogen Fusarium oxysporum to hydroxyurea in order to generate hypotheses that can be used in the future in development of a new class of pesticides. F. oxysporum causes severe damage to more than 100 agricultural crops and specifically threatens banana cultivation world-wide. Although the recovery of F. oxysporum from transient hydroxyurea exposure was similar to the one of Saccharomyces cerevisiae, colony formation was strongly inhibited in F. oxysporum in comparison with S. cerevisiae. As expected, genomic and phosphoproteomic analyses of F. oxysporum conidia (spores) exposed to hydroxyurea showed hallmarks of DNA replication perturbation and activation of recombination. Unexpectedly and strikingly, RNR was not induced by either hydroxyurea or the DNA-damaging agent methyl methanesulfonate as determined at the RNA and protein levels. Consequently, dNTP concentrations were significantly reduced, even in response to a low dose of hydroxyurea. Methyl methanesulfonate treatment did not induce dNTP pools in F. oxysporum, in contrast to the response of RNR and dNTP pools to DNA damage and hydroxyurea in several tested organisms. Our results are important because the lack of a feedback mechanism to increase RNR expression in F. oxysporum is expected to sensitize the pathogen to a fungal-specific ribonucleotide inhibitor. The potential impact of our observations on F. oxysporum genome stability and genome evolution is discussed.

Published
2019
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6. Dysregulated miRNA biogenesis downstream of cellular stress and ALS-causing mutations: a new mechanism for ALS.

Author

Emde, Anna, Emde, Anna, Eitan, Chen, Liou, Lee-Loung, Libby, Ryan T, Rivkin, Natali, Magen, Iddo, Reichenstein, Irit, Oppenheim, Hagar, Eilam, Raya, Silvestroni, Aurelio, Alajajian, Betty, Ben-Dov, Iddo Z, Aebischer, Julianne, Savidor, Alon, Levin, Yishai, Sons, Robert, Hammond, Scott M, Ravits, John M, Möller, Thomas, Hornstein, Eran, Emde, Anna, Emde, Anna, Eitan, Chen, Liou, Lee-Loung, Libby, Ryan T, Rivkin, Natali, Magen, Iddo, Reichenstein, Irit, Oppenheim, Hagar, Eilam, Raya, Silvestroni, Aurelio, Alajajian, Betty, Ben-Dov, Iddo Z, Aebischer, Julianne, Savidor, Alon, Levin, Yishai, Sons, Robert, Hammond, Scott M, Ravits, John M, Möller, Thomas, and Hornstein, Eran

Abstract

Interest in RNA dysfunction in amyotrophic lateral sclerosis (ALS) recently aroused upon discovering causative mutations in RNA-binding protein genes. Here, we show that extensive down-regulation of miRNA levels is a common molecular denominator for multiple forms of human ALS. We further demonstrate that pathogenic ALS-causing mutations are sufficient to inhibit miRNA biogenesis at the Dicing step. Abnormalities of the stress response are involved in the pathogenesis of neurodegeneration, including ALS. Accordingly, we describe a novel mechanism for modulating microRNA biogenesis under stress, involving stress granule formation and re-organization of DICER and AGO2 protein interactions with their partners. In line with this observation, enhancing DICER activity by a small molecule, enoxacin, is beneficial for neuromuscular function in two independent ALS mouse models. Characterizing miRNA biogenesis downstream of the stress response ties seemingly disparate pathways in neurodegeneration and further suggests that DICER and miRNAs affect neuronal integrity and are possible therapeutic targets.

Published
2015

7. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

Author

Lamour, Kurt H., Lamour, Kurt H., Mudge, Joann, Gobena, Daniel, Hurtado-Gonzales, Oscar P., Schmutz, Jeremy, Kuo, Alan, Miller, Neil A., Rice, Brandon J., Raffaele, Sylvain, Cano, Liliana M., Bharti, Arvind K., Donahoo, Ryan S., Finely, Sabra, Huitema, Edgar, Hulvey, Jon, Platt, Darren, Salamov, Asaf, Savidor, Alon, Sharma, Rahul, Stam, Remco, Sotrey, Dylan, Thines, Marco, Win, Joe, Haas, Brian J., Dinwiddie, Darrell L., Jenkins, Jerry, Knight, James R., Affourtit, Jason P., Han, Cliff S., Chertkov, Olga, Lindquist, Erika A., Detter, Chris, Grigoriev, Igor V., Kamoun, Sophien, Kingsmore, Stephen F., Lamour, Kurt H., Lamour, Kurt H., Mudge, Joann, Gobena, Daniel, Hurtado-Gonzales, Oscar P., Schmutz, Jeremy, Kuo, Alan, Miller, Neil A., Rice, Brandon J., Raffaele, Sylvain, Cano, Liliana M., Bharti, Arvind K., Donahoo, Ryan S., Finely, Sabra, Huitema, Edgar, Hulvey, Jon, Platt, Darren, Salamov, Asaf, Savidor, Alon, Sharma, Rahul, Stam, Remco, Sotrey, Dylan, Thines, Marco, Win, Joe, Haas, Brian J., Dinwiddie, Darrell L., Jenkins, Jerry, Knight, James R., Affourtit, Jason P., Han, Cliff S., Chertkov, Olga, Lindquist, Erika A., Detter, Chris, Grigoriev, Igor V., Kamoun, Sophien, and Kingsmore, Stephen F.

Abstract

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

Published
2012

8. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

Author

Lamour, Kurt H., Lamour, Kurt H., Mudge, Joann, Gobena, Daniel, Hurtado-Gonzales, Oscar P., Schmutz, Jeremy, Kuo, Alan, Miller, Neil A., Rice, Brandon J., Raffaele, Sylvain, Cano, Liliana M., Bharti, Arvind K., Donahoo, Ryan S., Finely, Sabra, Huitema, Edgar, Hulvey, Jon, Platt, Darren, Salamov, Asaf, Savidor, Alon, Sharma, Rahul, Stam, Remco, Sotrey, Dylan, Thines, Marco, Win, Joe, Haas, Brian J., Dinwiddie, Darrell L., Jenkins, Jerry, Knight, James R., Affourtit, Jason P., Han, Cliff S., Chertkov, Olga, Lindquist, Erika A., Detter, Chris, Grigoriev, Igor V., Kamoun, Sophien, Kingsmore, Stephen F., Lamour, Kurt H., Lamour, Kurt H., Mudge, Joann, Gobena, Daniel, Hurtado-Gonzales, Oscar P., Schmutz, Jeremy, Kuo, Alan, Miller, Neil A., Rice, Brandon J., Raffaele, Sylvain, Cano, Liliana M., Bharti, Arvind K., Donahoo, Ryan S., Finely, Sabra, Huitema, Edgar, Hulvey, Jon, Platt, Darren, Salamov, Asaf, Savidor, Alon, Sharma, Rahul, Stam, Remco, Sotrey, Dylan, Thines, Marco, Win, Joe, Haas, Brian J., Dinwiddie, Darrell L., Jenkins, Jerry, Knight, James R., Affourtit, Jason P., Han, Cliff S., Chertkov, Olga, Lindquist, Erika A., Detter, Chris, Grigoriev, Igor V., Kamoun, Sophien, and Kingsmore, Stephen F.

Abstract

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

Published
2012

9. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

Author

Haas, Brian J., Kamoun, Sophien, Zody, Michael C., Jiang, Rays H. Y., Handsaker, Robert E., Cano, Liliana M., Grabherr, Manfred, Kodira, Chinnappa D., Raffaele, Sylvain, Torto-Alalibo, Trudy, Bozkurt, Tolga O., Ah-Fong, Audrey M. V., Alvarado, Lucia, Anderson, Vicky L., Armstrong, Miles R., Avrova, Anna, Baxter, Laura, Beynon, Jim, Boevink, Petra C., Bollmann, Stephanie R., Bos, Jorunn I. B., Bulone, Vincent, Cai, Guohong, Cakir, Cahid, Carrington, James C., Chawner, Megan, Conti, Lucio, Costanzo, Stefano, Ewan, Richard, Fahlgren, Noah, Fischbach, Michael A., Fugelstad, Johanna, Gilroy, Eleanor M., Gnerre, Sante, Green, Pamela J., Grenville-Briggs, Laura J., Griffith, John, Gruenwald, Niklaus J., Horn, Karolyn, Horner, Neil R., Hu, Chia-Hui, Huitema, Edgar, Jeong, Dong-Hoon, Jones, Alexandra M. E., Jones, Jonathan D. G., Jones, Richard W., Karlsson, Elinor K., Kunjeti, Sridhara G., Lamour, Kurt, Liu, Zhenyu, Ma, LiJun, MacLean, Daniel, Chibucos, Marcus C., McDonald, Hayes, McWalters, Jessica, Meijer, Harold J. G., Morgan, William, Morris, Paul F., Munro, Carol A., O'Neill, Keith, Ospina-Giraldo, Manuel, Pinzon, Andres, Pritchard, Leighton, Ramsahoye, Bernard, Ren, Qinghu, Restrepo, Silvia, Roy, Sourav, Sadanandom, Ari, Savidor, Alon, Schornack, Sebastian, Schwartz, David C., Schumann, Ulrike D., Schwessinger, Ben, Seyer, Lauren, Sharpe, Ted, Silvar, Cristina, Song, Jing, Studholme, David J., Sykes, Sean, Thines, Marco, van de Vondervoort, Peter J. I., Phuntumart, Vipaporn, Wawra, Stephan, Weide, Rob, Win, Joe, Young, Carolyn, Zhou, Shiguo, Fry, William, Meyers, Blake C., van West, Pieter, Ristaino, Jean, Govers, Francine, Birch, Paul R. J., Whisson, Stephen C., Judelson, Howard S., Nusbaum, Chad, Haas, Brian J., Kamoun, Sophien, Zody, Michael C., Jiang, Rays H. Y., Handsaker, Robert E., Cano, Liliana M., Grabherr, Manfred, Kodira, Chinnappa D., Raffaele, Sylvain, Torto-Alalibo, Trudy, Bozkurt, Tolga O., Ah-Fong, Audrey M. V., Alvarado, Lucia, Anderson, Vicky L., Armstrong, Miles R., Avrova, Anna, Baxter, Laura, Beynon, Jim, Boevink, Petra C., Bollmann, Stephanie R., Bos, Jorunn I. B., Bulone, Vincent, Cai, Guohong, Cakir, Cahid, Carrington, James C., Chawner, Megan, Conti, Lucio, Costanzo, Stefano, Ewan, Richard, Fahlgren, Noah, Fischbach, Michael A., Fugelstad, Johanna, Gilroy, Eleanor M., Gnerre, Sante, Green, Pamela J., Grenville-Briggs, Laura J., Griffith, John, Gruenwald, Niklaus J., Horn, Karolyn, Horner, Neil R., Hu, Chia-Hui, Huitema, Edgar, Jeong, Dong-Hoon, Jones, Alexandra M. E., Jones, Jonathan D. G., Jones, Richard W., Karlsson, Elinor K., Kunjeti, Sridhara G., Lamour, Kurt, Liu, Zhenyu, Ma, LiJun, MacLean, Daniel, Chibucos, Marcus C., McDonald, Hayes, McWalters, Jessica, Meijer, Harold J. G., Morgan, William, Morris, Paul F., Munro, Carol A., O'Neill, Keith, Ospina-Giraldo, Manuel, Pinzon, Andres, Pritchard, Leighton, Ramsahoye, Bernard, Ren, Qinghu, Restrepo, Silvia, Roy, Sourav, Sadanandom, Ari, Savidor, Alon, Schornack, Sebastian, Schwartz, David C., Schumann, Ulrike D., Schwessinger, Ben, Seyer, Lauren, Sharpe, Ted, Silvar, Cristina, Song, Jing, Studholme, David J., Sykes, Sean, Thines, Marco, van de Vondervoort, Peter J. I., Phuntumart, Vipaporn, Wawra, Stephan, Weide, Rob, Win, Joe, Young, Carolyn, Zhou, Shiguo, Fry, William, Meyers, Blake C., van West, Pieter, Ristaino, Jean, Govers, Francine, Birch, Paul R. J., Whisson, Stephen C., Judelson, Howard S., and Nusbaum, Chad

Abstract

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

Published
2009
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10. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

Author

Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I.B., Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grunwald, N.J., Horn, K., Horner, N.R., Hu, C.H., Huitema, E., Jeong, D.H., Jones, A.M.E., Jones, J.D.G., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., Maclean, D., Chibucos, M.C., McDonald, H., McWalters, J., Meijer, H.J.G., Morgan, W., Morris, P.F., Munro, C.A., O'Neill, K., Ospina-Giraldo, M., Pinzon, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J.I., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S.C., Judelson, H.S., Nusbaum, C., Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I.B., Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grunwald, N.J., Horn, K., Horner, N.R., Hu, C.H., Huitema, E., Jeong, D.H., Jones, A.M.E., Jones, J.D.G., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., Maclean, D., Chibucos, M.C., McDonald, H., McWalters, J., Meijer, H.J.G., Morgan, W., Morris, P.F., Munro, C.A., O'Neill, K., Ospina-Giraldo, M., Pinzon, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J.I., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S.C., Judelson, H.S., and Nusbaum, C.

Abstract

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

Published
2009

11. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

Author

Tyler, Brett M., Tyler, Brett M., Tripathy, Sucheta, Zhang, Xuemin, Dehal, Paramvir, Jiang, Rays H. Y., Aerts, Andrea, Arredondo, Felipe D., Baxter, Laura, Bensasson, Douda, Beynon, JIm L., Chapman, Jarrod, Damasceno, Cynthia M. B., Dorrance, Anne E., Dou, Daolong, Dickerman, Allan W., Dubchak, Inna L., Garbelotto, Matteo, Gijzen, Mark, Gordon, Stuart G., Govers, Francine, Grunwald, NIklaus J., Huang, Wayne, Ivors, Kelly L., Jones, Richard W., Kamoun, Sophien, Krampis, Konstantinos, Lamour, Kurt H., Lee, Mi-Kyung, McDonald, W. Hayes, Medina, Monica, Meijer, Harold J. G., Nordberg, Erik K., Maclean, Donald J., Ospina-Giraldo, Manuel D., Morris, Paul F., Phuntumart, Vipaporn, Putnam, Nicholas J., Rash, Sam, Rose, Jocelyn K. C., Sakihama, Yasuko, Salamov, Asaf A., Savidor, Alon, Scheuring, Chantel F., Smith, Brian M., Sobral, Bruno W. S., Terry, Astrid, Torto-Alalibo, Trudy A., Win, Joe, Xu, Zhanyou, Zhang, Hongbin, Grigoriev, Igor V., Rokhsar, Daniel S., Boore, Jeffrey L., Tyler, Brett M., Tyler, Brett M., Tripathy, Sucheta, Zhang, Xuemin, Dehal, Paramvir, Jiang, Rays H. Y., Aerts, Andrea, Arredondo, Felipe D., Baxter, Laura, Bensasson, Douda, Beynon, JIm L., Chapman, Jarrod, Damasceno, Cynthia M. B., Dorrance, Anne E., Dou, Daolong, Dickerman, Allan W., Dubchak, Inna L., Garbelotto, Matteo, Gijzen, Mark, Gordon, Stuart G., Govers, Francine, Grunwald, NIklaus J., Huang, Wayne, Ivors, Kelly L., Jones, Richard W., Kamoun, Sophien, Krampis, Konstantinos, Lamour, Kurt H., Lee, Mi-Kyung, McDonald, W. Hayes, Medina, Monica, Meijer, Harold J. G., Nordberg, Erik K., Maclean, Donald J., Ospina-Giraldo, Manuel D., Morris, Paul F., Phuntumart, Vipaporn, Putnam, Nicholas J., Rash, Sam, Rose, Jocelyn K. C., Sakihama, Yasuko, Salamov, Asaf A., Savidor, Alon, Scheuring, Chantel F., Smith, Brian M., Sobral, Bruno W. S., Terry, Astrid, Torto-Alalibo, Trudy A., Win, Joe, Xu, Zhanyou, Zhang, Hongbin, Grigoriev, Igor V., Rokhsar, Daniel S., and Boore, Jeffrey L.

Abstract

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

Published
2006

12. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

Author

Tyler, Brett M., Tyler, Brett M., Tripathy, Sucheta, Zhang, Xuemin, Dehal, Paramvir, Jiang, Rays H. Y., Aerts, Andrea, Arredondo, Felipe D., Baxter, Laura, Bensasson, Douda, Beynon, JIm L., Chapman, Jarrod, Damasceno, Cynthia M. B., Dorrance, Anne E., Dou, Daolong, Dickerman, Allan W., Dubchak, Inna L., Garbelotto, Matteo, Gijzen, Mark, Gordon, Stuart G., Govers, Francine, Grunwald, NIklaus J., Huang, Wayne, Ivors, Kelly L., Jones, Richard W., Kamoun, Sophien, Krampis, Konstantinos, Lamour, Kurt H., Lee, Mi-Kyung, McDonald, W. Hayes, Medina, Monica, Meijer, Harold J. G., Nordberg, Erik K., Maclean, Donald J., Ospina-Giraldo, Manuel D., Morris, Paul F., Phuntumart, Vipaporn, Putnam, Nicholas J., Rash, Sam, Rose, Jocelyn K. C., Sakihama, Yasuko, Salamov, Asaf A., Savidor, Alon, Scheuring, Chantel F., Smith, Brian M., Sobral, Bruno W. S., Terry, Astrid, Torto-Alalibo, Trudy A., Win, Joe, Xu, Zhanyou, Zhang, Hongbin, Grigoriev, Igor V., Rokhsar, Daniel S., Boore, Jeffrey L., Tyler, Brett M., Tyler, Brett M., Tripathy, Sucheta, Zhang, Xuemin, Dehal, Paramvir, Jiang, Rays H. Y., Aerts, Andrea, Arredondo, Felipe D., Baxter, Laura, Bensasson, Douda, Beynon, JIm L., Chapman, Jarrod, Damasceno, Cynthia M. B., Dorrance, Anne E., Dou, Daolong, Dickerman, Allan W., Dubchak, Inna L., Garbelotto, Matteo, Gijzen, Mark, Gordon, Stuart G., Govers, Francine, Grunwald, NIklaus J., Huang, Wayne, Ivors, Kelly L., Jones, Richard W., Kamoun, Sophien, Krampis, Konstantinos, Lamour, Kurt H., Lee, Mi-Kyung, McDonald, W. Hayes, Medina, Monica, Meijer, Harold J. G., Nordberg, Erik K., Maclean, Donald J., Ospina-Giraldo, Manuel D., Morris, Paul F., Phuntumart, Vipaporn, Putnam, Nicholas J., Rash, Sam, Rose, Jocelyn K. C., Sakihama, Yasuko, Salamov, Asaf A., Savidor, Alon, Scheuring, Chantel F., Smith, Brian M., Sobral, Bruno W. S., Terry, Astrid, Torto-Alalibo, Trudy A., Win, Joe, Xu, Zhanyou, Zhang, Hongbin, Grigoriev, Igor V., Rokhsar, Daniel S., and Boore, Jeffrey L.

Abstract

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

Published
2006

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