J Plant Res DOI 10.1007/s10265-015-0718-7
JPR SYMPOSIUM
Reprogramming of plant cells as adaptive strategies
Plant cell reprogramming as an adaptive strategy Keiko Sugimoto1
Received: 27 February 2015 / Accepted: 2 March 2015 © The Botanical Society of Japan and Springer Japan 2015
Keywords Dedifferentiation · Redifferentiation · Totipotency · Pluripotency · Regeneration · Tissue culture · Wounding
Introduction When plants face severe mechanical or physiological damages, they often modify their intrinsic developmental programme as an adaptive strategy. Some extreme examples of these reprogramming can be found in various forms in nature; in some cases plants regenerate the whole or part of the plant body and in other cases they develop tumours or callus, a mass of unorganised cells, at the damage site. Exogenous application of plant hormones can also mimic some of these reprogramming events in the in vitro tissue culture and hormone-mediated callus generation followed by shoot or root regeneration has been adopted in many plant species. Thanks to the recent advances in plant cell and molecular biology, it is becoming increasingly clear that plant reprogramming, underlying organ regeneration or tumourgenesis, involves relatively a small population of cells (Ikeuchi et al. 2013). In some cases reprogramming starts from fully differentiated somatic cells and requires their dedifferentiation to a less differentiated state but there are some cases where relatively undifferentiated cells are reactivated or reprogrammed to have a new cell fate. In this special issue we highlight some of the recent progress in
our understanding of the molecular basis underlying plant reprogramming. In this editorial I give an overview of the articles included in this issue and discuss the future perspectives of plant reprogramming research.
Plant cell reprogramming: historical perspectives One of the most striking recent findings in the field of plant reprogramming is that the callus formation in the conventional tissue culture using Arabidopsis explants is mediated by the reactivation of relatively undifferentiated pericycle cells rather than dedifferentiation of mature somatic cells (Atta et al. 2009; Sugimoto et al. 2010). The study by Sugimoto et al. (2010) also showed that the callus induced by auxin-rich callus inducing medium resembles the root meristem both structurally and transcriptionally, demonstrating that at least this type of callus is not a mass of undifferentiated cells as previously thought. With this advance in mind, Sugiyama (2015) first provides a comprehensive historical review on this subject by carefully examining when the concept of cell dedifferentiation emerged in plant biology and what experimental basis supported this notion. Sugiyama (2015) also discusses cell dedifferentiation in the context of organ regeneration and somatic embryogenesis, and summarises our current understanding of their underlying molecular mechanisms.
Plant cell reprogramming in the tissue culture * Keiko Sugimoto [email protected] 1
RIKEN Center for Sustainable Resource Science, 1‑7‑22 Suehiro‑cho, Tsurumi, Yokohama, Kanagawa 230‑0045, Japan
The discovery that the combination of two plant hormones, auxin and cytokinin, promotes plant regeneration in the in vitro tissue culture has been a major historical breakthrough in plant biology but surprisingly little is known
13
as to how these hormones promote callus formation and subsequent shoot or root regeneration. Ohtani (2015) summarises an interesting link between in vitro organ regeneration and RNA metabolism and discusses, in particular, the requirement of rRNA biogenesis, pre-mRNA splicing and miRNA-mediated RNA degradation in in vitro organogenesis. In the accompanying research article Ohtani (2015) further demonstrate that organ regeneration in the in vitro tissue culture requires higher levels of small nuclear RNA, one of the non-coding RNA species involved in pre-mRNA splicing, compared to normal plant development.
J Plant Res
of reentry from late S phase occurring in Physcomitrella patens. How various environmental conditions, such as light and temperature, influence wound-induced regeneration has attracted attention of plant physiologists for many decades and light-stimulated regeneration in liverworts, for instance, was already documented in the early twentieth century (Cavers 1903). Nishihama et al. (2015) investigate how light modulates thallus regeneration in the liverwort Marchantia polymorpha and demonstrate that both phytochrome-mediated signalling and photosynthesis-derived sugar promote cell proliferation and morphogenesis during regeneration.
Plant cell reprogramming induced by wounding Despite the early documentation of callus induction at the wound site (for further info, see references in Sugiyama (2015) in this issue), the basic molecular mechanisms underlying this remarkable physiological response are far from clear. Examples of key unanswered questions include “what is the initial wound signal perceived by plants?” and “how do plants transduce these signals to start cellular reprogramming?” Asahina and Satoh (2015) address these questions in the context of tissue reunion in which cells adjacent to the incision site restart to proliferate in order to reconnect the two partially detached plant segments. Based on their previous findings, Asahina and Satoh (2015) discuss the context-dependent requirement of various plant hormones in the tomato and cucumber hypocotyls as well as Arabidopsis flowering stems. When Arabidopsis hypocotyls or roots are injured by cutting, they develop callus at the wound site. Iwase et al. (2011) previously showed that the wound induced dedifferentiation 1 (WIND1) family of the AP2/ERF transcription factors promotes callus formation in response to the wounding stimulus. In this issue Iwase et al. (2015) reports that WIND1 also increases the regenerative competency in the tissue culture and sequential activation of WIND1 and another differentiation-promoting regulator allows targeted cell fate manipulation. Based on these findings, Iwase et al. (2015) propose that the primary function of WIND proteins might be to potentiate plant cells for further reprogramming. Plant cell reprogramming is often associated with reentry into the mitotic cell cycle, thus one central question is how external stimuli, such as wounding, promotes cell cycle reentry. Ishikawa and Hasebe (2015) investigate this question in the moss Physcomitrella patens in which wounding induces reprogramming of fully differentiated leaf cells in gametophores into chloronema apical stem cells (Ishikawa et al. 2011). Ishikawa and Hasebe (2015) summarise several modes of cell cycle reentry known in animals and plants, and discuss the biological significance
13
Plant cell reprogramming induced by pathogens Plant cell reprogramming can be triggered by pathogenic infections, and crown gall tumour induced by Agrobacterium is among the most intensively studied examples. It is well established that the T-DNA transferred from Agrobacterium to the host plants encode enzymes for auxin and cytokinin biosynthesis and once inserted into the host genome, they promote the production of these plant hormones to facilitate gall formation. What is less clear is the role of other genes encoded in the T-DNA, including 6b of tumour-inducing Agrobacterium, and Ito and Machida (2015) provide a thorough summary of previous research investigating this question. Based on the series of earlier studies that have identified proteins interacting with 6b, Ito and Machida (2015) propose that 6b may act as a transcriptional coactivator that by binding to a set of transcription factors, promotes the expression of downstream target genes and/or as a chromatin remodeling factor that by mediating the nucleosome assembly, influences target gene expression.
Future perspectives How do plants reprogramme in response to external stimuli and what is the molecular basis underlying the high regenerative competence of plants compared to most animal counterparts? These are fundamental questions highly relevant in both basic and applied biology but we still do not understand many aspects of these molecular mechanisms. The two pathways to reprogramme plant cells, involving either dedifferentiation of somatic cells or reactivation of existing stem cells, should be governed by distinct molecular mechanisms. Therefore it is extremely important in current research to determine the cell types that contribute to reprogramming and investigate how diverse environmental stimuli activate each of these cellular processes.
J Plant Res
Identification of several master regulators such as WIND (Iwase et al. 2011), ANAC071 and RAP2.6L (Asahina et al. 2011) highlights the requirement of vast transcriptional change prior to reprogramming. Further elucidation of their downstream regulatory networks should help uncover the general physiological principles (and deviations from them) underlying different modes of reprogramming. It is also likely that various epigenetic regulators, such as histone modifiers and chromatin remodeling factors, contribute to the timely execution of reprogramming. Future studies should address how these epigenetic modifications intersect with transcriptional regulation to coordinately control reprogramming. Given that most of these genetic or epigenetic regulators act very locally, for instance, at the site of injury or pathogen infection, single-cell resolution approaches will be the key for the full spatiotemporal understanding of reprogramming. It is known that some plant species or even some cultivars wihtin the same plant species are more regenerative compared to their close relatives and younger tissues tend to be more regenerative compared to older tissues of the same plant. These differences in the regenerative competency might arise from relatively small genetic or epigenetic variations and unveiling the molecular basis of these variations should also facilitate our better understanding of plant reprogramming. Acknowledgments I thank Masaki Ito and Akira Iwase for comments and suggestions on this manuscript. The work on reprogramming in my laboratory is supported by Grants-in-Aid for Scientific Research on Innovative Areas (Grant No. 22119010) and as a part of the Research and Development Projects for Application in Promoting New Policy of Agriculture, Forestry and Fisheries.
References Asahina M, Satoh S (2015) Molecular and physiological mechanisms regulating tissue reunion in incised plant tissues. J Plant Res. doi:10.1007/s10265-015-0705-z
Asahina M, Azuma K, Pitaksaringkarn W, Yamazaki T, Mitsuda N, Ohme-Takagi M, Yamaguchi S, Kamiya Y, Okada K, Nishimura T, Koshiba T, Yokota T, Kamada H, Satoh S (2011) Spatially selective hormonal control of RAP2.6L and ANAC071 transcription factors involved in tissue reunion in Arabidopsis. Proc Natl Acad Sci 108:16128–16132 Atta R, Laurens L, Boucheron-Dubuisson E, Guivarc’h A, Carnero E, Giraudat-Pautot V, Rech P, Chriqui D (2009) Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grown in vitro. Plant J 57:626–644 Cavers F (1903) On asexual reproduction and regeneration in Hepaticae. New Phytol 2:121–133 Ikeuchi M, Sugimoto K, Iwase A (2013) Plant callus: mechanisms of induction and repression. Plant Cell 25:3159–3173 Ishikawa M, Hasebe M (2015) Cell cycle reentry from the late S phase: implications from stem cell formation in the moss Physcomitrella patens. J Plant Res. doi:10.1007/s10265-015-0713-z Ishikawa M, Murata T, Sato Y, Nishiyama T, Hiwatashi Y, Imai A, Kimura M, Sugimoto N, Akita A, Oguri Y, Friedman WE, Hasebe M, Kubo M (2011) Physcomitrella cyclin-dependent kinase a links cell cycle reactivation to other cellular changes during reprogramming of leaf cells. Plant Cell 23:2924–2938 Ito M, Machida Y (2015) Reprogramming of plant cells by 6b oncoproteins from the plant pathogen Agrobacterium. J Plant Res. doi:10.1007/s10265-014-0694-3 Iwase A, Mitsuda N, Koyama T, Hiratsu K, Kojima M, Arai T, Inoue Y, Seki M, Sakakibara H, Sugimoto K, Ohme-Takagi M (2011) The AP2/ERF transcription factor WIND1 controls cell dedifferentiation. Curr Biol 21:506–514 Iwase A, Mita K, Nonaka S, Ikeuchi M, Koizuka C, Ohnuma M, Ezura H, Imamura J, Sugimoto K (2015) WIND1-based acquisition of regeneration competency in Arabidopsis and rapeseed. J Plant Res (in press) Nishihama R, Ishizaki K, Hosaka M, Matsuda Y, Kubota A, Kohchi T (2015) Phytochrome-mediated regulation of cell division and growth during regeneration and sporeling development in the liverwort Marchantia polymorpha. J Plant Res. doi:10.1007/ s10265-015-0724-9 Ohtani M (2015) Regulation of RNA metabolism is important for in vitro dedifferentiation of plant cells. J Plant Res. doi:10.1007/ s10265-015-0700-4 Sugimoto K, Jiao Y, Meyerowitz EM (2010) Arabidopsis regeneration from multiple tissues occurs via a root development pathway. Dev Cell 18:463–471 Sugiyama M (2015) Historical review of researches on plant cell dedifferentiation. J Plant Res. doi:10.1007/s10265-015-0706-y
13
JPR SYMPOSIUM
Reprogramming of plant cells as adaptive strategies
Plant cell reprogramming as an adaptive strategy Keiko Sugimoto1
Received: 27 February 2015 / Accepted: 2 March 2015 © The Botanical Society of Japan and Springer Japan 2015
Keywords Dedifferentiation · Redifferentiation · Totipotency · Pluripotency · Regeneration · Tissue culture · Wounding
Introduction When plants face severe mechanical or physiological damages, they often modify their intrinsic developmental programme as an adaptive strategy. Some extreme examples of these reprogramming can be found in various forms in nature; in some cases plants regenerate the whole or part of the plant body and in other cases they develop tumours or callus, a mass of unorganised cells, at the damage site. Exogenous application of plant hormones can also mimic some of these reprogramming events in the in vitro tissue culture and hormone-mediated callus generation followed by shoot or root regeneration has been adopted in many plant species. Thanks to the recent advances in plant cell and molecular biology, it is becoming increasingly clear that plant reprogramming, underlying organ regeneration or tumourgenesis, involves relatively a small population of cells (Ikeuchi et al. 2013). In some cases reprogramming starts from fully differentiated somatic cells and requires their dedifferentiation to a less differentiated state but there are some cases where relatively undifferentiated cells are reactivated or reprogrammed to have a new cell fate. In this special issue we highlight some of the recent progress in
our understanding of the molecular basis underlying plant reprogramming. In this editorial I give an overview of the articles included in this issue and discuss the future perspectives of plant reprogramming research.
Plant cell reprogramming: historical perspectives One of the most striking recent findings in the field of plant reprogramming is that the callus formation in the conventional tissue culture using Arabidopsis explants is mediated by the reactivation of relatively undifferentiated pericycle cells rather than dedifferentiation of mature somatic cells (Atta et al. 2009; Sugimoto et al. 2010). The study by Sugimoto et al. (2010) also showed that the callus induced by auxin-rich callus inducing medium resembles the root meristem both structurally and transcriptionally, demonstrating that at least this type of callus is not a mass of undifferentiated cells as previously thought. With this advance in mind, Sugiyama (2015) first provides a comprehensive historical review on this subject by carefully examining when the concept of cell dedifferentiation emerged in plant biology and what experimental basis supported this notion. Sugiyama (2015) also discusses cell dedifferentiation in the context of organ regeneration and somatic embryogenesis, and summarises our current understanding of their underlying molecular mechanisms.
Plant cell reprogramming in the tissue culture * Keiko Sugimoto [email protected] 1
RIKEN Center for Sustainable Resource Science, 1‑7‑22 Suehiro‑cho, Tsurumi, Yokohama, Kanagawa 230‑0045, Japan
The discovery that the combination of two plant hormones, auxin and cytokinin, promotes plant regeneration in the in vitro tissue culture has been a major historical breakthrough in plant biology but surprisingly little is known
13
as to how these hormones promote callus formation and subsequent shoot or root regeneration. Ohtani (2015) summarises an interesting link between in vitro organ regeneration and RNA metabolism and discusses, in particular, the requirement of rRNA biogenesis, pre-mRNA splicing and miRNA-mediated RNA degradation in in vitro organogenesis. In the accompanying research article Ohtani (2015) further demonstrate that organ regeneration in the in vitro tissue culture requires higher levels of small nuclear RNA, one of the non-coding RNA species involved in pre-mRNA splicing, compared to normal plant development.
J Plant Res
of reentry from late S phase occurring in Physcomitrella patens. How various environmental conditions, such as light and temperature, influence wound-induced regeneration has attracted attention of plant physiologists for many decades and light-stimulated regeneration in liverworts, for instance, was already documented in the early twentieth century (Cavers 1903). Nishihama et al. (2015) investigate how light modulates thallus regeneration in the liverwort Marchantia polymorpha and demonstrate that both phytochrome-mediated signalling and photosynthesis-derived sugar promote cell proliferation and morphogenesis during regeneration.
Plant cell reprogramming induced by wounding Despite the early documentation of callus induction at the wound site (for further info, see references in Sugiyama (2015) in this issue), the basic molecular mechanisms underlying this remarkable physiological response are far from clear. Examples of key unanswered questions include “what is the initial wound signal perceived by plants?” and “how do plants transduce these signals to start cellular reprogramming?” Asahina and Satoh (2015) address these questions in the context of tissue reunion in which cells adjacent to the incision site restart to proliferate in order to reconnect the two partially detached plant segments. Based on their previous findings, Asahina and Satoh (2015) discuss the context-dependent requirement of various plant hormones in the tomato and cucumber hypocotyls as well as Arabidopsis flowering stems. When Arabidopsis hypocotyls or roots are injured by cutting, they develop callus at the wound site. Iwase et al. (2011) previously showed that the wound induced dedifferentiation 1 (WIND1) family of the AP2/ERF transcription factors promotes callus formation in response to the wounding stimulus. In this issue Iwase et al. (2015) reports that WIND1 also increases the regenerative competency in the tissue culture and sequential activation of WIND1 and another differentiation-promoting regulator allows targeted cell fate manipulation. Based on these findings, Iwase et al. (2015) propose that the primary function of WIND proteins might be to potentiate plant cells for further reprogramming. Plant cell reprogramming is often associated with reentry into the mitotic cell cycle, thus one central question is how external stimuli, such as wounding, promotes cell cycle reentry. Ishikawa and Hasebe (2015) investigate this question in the moss Physcomitrella patens in which wounding induces reprogramming of fully differentiated leaf cells in gametophores into chloronema apical stem cells (Ishikawa et al. 2011). Ishikawa and Hasebe (2015) summarise several modes of cell cycle reentry known in animals and plants, and discuss the biological significance
13
Plant cell reprogramming induced by pathogens Plant cell reprogramming can be triggered by pathogenic infections, and crown gall tumour induced by Agrobacterium is among the most intensively studied examples. It is well established that the T-DNA transferred from Agrobacterium to the host plants encode enzymes for auxin and cytokinin biosynthesis and once inserted into the host genome, they promote the production of these plant hormones to facilitate gall formation. What is less clear is the role of other genes encoded in the T-DNA, including 6b of tumour-inducing Agrobacterium, and Ito and Machida (2015) provide a thorough summary of previous research investigating this question. Based on the series of earlier studies that have identified proteins interacting with 6b, Ito and Machida (2015) propose that 6b may act as a transcriptional coactivator that by binding to a set of transcription factors, promotes the expression of downstream target genes and/or as a chromatin remodeling factor that by mediating the nucleosome assembly, influences target gene expression.
Future perspectives How do plants reprogramme in response to external stimuli and what is the molecular basis underlying the high regenerative competence of plants compared to most animal counterparts? These are fundamental questions highly relevant in both basic and applied biology but we still do not understand many aspects of these molecular mechanisms. The two pathways to reprogramme plant cells, involving either dedifferentiation of somatic cells or reactivation of existing stem cells, should be governed by distinct molecular mechanisms. Therefore it is extremely important in current research to determine the cell types that contribute to reprogramming and investigate how diverse environmental stimuli activate each of these cellular processes.
J Plant Res
Identification of several master regulators such as WIND (Iwase et al. 2011), ANAC071 and RAP2.6L (Asahina et al. 2011) highlights the requirement of vast transcriptional change prior to reprogramming. Further elucidation of their downstream regulatory networks should help uncover the general physiological principles (and deviations from them) underlying different modes of reprogramming. It is also likely that various epigenetic regulators, such as histone modifiers and chromatin remodeling factors, contribute to the timely execution of reprogramming. Future studies should address how these epigenetic modifications intersect with transcriptional regulation to coordinately control reprogramming. Given that most of these genetic or epigenetic regulators act very locally, for instance, at the site of injury or pathogen infection, single-cell resolution approaches will be the key for the full spatiotemporal understanding of reprogramming. It is known that some plant species or even some cultivars wihtin the same plant species are more regenerative compared to their close relatives and younger tissues tend to be more regenerative compared to older tissues of the same plant. These differences in the regenerative competency might arise from relatively small genetic or epigenetic variations and unveiling the molecular basis of these variations should also facilitate our better understanding of plant reprogramming. Acknowledgments I thank Masaki Ito and Akira Iwase for comments and suggestions on this manuscript. The work on reprogramming in my laboratory is supported by Grants-in-Aid for Scientific Research on Innovative Areas (Grant No. 22119010) and as a part of the Research and Development Projects for Application in Promoting New Policy of Agriculture, Forestry and Fisheries.
References Asahina M, Satoh S (2015) Molecular and physiological mechanisms regulating tissue reunion in incised plant tissues. J Plant Res. doi:10.1007/s10265-015-0705-z
Asahina M, Azuma K, Pitaksaringkarn W, Yamazaki T, Mitsuda N, Ohme-Takagi M, Yamaguchi S, Kamiya Y, Okada K, Nishimura T, Koshiba T, Yokota T, Kamada H, Satoh S (2011) Spatially selective hormonal control of RAP2.6L and ANAC071 transcription factors involved in tissue reunion in Arabidopsis. Proc Natl Acad Sci 108:16128–16132 Atta R, Laurens L, Boucheron-Dubuisson E, Guivarc’h A, Carnero E, Giraudat-Pautot V, Rech P, Chriqui D (2009) Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grown in vitro. Plant J 57:626–644 Cavers F (1903) On asexual reproduction and regeneration in Hepaticae. New Phytol 2:121–133 Ikeuchi M, Sugimoto K, Iwase A (2013) Plant callus: mechanisms of induction and repression. Plant Cell 25:3159–3173 Ishikawa M, Hasebe M (2015) Cell cycle reentry from the late S phase: implications from stem cell formation in the moss Physcomitrella patens. J Plant Res. doi:10.1007/s10265-015-0713-z Ishikawa M, Murata T, Sato Y, Nishiyama T, Hiwatashi Y, Imai A, Kimura M, Sugimoto N, Akita A, Oguri Y, Friedman WE, Hasebe M, Kubo M (2011) Physcomitrella cyclin-dependent kinase a links cell cycle reactivation to other cellular changes during reprogramming of leaf cells. Plant Cell 23:2924–2938 Ito M, Machida Y (2015) Reprogramming of plant cells by 6b oncoproteins from the plant pathogen Agrobacterium. J Plant Res. doi:10.1007/s10265-014-0694-3 Iwase A, Mitsuda N, Koyama T, Hiratsu K, Kojima M, Arai T, Inoue Y, Seki M, Sakakibara H, Sugimoto K, Ohme-Takagi M (2011) The AP2/ERF transcription factor WIND1 controls cell dedifferentiation. Curr Biol 21:506–514 Iwase A, Mita K, Nonaka S, Ikeuchi M, Koizuka C, Ohnuma M, Ezura H, Imamura J, Sugimoto K (2015) WIND1-based acquisition of regeneration competency in Arabidopsis and rapeseed. J Plant Res (in press) Nishihama R, Ishizaki K, Hosaka M, Matsuda Y, Kubota A, Kohchi T (2015) Phytochrome-mediated regulation of cell division and growth during regeneration and sporeling development in the liverwort Marchantia polymorpha. J Plant Res. doi:10.1007/ s10265-015-0724-9 Ohtani M (2015) Regulation of RNA metabolism is important for in vitro dedifferentiation of plant cells. J Plant Res. doi:10.1007/ s10265-015-0700-4 Sugimoto K, Jiao Y, Meyerowitz EM (2010) Arabidopsis regeneration from multiple tissues occurs via a root development pathway. Dev Cell 18:463–471 Sugiyama M (2015) Historical review of researches on plant cell dedifferentiation. J Plant Res. doi:10.1007/s10265-015-0706-y
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