Cytokinin-CLAVATA cross-talk is an ancient mechanism regulating shoot meristem homeostasis in land plants

CLE peptides act via the receptor-like kinase CRINKLY 4 in Physcomitrium patens gametophore development

The CLAVATA pathway plays a key role in the regulation of multicellular shoot and root meristems in flowering plants. In Arabidopsis, CLAVATA 3-like signaling peptides (CLEs) act via receptor-like kinases CLAVATA 1 and CRINKLY 4 (CR4). In the moss Physcomitrium patens, PpCLAVATA and PpCR4 were previously studied independently and shown to play conserved roles in the regulation of cell proliferation and differentiation. The plant calpain DEFECTIVE KERNEL 1 (DEK1) has been identified as another key regulator of cell division and cell fate in vascular plants and bryophytes. The functional interaction between CLAVATA, CR4, and DEK1 remains unknown. Here, we show that P. patens crinkly4 and dek1 mutants respond differently to CLE peptide treatments suggesting their distinct roles in the CLAVATA pathway. Reduced CLAVATA-mediated suppression of leafy shoot growth in Δcr4 mutants indicates that PpCR4 is involved in CLV3p perception, most likely as a receptor. The CLV3p strongly suppressed leaf vein development in Δcr4 mutants, suggesting that other receptors are involved in these processes and indicating a potential role of PpCR4 in organ sensitization to CLEs.

Identification of a novel gene, Bryophyte Co-retained Gene 1, that has a positive role in desiccation tolerance in the moss Physcomitrium patens

The moss Physcomitrium patens is a model system for the evolutionary study of land plants, and as such, it may contain as yet unannotated genes with functions related to the adaptation to water deficiency that was required during the water-to-land transition. In this study, we identified a novel gene, Bryophyte Co-retained Gene 1 (BCG1), in P. patens that is responsive to dehydration and rehydration. Under de- and rehydration treatments, BCG1 was significantly co-expressed with DHNA, which encodes a dehydrin (DHN). Examination of previous microarray data revealed that BCG1 is highly expressed in spores, archegonia (female reproductive organ), and mature sporophytes. In addition, the bcg1 mutant showed reduced dehydration tolerance, and this was accompanied by a relatively low level of chlorophyll content during recovery. Comprehensive transcriptomics uncovered a detailed set of regulatory processes that were affected by the disruption to BCG1. Experimental evidence showed that BCG1 might function in antioxidant activity, the abscisic acid pathway, and in intracellular Ca2+ homeostasis to resist desiccation. Overall, our results provide insights into the role of a bryophyte co-retained gene in desiccation tolerance.

Cytokinin and ALOG proteins regulate pluripotent stem cell identity in the moss Physcomitrium patens

The shoot apical meristem (SAM) contains pluripotent stem cells that produce all the aerial parts of the plant. Stem cells undergo asymmetric cell divisions to self-renew and to produce differentiating cells. Our research focused on unraveling the mechanisms governing the specification of these two distinct cell fates following the stem cell division. For this purpose, we used the model organism Physcomitrium patens, which features a singular pluripotent stem cell known as the gametophore apical cell. We show that the activity of cytokinins, critical stem cell regulators, is restricted to the gametophore apical cell due to the specific localization of PpLOG, the enzyme responsible for cytokinin activation. In turn, PpTAW, which promotes differentiating cell identity of the merophyte, is excluded from the gametophore apical cell by the action of cytokinins. We propose a cytokinin-based model for the establishment of asymmetry in the pluripotent stem cell division.

Male Germ Cell Specification in Plants

Germ cells (GCs) serve as indispensable carriers in both animals and plants, ensuring genetic continuity across generations. While it is generally acknowledged that the timing of germline segregation differs significantly between animals and plants, ongoing debates persist as new evidence continues to emerge. In this review, we delve into studies focusing on male germ cell specifications in plants, and we summarize the core gene regulatory circuits in germ cell specification, which show remarkable parallels to those governing meristem homeostasis. The similarity in germline establishment between animals and plants is also discussed.

Re-examining meristems through the lens of evo-devo

The concept of the meristem was introduced in 1858 to characterize multicellular, formative, and proliferative tissues that give rise to the entire plant body, based on observations of vascular plants. Although its original definition did not encompass bryophytes, this concept has been used and continuously refined over the past 165 years to describe the diverse apices of all land plants. Here, we re-examine this matter in light of recent evo-devo research and show that, despite displaying high anatomical diversity, land plant meristems are unified by shared genetic control. We also propose a modular view of meristem function and highlight multiple evolutionary mechanisms that are likely to have contributed to the assembly and diversification of the varied meristems during the course of plant evolution.

Hormonal and genetic control of pluripotency in bryophyte model systems

Land plant meristems are reservoirs of pluripotent stem cells where new tissues emerge, grow and eventually differentiate into specific cell identities. Compared to algae, where cells are produced in two-dimensional tissues via tip or marginal growth, land plants have meristems that allow three-dimensional growth for successful exploration of the terrestrial environment. In land plants, meristem maintenance leads to indeterminate growth and the production of new meristems leads to branching or regeneration via reprogramming of wounded somatic cells. Emerging model systems in the haploid dominant and monophyletic bryophytes are allowing comparative analyses of meristem gene regulatory networks to address whether all plants use common or diverse programs to organise, maintain, and regenerate meristems. In this piece we aim to discuss recent advances in genetic and hormonal control of bryophyte meristems and possible convergence or discrepancies in an exciting and emerging field in plant biology.

Cultivating potential: Harnessing plant stem cells for agricultural crop improvement

Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement. Developmental regulators control the balance and rate of cell divisions within the meristem. Altering these regulators impacts meristem architecture and, as a consequence, plant form. In this review, we discuss genes involved in regulating the shoot apical meristem, inflorescence meristem, axillary meristem, root apical meristem, and vascular cambium in plants. We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns. Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible. We discuss recent advances on plant transformation made possible by studying genes controlling meristem development. Finally, we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.

The ratio of auxin to cytokinin controls leaf development and meristem initiation in Physcomitrium patens

Crosstalk between auxin and cytokinin contributes to widespread developmental processes, including root and shoot meristem maintenance, phyllotaxy, and vascular patterning. However, our understanding of crosstalk between these hormones is limited primarily to angiosperms. The moss Physcomitrium patens (formerly Physcomitrella patens) is a powerful system for studying plant hormone function. Auxin and cytokinin play similar roles in regulating moss gametophore (shoot) architecture, to those in flowering plant shoots. However, auxin-cytokinin crosstalk is poorly understood in moss. Here we find that the ratio of auxin to cytokinin is an important determinant of development in P. patens, especially during leaf development and branch stem cell initiation. Addition of high levels of auxin to P. patens gametophores blocks leaf outgrowth. However, simultaneous addition of high levels of both auxin and cytokinin partially restores leaf outgrowth, suggesting that the ratio of these hormones is the predominant factor. Likewise, during branch initiation and outgrowth, chemical inhibition of auxin synthesis phenocopies cytokinin application. Finally, cytokinin-insensitive mutants resemble plants with altered auxin signaling and are hypersensitive to auxin. In summary, our results suggest that the ratio between auxin and cytokinin signaling is the basis for developmental decisions in the moss gametophore.

Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification

PREMISE

Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear.

METHODS

Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.

RESULTS

The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology.

CONCLUSIONS

We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.

Complex peptide hormone signaling in plant stem cells

Peptide hormones influence diverse aspects of plant development through highly coordinated cell-cell signaling pathways. Many peptide hormone families play key roles in stem cell maintenance across land plants. In this review, we focus on recent work in two conserved peptide hormone families, CLAVATA3/EMBRYO-SURROUNDING REGION (CLEs) and ROOT MERISTEM GROWTH FACTOR (RGFs), and their roles in regulating plant stem cells. We discuss recent work establishing downstream crosstalk between peptide hormones and other conserved signaling mechanisms in meristem maintenance as well as highlight advances in peptide hormone gene identification that provide important context for CLE/RGF family evolution across diverse plant lineages. CLE and RGF gene families have greatly expanded in angiosperms, contributing to the complex genetic regulation of stem cell homeostasis observed in model systems over the last 30 years. Peptide hormone duplications have resulted in genetic compensation mechanisms that ensure robust development through the function of paralogous genes. Broad conservation of genetic compensation across angiosperms highlights the importance of these mechanisms in developmental signaling and understanding their regulation could inform broader understanding of morphological diversity and evolutionary innovation.

What can hornworts teach us?

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

Advances in Receptor-like Protein Kinases in Balancing Plant Growth and Stress Responses

Accompanying the process of growth and development, plants are exposed to ever-changing environments, which consequently trigger abiotic or biotic stress responses. The large protein family known as receptor-like protein kinases (RLKs) is involved in the regulation of plant growth and development, as well as in the response to various stresses. Understanding the biological function and molecular mechanism of RLKs is helpful for crop breeding. Research on the role and mechanism of RLKs has recently received considerable attention regarding the balance between plant growth and environmental adaptability. In this paper, we systematically review the classification of RLKs, the regulatory roles of RLKs in plant development (meristem activity, leaf morphology and reproduction) and in stress responses (disease resistance and environmental adaptation). This review focuses on recent findings revealing that RLKs simultaneously regulate plant growth and stress adaptation, which may pave the way for the better understanding of their function in crop improvement. Although the exact crosstalk between growth constraint and plant adaptation remains elusive, a profound study on the adaptive mechanisms for decoupling the developmental processes would be a promising direction for the future research.

Cell Division and Meristem Dynamics in Fern Gametophytes

One of the most important questions in all multicellular organisms is how to define and maintain different cell fates during continuous cell division and proliferation. Plant meristems provide a unique research system to address this fundamental question because meristems dynamically maintain themselves and sustain organogenesis through balancing cell division and cell differentiation. Different from the gametophytes of seed plants that depend on their sporophytes and lack meristems, the gametophytes of seed-free ferns develop different types of meristems (including apical cell-based meristems and multicellular apical and marginal meristems) to promote independent growth and proliferation during the sexual gametophyte phase. Recent studies combining confocal time-lapse imaging and computational image analysis reveal the cellular basis of the initiation and proliferation of different types of meristems in fern gametophytes, providing new insights into the evolution of meristems in land plants. In this review, we summarize the recent progress in understanding the cell growth dynamics in fern gametophytes and discuss both conserved and diversified mechanisms underlying meristem cell proliferation in seed-free vascular plants.

CURLY LEAF is required for the auxin-dependent regulation of 3-dimensional growth specification in Physcomitrium patens

The no gametophores 4 ( nog4-R ) mutant cannot make the transition from 2-dimensional (2D) to 3-dimensional (3D) growth in Physcomitrium patens and forms side branch initials that are largely fated to become sporophyte-like structures. We describe the three different developmental trajectories adopted by the nog4-R mutant, all of which result in indeterminate growth and defects in cell division plane orientation. A candidate gene approach confirmed that the causative mutation resided in the CURLY LEAF gene, and we highlight a previously uncharacterized role for CURLY LEAF in maintaining auxin homeostasis in P. patens .

Unravelling 3D growth in the moss Physcomitrium patens

The colonization of land by plants, and the greening of the terrestrial biosphere, was one of the most important events in the history of life on Earth. The transition of plants from water to land was accompanied, and largely facilitated, by the acquisition of apical cells with three or more cutting faces (3D growth). This enabled plants to develop the morphological characteristics required to survive and reproduce effectively on land and to colonize progressively drier habitats. Most plants develop in such a way that makes genetic studies of 3D growth difficult as the onset of 3D growth is established early during embryo development. On the other hand, in the moss Physcomitrium patens, the onset of 3D growth is preceded by a protracted 2D filamentous phase of the life cycle that can be continuously propagated. P. patens is an ideal model system in which to identify the genetic toolkit underpinning the 2D to 3D growth transition, and this is because 3D growth is not a pre-requisite for survival. Thus, insights into the mechanisms underpinning the formation of apical cells and the subsequent establishment and maintenance of 3D growth have largely been gained through studies in P. patens. This review summarizes the most recently published articles that have provided new and important insights into the mechanisms underpinning 3D growth in P. patens.

How was apical growth regulated in the ancestral land plant? Insights from the development of non-seed plants

Land plant life cycles are separated into distinct haploid gametophyte and diploid sporophyte stages. Indeterminate apical growth evolved independently in bryophyte (moss, liverwort, and hornwort) and fern gametophytes, and tracheophyte (vascular plant) sporophytes. The extent to which apical growth in tracheophytes co-opted conserved gametophytic gene networks, or exploited ancestral sporophytic networks, is a long-standing question in plant evolution. The recent phylogenetic confirmation of bryophytes and tracheophytes as sister groups has led to a reassessment of the nature of the ancestral land plant. Here, we review developmental genetic studies of apical regulators and speculate on their likely evolutionary history.

Evolution of meristem zonation by CLE gene duplication in land plants

In angiosperms, a negative feedback pathway involving CLAVATA3 (CLV3) peptide and WUSCHEL transcription factor maintains the stem-cell population in the shoot apical meristem and is central for continued shoot growth and organogenesis. An intriguing question is how this cell-signalling system was established during the evolution of land plants. On the basis of two recent studies on CLV3/ESR-related (CLE) genes, this paper proposes a model for the evolution of meristem zonation. The model suggests that a stem-cell-limiting CLV3 pathway is derived from stem-cell-promoting CLE pathways conserved in land pants by gene duplication in the angiosperm lineage. The model can be examined in the future by genomic and developmental studies on diverse plant species.