The DEK1 Calpain Linker Functions in Three-Dimensional Body Patterning in Physcomitrella patens

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.

Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens

Calpains are cysteine proteases that control cell fate transitions whose loss of function causes severe, pleiotropic phenotypes in eukaryotes. Although mainly considered as modulatory proteases, human calpain targets are directed to the N-end rule degradation pathway. Several such targets are transcription factors, hinting at a gene-regulatory role. Here, we analyze the gene-regulatory networks of the moss Physcomitrium patens and characterize the regulons that are misregulated in mutants of the calpain DEFECTIVE KERNEL1 (DEK1). Predicted cleavage patterns of the regulatory hierarchies in five DEK1-controlled subnetworks are consistent with a pleiotropic and regulatory role during cell fate transitions targeting multiple functions. Network structure suggests DEK1-gated sequential transitions between cell fates in 2D-to-3D development. Our method combines comprehensive phenotyping, transcriptomics and data science to dissect phenotypic traits, and our model explains the protease function as a switch gatekeeping cell fate transitions potentially also beyond plant development.

Membrane-anchored calpains - hidden regulators of growth and development beyond plants?

Calpains are modulatory proteases that modify diverse cellular substrates and play essential roles in eukaryots. The best studied are animal cytosolic calpains. Here, we focus on enigmatic membrane-anchored calpains, their structural and functional features as well as phylogenetic distribution. Based on domain composition, we identified four types of membrane-anchored calpains. Type 1 and 2 show broad phylogenetic distribution among unicellular protists and streptophytes suggesting their ancient evolutionary origin. Type 3 and 4 diversified early and are present in brown algae and oomycetes. The plant DEK1 protein is the only representative of membrane-anchored calpains that has been functionally studied. Here, we present up to date knowledge about its structural features, putative regulation, posttranslational modifications, and biological role. Finally, we discuss potential model organisms and available tools for functional studies of membrane-anchored calpains with yet unknown biological role. Mechanistic understanding of membrane-anchored calpains may provide important insights into fundamental principles of cell polarization, cell fate control, and morphogenesis beyond plants.

Improved prime editing allows for routine predictable gene editing in Physcomitrium patens

Efficient and precise gene editing is the gold standard of any reverse genetic study. The recently developed prime editing approach, a modified CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein] editing method, has reached the precision goal but its editing rate can be improved. We present an improved methodology that allows for routine prime editing in the model plant Physcomitrium patens, whilst exploring potential new prime editing improvements. Using a standardized protoplast transfection procedure, multiple prime editing guide RNA (pegRNA) structural and prime editor variants were evaluated targeting the APT reporter gene through direct plant selection. Together, enhancements of expression of the prime editor, modifications of the 3' extension of the pegRNA, and the addition of synonymous mutation in the reverse transcriptase template sequence of the pegRNA dramatically improve the editing rate without affecting the quality of the edits. Furthermore, we show that prime editing is amenable to edit a gene of interest through indirect selection, as demonstrated by the generation of a Ppdek10 mutant. Additionally, we determine that a plant retrotransposon reverse transcriptase enables prime editing. Finally, we show for the first time the possibility of performing prime editing with two independently coded peptides.

Genome-wide alternative polyadenylation dynamics underlying plant growth retardant-induced dwarfing of pomegranate

Dwarfed stature is a desired agronomic trait for pomegranate (Punica granatum L.), with its advantages such as lower cost and increased yield. A comprehensive understanding of regulatory mechanisms underlying the growth repression would provide a genetic foundation to molecular-assisted dwarfing cultivation of pomegranate. Our previous study induced dwarfed pomegranate seedlings via exogenous application of plant growth retardants (PGRs) and highlighted the important roles of differential expression of plant growth-related genes in eliciting the dwarfed phenotype of pomegranate. Alternative polyadenylation (APA) is an important post-transcriptional mechanism and has been demonstrated to act as a key regulator in plant growth and development. However, no attention has been paid to the role of APA in PGR-induced dwarfing in pomegranate. In this study, we characterized and compared APA-mediated regulation events underlying PGR-induced treatments and normal growth condition. Genome-wide alterations in the usage of poly(A) sites were elicited by PGR treatments, and these changes were involved in modulating the growth and development of pomegranate seedlings. Importantly, ample specificities were observed in APA dynamics among the different PGR treatments, which mirrors their distinct nature. Despite the asynchrony between APA events and differential gene expression, APA was found to regulate transcriptome via influencing microRNA (miRNA)-mediated mRNA cleavage or translation inhibition. A global preference for lengthening of 3' untranslated regions (3' UTRs) was observed under PGR treatments, which was likely to host more miRNA target sites in 3' UTRs and thus suppress the expression of the corresponding genes, especially those associated with developmental growth, lateral root branching, and maintenance of shoot apical meristem. Together, these results highlighted the key role of APA-mediated regulations in fine-tuning the PGR-induced dwarfed stature of pomegranate, which provides new insights into the genetic basis underlying the growth and development of pomegranate.

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.

The bryophytes Physcomitrium patens and Marchantia polymorpha as model systems for studying evolutionary cell and developmental biology in plants

Bryophytes are nonvascular spore-forming plants. Unlike in flowering plants, the gametophyte (haploid) generation of bryophytes dominates the sporophyte (diploid) generation. A comparison of bryophytes with flowering plants allows us to answer some fundamental questions raised in evolutionary cell and developmental biology. The moss Physcomitrium patens was the first bryophyte with a sequenced genome. Many cell and developmental studies have been conducted in this species using gene targeting by homologous recombination. The liverwort Marchantia polymorpha has recently emerged as an excellent model system with low genomic redundancy in most of its regulatory pathways. With the development of molecular genetic tools such as efficient genome editing, both P. patens and M. polymorpha have provided many valuable insights. Here, we review these advances with a special focus on polarity formation at the cell and tissue levels. We examine current knowledge regarding the cellular mechanisms of polarized cell elongation and cell division, including symmetric and asymmetric cell division. We also examine the role of polar auxin transport in mosses and liverworts. Finally, we discuss the future of evolutionary cell and developmental biological studies in plants.

PpGRAS12 acts as a positive regulator of meristem formation in Physcomitrium patens

This study focused on the key regulatory function of Physcomitrium patens GRAS12 gene underlying an increasing plant complexity, an important step in plant terrestrialization and the evolutionary history of life. The miR171-GRAS module has been identified as a key player in meristem maintenance in angiosperms. PpGRAS12 is a member of the GRAS family and a validated target for miR171 in Physcomitrium (Physcomitrella) patens. Here we show a regulatory function of miR171 at the gametophytic vegetative growth stage and targeted deletion of the PpGRAS12 gene adversely affects sporophyte production since fewer sporophytes were produced in ΔPpGRAS12 knockout lines compared to wild type moss. Furthermore, highly specific and distinct growth arrests were observed in inducible PpGRAS12 overexpression lines at the protonema stage. Prominent phenotypic aberrations including the formation of multiple apical meristems at the gametophytic vegetative stage in response to elevated PpGRAS12 transcript levels were discovered via scanning electron microscopy. The production of multiple buds in the PpGRAS12 overexpression lines similar to ΔPpCLV1a/1b disruption mutants is accompanied by an upregulation of PpCLE and downregulation of PpCLV1, PpAPB, PpNOG1, PpDEK1, PpRPK2 suggesting that PpGRAS12 acts upstream of these genes and negatively regulates the proposed pathway to specify simplex meristem formation. As CLV signaling pathway components are not present in the chlorophytic or charophytic algae and arose with the earliest land plants, we identified a key regulatory function of PpGRAS12 underlying an increasing plant complexity, an important step in plant terrestrialization and the evolutionary history of life.

Physcomitrium patens: A Single Model to Study Oriented Cell Divisions in 1D to 3D Patterning

Development in multicellular organisms relies on cell proliferation and specialization. In plants, both these processes critically depend on the spatial organization of cells within a tissue. Owing to an absence of significant cellular migration, the relative position of plant cells is virtually made permanent at the moment of division. Therefore, in numerous plant developmental contexts, the (divergent) developmental trajectories of daughter cells are dependent on division plane positioning in the parental cell. Prior to and throughout division, specific cellular processes inform, establish and execute division plane control. For studying these facets of division plane control, the moss Physcomitrium (Physcomitrella) patens has emerged as a suitable model system. Developmental progression in this organism starts out simple and transitions towards a body plan with a three-dimensional structure. The transition is accompanied by a series of divisions where cell fate transitions and division plane positioning go hand in hand. These divisions are experimentally highly tractable and accessible. In this review, we will highlight recently uncovered mechanisms, including polarity protein complexes and cytoskeletal structures, and transcriptional regulators, that are required for 1D to 3D body plan formation.

Challenges of in vivo protein localization in plants seen through the DEK1 protein lens

During the last 25 y, fluorescent protein tagging has become a tool of choice to investigate protein function in a cellular context. The information gathered with this approach is not only providing insights into protein subcellular localization but also allows contextualizing protein function in multicellular settings. Here we illustrate the power of this method by commenting on the recent successful localization of the large membrane DEK1 protein during three-dimensional body formation in the moss Physcomitrella patens. But as many approaches, protein tagging is not exempt of caveats. The multiple infructuous (failed) attempts to detect DEK1 using a fluorescent protein tag present a good overview of such potential problems. Here we discuss the insertion of different fluorescent proteins at different positions in the PpDEK1 protein and the resulting unintended range of mutant phenotypes. Albeit none of these mutants generated a detectable fluorescent signal they can still provide interesting biological information about DEK1 function.

Genetic Regulation of the 2D to 3D Growth Transition in the Moss Physcomitrella patens

One of the most important events in the history of life on earth was the colonization of land by plants; this transition coincided with and was most likely enabled by the evolution of 3-dimensional (3D) growth. Today, the diverse morphologies exhibited across the terrestrial biosphere arise from the differential regulation of 3D growth processes during development. In many plants, 3D growth is initiated during the first few divisions of the zygote, and therefore, the genetic basis cannot be dissected because mutants do not survive. However, in mosses, which are representatives of the earliest land plants, 3D shoot growth is preceded by a 2D filamentous phase that can be maintained indefinitely. Here, we used the moss Physcomitrella patens to identify genetic regulators of the 2D to 3D transition. Mutant screens yielded individuals that could only grow in 2D, and through an innovative strategy that combined somatic hybridization with bulk segregant analysis and genome sequencing, the causative mutation was identified in one of them. The NO GAMETOPHORES 1 (NOG1) gene, which encodes a ubiquitin-associated protein, is present only in land plant genomes. In mutants that lack PpNOG1 function, transcripts encoding 3D-promoting PpAPB transcription factors [1] are significantly reduced, and apical initial cells specified for 3D growth are not formed. PpNOG1 acts at the earliest identified stage of the 2D to 3D transition, possibly through degradation of proteins that suppress 3D growth. The acquisition of NOG1 function in land plants could thus have enabled the evolution and development of 3D morphology.

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NO GAMETOPHORES 1 (PpNOG1) regulates the 2D to 3D growth transition in P. patens

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PpNOG1 acts upstream of 3D-promoting PpAPB transcription factors

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PpNOG1 is required for the formation of apical initial cells specified for 3D growth

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NOG1 genes are found only in land plants and thus evolved coincident with 3D growth

An intragenic mutagenesis strategy in Physcomitrella patens to preserve intron splicing

Gene targeting is a powerful reverse genetics technique for site-specific genome modification. Intrinsic homologous recombination in the moss Physcomitrella patens permits highly effective gene targeting, a characteristic that makes this organism a valuable model for functional genetics. Functional characterization of domains located within a multi-domain protein depends on the ability to generate mutants harboring genetic modifications at internal gene positions while maintaining the reading-frames of the flanking exons. In this study, we designed and evaluated different gene targeting constructs for targeted gene manipulation of sequences corresponding to internal domains of the DEFECTIVE KERNEL1 protein in Physcomitrella patens. Our results show that gene targeting-associated mutagenesis of introns can have adverse effects on splicing, corrupting the normal reading frame of the transcript. We show that successful genetic modification of internal sequences of multi-exon genes depends on gene-targeting strategies which insert the selection marker cassette into the 5' end of the intron and preserve the nucleotide sequence of the targeted intron.