Wound signaling of regenerative cell reprogramming

Morpho-histology of co-occurrence of somatic embryos, shoots, and inflorescences within a callus of Limonium 'Misty Blue'

This is the first attempt to report the co-occurrence of somatic embryos, shoots, and inflorescences and their sequential development from stem cell niches of an individual callus mass through morpho-histological study of any angiosperm. In the presence of a proper auxin/cytokinin combination, precambial stem cells from the middle layer of a compact callus, which was derived from the thin cell layer of the inflorescence rachis of Limonium, expressed the highest level of totipotency and pluripotency and simultaneously developed somatic embryos, shoots, and inflorescences. This study also proposed the concept of programmed cell death during bipolar somatic embryo and unipolar shoot bud pattern formation. The unique feature of this research was the stepwise histological description of in vitro racemose inflorescence development. Remarkably, during the initiation of inflorescence development, either a unipolar structure with open vascular elements or an independent bipolar structure with closed vascular elements were observed. The protocol predicted the production of 6.6 ± 0.24 and 7.4 ± 0.24 somatic embryos and shoots, respectively, from 400 mg of callus, which again multiplied, rooted, and acclimatised. The plants' ploidy level and genetic fidelity were assessed randomly before acclimatisation by flow cytometry and inter simple sequence repeats (ISSR) marker analysis. Finally, the survivability and flower quality of the regenerated plants were evaluated in the field.

Wounding-Related Signaling Is Integrated within the Auxin-Response Framework to Induce Adventitious Rooting in Chestnut

Wounding and exogenous auxin are needed to induce adventitious roots in chestnut microshoots. However, the specific inductive role of wounding has not been characterized in this species. In the present work, two main goals were established: First, we prompted to optimize exogenous auxin treatments to improve the overall health status of the shoots at the end of the rooting cycle. Second, we developed a time-series transcriptomic analysis to compare gene expression in response to wounding alone and wounding plus auxin, focusing on the early events within the first days after treatments. Results suggest that the expression of many genes involved in the rooting process is under direct or indirect control of both stimuli. However, specific levels of expression of relevant genes are only attained when both treatments are applied simultaneously, leading to the successful development of roots. In this sense, we have identified four transcription factors upregulated by auxin (CsLBD16, CsERF113, Cs22D and CsIAA6), with some of them also being induced by wounding. The highest expression levels of these genes occurred when wounding and auxin treatments were applied simultaneously, correlating with the rooting response of the shoots. The results of this work clarify the genetic nature of the wounding response in chestnut, its relation to adventitious rooting, and might be helpful in the development of more specific protocols for the vegetative propagation of this species.

Fine-tuned nitric oxide and hormone interface in plant root development and regeneration

Plant root growth and developmental capacities reside in a few stem cells of the root apical meristem (RAM). Maintenance of these stem cells requires regenerative divisions of the initial stem cell niche (SCN) cells, self-maintenance, and proliferative divisions of the daughter cells. This ensures sufficient cell diversity to guarantee the development of complex root tissues in the plant. Damage in the root during growth involves the formation of a new post-embryonic root, a process known as regeneration. Post-embryonic root development and organogenesis processes include primary root development and SCN maintenance, plant regeneration, and the development of adventitious and lateral roots. These developmental processes require a fine-tuned balance between cell proliferation and maintenance. An important regulator during root development and regeneration is the gasotransmitter nitric oxide (NO). In this review we have sought to compile how NO regulates cell rate proliferation, cell differentiation, and quiescence of SCNs, usually through interaction with phytohormones, or other molecular mechanisms involved in cellular redox homeostasis. NO exerts a role on molecular components of the auxin and cytokinin signaling pathways in primary roots that affects cell proliferation and maintenance of the RAM. During root regeneration, a peak of auxin and cytokinin triggers specific molecular programs. Moreover, NO participates in adventitious root formation through its interaction with players of the brassinosteroid and cytokinin signaling cascade. Lately, NO has been implicated in root regeneration under hypoxia conditions by regulating stem cell specification through phytoglobins.

A Common Molecular Signature Indicates the Pre-Meristematic State of Plant Calli

In response to different degrees of mechanical injury, certain plant cells re-enter the division cycle to provide cells for tissue replenishment, tissue rejoining, de novo organ formation, and/or wound healing. The intermediate tissue formed by the dividing cells is called a callus. Callus formation can also be induced artificially in vitro by wounding and/or hormone (auxin and cytokinin) treatments. The callus tissue can be maintained in culture, providing starting material for de novo organ or embryo regeneration and thus serving as the basis for many plant biotechnology applications. Due to the biotechnological importance of callus cultures and the scientific interest in the developmental flexibility of somatic plant cells, the initial molecular steps of callus formation have been studied in detail. It was revealed that callus initiation can follow various ways, depending on the organ from which it develops and the inducer, but they converge on a seemingly identical tissue. It is not known, however, if callus is indeed a special tissue with a defined gene expression signature, whether it is a malformed meristem, or a mass of so-called "undifferentiated" cells, as is mostly believed. In this paper, I review the various mechanisms of plant regeneration that may converge on callus initiation. I discuss the role of plant hormones in the detour of callus formation from normal development. Finally, I compare various Arabidopsis gene expression datasets obtained a few days, two weeks, or several years after callus induction and identify 21 genes, including genes of key transcription factors controlling cell division and differentiation in meristematic regions, which were upregulated in all investigated callus samples. I summarize the information available on all 21 genes that point to the pre-meristematic nature of callus tissues underlying their wide regeneration potential.

An auxin-mediated ultradian rhythm positively influences root regeneration via EAR1/EUR1 in Arabidopsis

Ultradian rhythms have been proved to be critical for diverse biological processes. However, comprehensive understanding of the short-period rhythms remains limited. Here, we discover that leaf excision triggers a gene expression rhythm with ~3-h periodicity, named as the excision ultradian rhythm (UR), which is regulated by the plant hormone auxin. Promoter-luciferase analyses showed that the spatiotemporal patterns of the excision UR were positively associated with de novo root regeneration (DNRR), a post-embryonic developmental process. Transcriptomic analysis indicated more than 4,000 genes including DNRR-associated genes were reprogramed toward ultradian oscillation. Genetic studies showed that EXCISION ULTRADIAN RHYTHM 1 (EUR1) encoding ENHANCER OF ABSCISIC ACID CO-RECEPTOR1 (EAR1), an abscisic acid signaling regulator, was required to generate the excision ultradian rhythm and enhance root regeneration. The eur1 mutant exhibited the absence of auxin-induced excision UR generation and partial failure during rescuing root regeneration. Our results demonstrate a link between the excision UR and adventitious root formation via EAR1/EUR1, implying an additional regulatory layer in plant regeneration.

Full-length transcriptome-referenced analysis reveals crucial roles of hormone and wounding during induction of aerial bulbils in lily

Aerial bulbils are important vegetative reproductive organs in Lilium. They are often perpetually dormant in most Lilium species, and little is known about the induction of these vegetative structures. The world-famous Oriental hybrid lily cultivar 'Sorbonne', which blooms naturally devoid of aerial bulbils, is known for its lovely appearance and sweet fragrance. We found that decapitation stimulated the outgrowth of aerial bulbils at lower stems (LSs) and then application of low and high concentrations of IAA promoted aerial bulbils emergence around the wound at upper stems (USs) of 'Sorbonne'. However, the genetic basis of aerial bulbil induction is still unclear. Herein, 'Sorbonne' transcriptome has been sequenced for the first time using the combination of third-generation long-read and next-generation short-read technology. A total of 46,557 high-quality non-redundant full-length transcripts were generated. Transcriptomic profiling was performed on seven tissues and stems with treatments of decapitation and application of low and high concentrations of IAA, respectively. Functional annotation of 1918 DEGs within stem samples of different treatments showed that hormone signaling, sugar metabolism and wound-induced genes were crucial to bulbils outgrowth. The expression pattern of auxin-, shoot branching hormone-, plant defense hormone- and wound-inducing-related genes indicated their crucial roles in bulbil induction. Then we established five hormone- and wounding-regulated co-expression modules and identified some candidate transcriptional factors, such as MYB, bZIP, and bHLH, that may function in inducing bulbils. High connectivity was observed among hormone signaling genes, wound-induced genes, and some transcriptional factors, suggesting wound- and hormone-invoked signals exhibit extensive cross-talk and regulate bulbil initiation-associated genes via multilayered regulatory cascades. We propose that the induction of aerial bulbils at LSs after decapitation can be explained as the release of apical dominance. In contrast, the induction of aerial bulbils at the cut surface of USs after IAA application occurs via a process similar to callus formation. This study provides abundant candidate genes that will deepen our understanding of the regulation of bulbil outgrowth, paving the way for further molecular breeding of lily.

Comparative Transcriptome Analysis of Two Kalanchoë Species during Plantlet Formation

Few species in the Kalanchoë genus form plantlets on their leaf margins as an asexual reproduction strategy. The limited molecular studies on plantlet formation show that an organogenesis ortholog, SHOOTMERISTEMLESS (STM) and embryogenesis genes, such as LEAFY COTYLEDON1 (LEC1) and FUSCA3 are recruited during plantlet formation. To understand the mechanisms of two Kalanchoë plantlet-forming species with different modes of plantlet formation, RNA-sequencing analysis was performed. Differentially expressed genes between the developmental stages were clustered in K. daigremontiana (Raym.-Hamet and H. Perrier) and K. pinnata (Lam. Pers.), respectively. Of these gene clusters, GO terms that may be involved in plantlet formation of both species, such as signaling, response to wounding, reproduction, regulation of hormone level, and response to karrikin were overrepresented. Compared with the common GO terms, there were more unique GO terms overrepresented during the plantlet formation of each species. A more in-depth investigation is required to understand how these pathways are participating in plantlet formation. Nonetheless, this transcriptome analysis is presented as a reliable basis for future studies on plantlet formation and development in two Kalanchoë plantlet-forming species.

The Arabinogalactan Protein Family of Centaurium erythraea Rafn

Centaurium erythraea (centaury) is a medicinal plant with exceptional developmental plasticity in vitro and vigorous, often spontaneous, regeneration via shoot organogenesis and somatic embryogenesis, during which arabinogalactan proteins (AGPs) play an important role. AGPs are highly glycosylated proteins belonging to the super family of O-glycosylated plant cell surface hydroxyproline-rich glycoproteins (HRGPs). HRGPs/AGPs are intrinsically disordered and not well conserved, making their homology-based mining ineffective. We have applied a recently developed pipeline for HRGP/AGP mining, ragp, which is based on machine learning prediction of proline hydroxylation, to identify HRGP sequences in centaury transcriptome and to classify them into motif and amino acid bias (MAAB) classes. AGP sequences with low AG glycomotif representation were also identified. Six members of each of the three AGP subclasses, fasciclin-like AGPs, receptor kinase-like AGPs and AG peptides, were selected for phylogenetic and expression analyses. The expression of these 18 genes was recorded over 48 h following leaf mechanical wounding, as well as in 16 tissue samples representing plants from nature, plants cultivated in vitro, and developmental stages during shoot organogenesis and somatic embryogenesis. None of the selected genes were upregulated during both wounding recovery and regeneration. Possible functions of AGPs with the most interesting expression profiles are discussed.

Genome-wide profiling of long noncoding RNAs involved in wheat spike development

BACKGROUND

Long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of plant growth and development. Recent transcriptomic analyses have revealed the gene expression profiling in wheat spike development, however, the possible regulatory roles of lncRNAs in wheat spike morphogenesis remain largely unclear.

RESULTS

Here, we analyzed the genome-wide profiling of lncRNAs during wheat spike development at six stages, and identified a total of 8,889 expressed lncRNAs, among which 2,753 were differentially expressed lncRNAs (DE lncRNAs) at various developmental stages. Three hundred fifteen differentially expressed cis- and trans-regulatory lncRNA-mRNA pairs comprised of 205 lncRNAs and 279 genes were predicted, which were found to be mainly involved in the stress responses, transcriptional and enzymatic regulations. Moreover, the 145 DE lncRNAs were predicted as putative precursors or target mimics of miRNAs. Finally, we identified the important lncRNAs that participate in spike development by potentially targeting stress response genes, TF genes or miRNAs.

CONCLUSIONS

This study outlines an overall view of lncRNAs and their possible regulatory networks during wheat spike development, which also provides an alternative resource for genetic manipulation of wheat spike architecture and thus yield.

Application of naturally occurring mechanical forces in in vitro plant tissue culture and biotechnology

Cues and signals of the environment in nature can be either beneficial or detrimental from the growth and developmental perspectives. Plants, despite their limited spatial mobility, have developed advanced strategies to overcome the various and changing environmental impacts including stresses. In vitro plantlets, tissues and cells are constantly exposed to the influence of their environment that is well controlled. Light has a widely known morphogenetic effect on plants; however, other physical cues and signals are at least as important but were often neglected. In this review, I summarize our knowledge about the role of the mechanical stimuli, like sound, ultrasound, touch, or wounding in in vitro plant cultures. I summarize the molecular, biochemical, physiological, growth, and developmental changes they cause and how these processes are controlled; moreover, how their regulating or stimulating roles are applied in various plant biotechnological applications. Recent studies revealed that mechanical forces can be used for affecting the plant development and growth in plant tissue culture efficiently, and for increasing the efficacy of other plant biotechnological methods, like genetic transformation and secondary metabolite production.

Somatic Embryogenesis in Centaurium erythraea Rafn-Current Status and Perspectives: A Review

Centaurium erythraea (centaury) is a traditionally used medicinal plant, with a spectrum of secondary metabolites with confirmed healing properties. Centaury is an emerging model in plant developmental biology due to its vigorous regenerative potential and great developmental plasticity when cultured in vitro. Hereby, we review nearly two decades of research on somatic embryogenesis (SE) in centaury. During SE, somatic cells are induced by suitable culture conditions to express their totipotency, acquire embryogenic characteristics, and eventually give rise to somatic embryos. When SE is initiated from centaury root explants, the process occurs spontaneously (on hormone-free medium), directly (without the callusing phase), and the somatic embryos are of unicellular origin. SE from leaf explants has to be induced by plant growth regulators and is indirect (preceded by callusing). Histological observations and culture conditions are compared in these two systems. The changes in antioxidative enzymes were followed during SE from the leaf explants. Special focus is given to the role of arabinogalactan proteins during SE, which were analyzed using a variety of approaches. The newest and preliminary results, including centaury transcriptome, novel potential SE markers, and novel types of arabinogalactan proteins, are discussed as perspectives of centaury research.

Recent Advances in Adventitious Root Formation in Chestnut

The genus Castanea includes several tree species that are relevant because of their geographical extension and their multipurpose character, that includes nut and timber production. However, commercial exploitation of the trees is hindered by several factors, particularly by their limited regeneration ability. Regardless of recent advances, there exists a serious limitation for the propagation of elite genotypes of chestnut due to decline of rooting ability as the tree ages. In the present review, we summarize the research developed in this genus during the last three decades concerning the formation of adventitious roots (ARs). Focusing on cuttings and in vitro microshoots, we gather the information available on several species, particularly C. sativa, C. dentata and the hybrid C.sativa × C. crenata, and analyze the influence of several factors on the achievements of the applied protocols, including genotype, auxin treatment, light regime and rooting media. We also pay attention to the acclimation phase, as well as compile the information available about biochemical and molecular related aspects. Furthermore, we considerate promising biotechnological approaches that might enable the improvement of the current protocols.

Advances in Plant Regeneration: Shake, Rattle and Roll

Some plant cells are able to rebuild new organs after tissue damage or in response to definite stress treatments and/or exogenous hormone applications. Whole plants can develop through de novo organogenesis or somatic embryogenesis. Recent findings have enlarged our understanding of the molecular and cellular mechanisms required for tissue reprogramming during plant regeneration. Genetic analyses also suggest the key role of epigenetic regulation during de novo plant organogenesis. A deeper understanding of plant regeneration might help us to enhance tissue culture optimization, with multiple applications in plant micropropagation and green biotechnology. In this review, we will provide additional insights into the physiological and molecular framework of plant regeneration, including both direct and indirect de novo organ formation and somatic embryogenesis, and we will discuss the key role of intrinsic and extrinsic constraints for cell reprogramming during plant regeneration.

Cellular, Molecular, and Physiological Aspects of In Vitro Plant Regeneration

Plants generally have the highest regenerative ability because they show a high degree of developmental plasticity. Although the basic principles of plant regeneration date back many years, understanding the cellular, molecular, and physiological mechanisms based on these principles is currently in progress. In addition to the significant effects of some factors such as medium components, phytohormones, explant type, and light on the regeneration ability of an explant, recent reports evidence the involvement of molecular signals in organogenesis and embryogenesis responses to explant wounding, induced plant cell death, and phytohormones interaction. However, some cellular behaviors such as the occurrence of somaclonal variations and abnormalities during the in vitro plant regeneration process may be associated with adverse effects on the efficacy of plant regeneration. A review of past studies suggests that, in some cases, regeneration in plants involves the reprogramming of distinct somatic cells, while in others, it is induced by the activation of relatively undifferentiated cells in somatic tissues. However, this review covers the most important factors involved in the process of plant regeneration and discusses the mechanisms by which plants monitor this process.

Multi-tissue to whole plant metabolic modelling

Genome-scale metabolic models have been successfully applied to study the metabolism of multiple plant species in the past decade. While most existing genome-scale modelling studies have focussed on studying the metabolic behaviour of individual plant metabolic systems, there is an increasing focus on combining models of multiple tissues or organs to produce multi-tissue models that allow the investigation of metabolic interactions between tissues and organs. Multi-tissue metabolic models were constructed for multiple plants including Arabidopsis, barley, soybean and Setaria. These models were applied to study various aspects of plant physiology including the division of labour between organs, source and sink tissue relationship, growth of different tissues and organs and charge and proton balancing. In this review, we outline the process of constructing multi-tissue genome-scale metabolic models, discuss the strengths and challenges in using multi-tissue models, review the current status of plant multi-tissue and whole plant metabolic models and explore the approaches for integrating genome-scale metabolic models into multi-scale plant models.

High frequency in vitro regeneration of adventitious shoots in daylilies (Hemerocallis sp) stem tissue using thidiazuron

BACKGROUND

Daylilies are a lucrative crop used for its floral beauty, medicinal proprieties, landscaping, fire prevention, nutritional value, and research. Despite the importance, daylilies remain extremely challenging for multiplying in vitro. The response difficulty is exacerbated because a few good protocols for daylilies micropropagation are generally difficult to reproduce across genotypes. An efficient strategy, currently applied at Langston University, is to systematically explore individual tissues or organs for their potential to micropropagation. This article is a partial report of the investigation carried out under room environmental conditions and focuses on developing an efficient daylilies in vitro propagation protocol that uses the stem tissue as the principal explant.

RESULTS

In less than three months, using thidiazuron, the use of the stem tissue as the in vitro experimental explant was successful in inducing multiple shoots several folds greater than current daylilies shoot organogenesis protocols. The study showed that tissue culture can be conducted successfully under unrestricted room environmental conditions as well as under the controlled environment of a growth chamber. It also showed that splitting lengthwise stem explants formed multiple shoots several folds greater than cross-sectioned and inverted explants. Shoot conversion rate was mostly independent of the number of shoots formed per explants. The overall response was explant and genotype-dependent. Efficient responses were observed in all thidiazuron treatments.

CONCLUSION

An efficient protocol, which can be applied for mass multiple shoots formation using the daylilies stem tissue as the main explant, was successfully developed. This could lead to a broad and rapid propagation of the crop under an array of environmental conditions to meet the market demand and hasten exogenous gene transfer and breeding selection processes.

Auxin transport and stem vascular reconnection - has our thinking become canalized?

BACKGROUND

The presence of a polar auxin transport stream has long been correlated with the differentiation and patterning of vascular cells across vascular plants. As our understanding of auxin transport and vascular development has grown, so too has evidence for the correlation between these processes. However, a clear understanding of the cellular and molecular mechanisms driving this correlation has not been elucidated.

SCOPE

This article examines the hypothesis that canalization via polar auxin transport regulates vascular reconnection and patterning in the stem after wounding or grafting. We examine the evidence for the causal nature of the relationship and the suggested role that other hormones may play. Data are presented indicating that in grafted plants the degree of auxin transport may not always correlate with vascular reconnection. Furthermore, data on grafting success using plants with a range of hormone-related mutations indicate that these hormones may not be critical for vascular reconnection.

CONCLUSIONS

In the past, excellent work examining elements of auxin synthesis, transport and response in relation to vascular development has been carried out. However, new experimental approaches are required to test more directly the hypothesis that auxin transport regulates stem vascular reconnection after wounding or grafting. This could include studies on the timing of the re-establishment of auxin transport and vascular reconnection after grafting and the influence of auxin transport mutants and inhibitors on these processes using live imaging.

A Network-Guided Genetic Approach to Identify Novel Regulators of Adventitious Root Formation in Arabidopsis thaliana

Adventitious roots (ARs) are formed de novo during post-embryonic development from non-root tissues, in processes that are highly dependent on environmental inputs. Whole root excision from young seedlings has been previously used as a model to study adventitious root formation in Arabidopsis thaliana hypocotyls. To identify novel regulators of adventitious root formation, we analyzed adventitious rooting in the hypocotyl after whole root excision in 112 T-DNA homozygous leaf mutants, which were selected based on the dynamic expression profiles of their annotated genes during hormone-induced and wound-induced tissue regeneration. Forty-seven T-DNA homozygous lines that displayed low rooting capacity as regards their wild-type background were dubbed as the less adventitious roots (lars) mutants. We identified eight lines with higher rooting capacity than their wild-type background that we named as the more adventitious roots (mars) mutants. A relatively large number of mutants in ribosomal protein-encoding genes displayed a significant reduction in adventitious root number in the hypocotyl after whole root excision. In addition, gene products related to gibberellin (GA) biosynthesis and signaling, auxin homeostasis, and xylem differentiation were confirmed to participate in adventitious root formation. Nearly all the studied mutants tested displayed similar rooting responses from excised whole leaves, which suggest that their affected genes participate in shared regulatory pathways required for de novo organ formation in different organs.

Effects of the Extracts from Fruit and Stem of Camellia japonica on Induced Pluripotency and Wound Healing

Small molecules that improve reprogramming, stem cell properties, and regeneration can be widely applied in regenerative medicine. Natural plant extracts represent an abundant and valuable source of bioactive small molecules for drug discovery. Natural products themselves or direct derivatives of them have continued to provide small molecules that have entered clinical trials, such as anticancer and antimicrobial drugs. Here, we tested 3695 extracts from native plants to examine whether they can improve induced pluripotent stem cell (iPSC) generation using genetically homogeneous secondary mouse embryonic fibroblasts (MEFs) harboring doxycycline (dox)-inducible reprograming transgenes. Among the tested extracts, extracts from the fruit and stem of Camellia japonica (CJ) enhanced mouse and human iPSC generation and promoted efficient wound healing in an in vivo mouse wound model. CJ is one of the best-known species of the genus Camellia that belongs to the Theaceae family. Our findings identified the natural plant extracts from the fruit and stem of CJ as novel regulators capable of enhancing cellular reprogramming and wound healing, providing a useful supplement in the development of a more efficient and safer method to produce clinical-grade iPSCs and therapeutics.

Callus Initiation from Root Explants Employs Different Strategies in Rice and Arabidopsis

Callus formation in tissue culture follows the rooting pathway, and newly formed callus seems to be a group of root primordium-like cells. However, it is not clear whether there are multiple mechanisms of callus initiation in different species and in different organs. Here we show that the OsIAA11-mediated pathway is specifically and strictly required for callus initiation in the lateral root (LR) formation region of the primary root (PR) but not for callus initiation at the root tip or the stem base in rice. OsIAA11 and its Arabidopsis homolog AtIAA14 are key players in lateral rooting. However, the AtIAA14-mediated pathway is not strictly required for callus initiation in the LR formation region in Arabidopsis. LRs can be initiated through either the AtIAA14-mediated or AtWOX11-mediated pathway in the Arabidopsis PR, therefore providing optional pathways for callus initiation. In contrast, OsIAA11 is strictly required for lateral rooting in the rice PR, meaning that the OsIAA11 pathway is the only choice for callus initiation. Our study suggests that multiple pathways may converge to WOX5 activation during callus formation in different organs and different species.

Stem cells and plant regeneration

Multicellular organisms show the ability to replace damage cells, tissues and even whole organs through regeneration mechanisms. Plants show a remarkable regenerative potential. While the basic principles of plant regeneration have been known for a number of decades, the molecular and cellular mechanisms underlying such principles are currently starting to emerge. Some of these mechanisms point to the existence of highly reprogrammable cells. Developmental plasticity is a hallmark for stem cells, and stem cells are responsible for the generation of distinctive cell types forming plants. In the last years, a number of players and molecular mechanism regulating stem cell maintenance have been described, and some of them have also been involved in regenerative processes. These discoveries in plant stem cell regulation and regeneration invite us to rethink several of the classical concepts in plant biology such as cell fate specification and even the actual meaning of what we consider stem cells in plants. In this review we will cover some of these discoveries, focusing on the role of the plant stem cell function and regulation during cell and organ regeneration.

Intermediate Developmental Phases During Regeneration

The initial view that regeneration can be a continuum in terms of regulatory mechanisms is gradually changing, and recent evidence points towards the presence of discrete regulatory steps and intermediate phases. Furthermore, regeneration presents an excellent example of a process generating order and pattern, i.e. a self-organization process. It is likely that the process traverses a set of intermediate phases before reaching an endpoint. Although some progress has been made in deciphering the identity of these intermediate phases, a lot more work is needed to derive a comprehensive and complete picture. Here, we discuss the intermediate developmental phases in plant regeneration and compare them with the possible intermediate developmental phases in animal regeneration.

De novo root regeneration from leaf explants: wounding, auxin, and cell fate transition

Root organogenesis after tissue damage is a type of plant regeneration known as de novo root regeneration (DNRR). The DNRR process is widely exploited in agricultural technologies, such as cuttings for vegetative propagation. This review summarizes recent advances in our understanding of the cellular and molecular framework of DNRR, mainly focusing on rooting from Arabidopsis thaliana leaf explants. The framework comprises three successive phases, that is, early signaling, auxin accumulation, and cell fate transition, and involves two types of cells with different functions: the converter cell that converts the early signals as the input into auxin flux as the output; and the regeneration-competent cell that undergoes fate transition guided by auxin.

An Alternative Nested Reading Frame May Participate in the Stress-Dependent Expression of a Plant Gene

Although plants as sessile organisms are affected by a variety of stressors in the field, the stress factors for the above-ground and underground parts of the plant and their gene expression profiles are not the same. Here, we investigated NbKPILP, a gene encoding a new member of the ubiquitous, pathogenesis-related Kunitz peptidase inhibitor (KPI)-like protein family, that we discovered in the genome of Nicotiana benthamiana and other representatives of the Solanaceae family. The NbKPILP gene encodes a protein that has all the structural elements characteristic of KPI but in contrast to the proven A. thaliana KPI (AtKPI), it does not inhibit serine peptidases. Unlike roots, NbKPILP mRNA and its corresponding protein were not detected in intact leaves, but abiotic and biotic stressors drastically affected NbKPILP mRNA accumulation. In search of the causes of suppressed NbKPILP mRNA accumulation in leaves, we found that the NbKPILP gene is "matryoshka," containing an alternative nested reading frame (ANRF) encoding a 53-amino acid (aa) polypeptide (53aa-ANRF) which has an amphipathic helix (AH). We confirmed ANRF expression experimentally. A vector containing a GFP-encoding sequence was inserted into the NbKPILP gene in frame with 53aa-ANRF, resulting in a 53aa-GFP fused protein that localized in the membrane fraction of cells. Using the 5'-RACE approach, we have shown that the expression of ANRF was not explained by the existence of a cryptic promoter within the NbKPILP gene but was controlled by the maternal NbKPILP mRNA. We found that insertion of mutations destroying the 53aa-ANRF AH resulted in more than a two-fold increase of the NbKPILP mRNA level. The NbKPILP gene represents the first example of ANRF functioning as a repressor of a maternal gene in an intact plant. We proposed a model where the stress influencing the translation initiation promotes the accumulation of NbKPILP and its mRNA in leaves.

Mechanical wounding promotes local and long distance response in the halophyte Cakile maritima through the involvement of the ROS and RNS metabolism

Mechanical wounding in plants, which are capable of generating defense responses possibly associated with nitro-oxidative stress, can be caused by (a)biotic factors such as rain, wind, herbivores and insects. Sea rocket (Cakile maritima L.), a halophyte plant belonging to the mustard family Brassicaceae, is commonly found on sandy coasts throughout Europe. Using 7-day-old Cakile maritima L. seedlings, mechanical wounding was induced in hypocotyls by pinching with a striped-tip forceps; after 3 h, several biochemical parameters were analyzed in both the damaged and unwounded organs (green cotyledons and roots). We thus determined NO production, H₂O₂ content, lipid oxidation as well as protein nitration patterns; we also identified several antioxidant enzymes including catalase, superoxide dismutase (SOD) isozymes, peroxidases, ascorbate-glutathione cycle enzymes and NADP-dehydrogenases. All these parameters were differentially modulated in the damaged (hypocotyls) and unwounded organs, which clearly indicated an induction of CuZnSOD V in the three organs, an increase in protein nitration in green cotyledons and an induction of NADP-isocitrate dehydrogenase activity in roots. On the whole, our results indicate that the wounding of hypocotyls, which showed an active ROS metabolism and oxidative stress, causes long-distance signals that also trigger responses in unwounded tissues with a more active RNS metabolism. These data therefore confirm the existence of local and long-distance responses which counteract negative effects and provide appropriate responses, enabling the wounded seedlings to survive.

The ISWI remodeler in plants: protein complexes, biochemical functions, and developmental roles

Imitation Switch (ISWI) is a member of the ATP-dependent chromatin remodeling factor family, whose members move or restructure nucleosomes using energy derived from ATP hydrolysis. ISWI proteins are conserved in eukaryotes and usually form complexes with DDT (DNA-binding homeobox and different transcription factors)-domain proteins. Here, we review recent research on ISWI in the model plant Arabidopsis thaliana (AtISWI). AtISWI forms complexes with AtDDT-domain proteins, many of which have domain structures that differ from those of DDT-domain proteins in yeast and animals. This might suggest that plant ISWI complexes have unique roles. In vivo studies have shown that AtISWI is involved in the formation of the evenly spaced pattern of nucleosome arrangement in gene bodies-this pattern is associated with high transcriptional levels of genes. In addition, AtISWI and the AtDDT-domain protein RINGLET (RLT) are involved in many developmental processes in A. thaliana, including meristem fate transition and organ formation. Studies on the functions of AtISWI may shed light on how chromatin remodeling functions in plants and also provide new information about the evolution of ISWI remodeling complexes in eukaryotes.

Wound signaling: The missing link in plant regeneration

Wounding is the first event that occurs in plant regeneration. However, wound signaling in plant regeneration is barely understood. Using a simple system of de novo root organogenesis from Arabidopsis thaliana leaf explants, we analyzed the genes downstream of wound signaling. Leaf explants may produce at least two kinds of wound signals to trigger short-term and long-term wound signaling. Short-term wound signaling is primarily involved in controlling auxin behavior and the fate transition of regeneration-competent cells, while long-term wound signaling mainly modulates the cellular environment at the wound site and maintains the auxin level in regeneration-competent cells. YUCCA (YUC) genes, which are involved in auxin biogenesis, are targets of short-term wound signaling in mesophyll cells and of long-term wound signaling in regeneration-competent cells. The expression patterns of YUCs provide important information about the molecular basis of wound signaling in plant regeneration.