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ent-Kaurene is a biosynthetic intermediate diterpene of phytohormone gibberellins, and is biosynthesized from geranylgeranyl diphosphate via ent-copalyl diphosphate (ent-CDP). The successive cyclization is catalyzed by two distinct diterpene synthases, ent-CDP synthase (ent-CPS) and ent-kaurene synthase (KS). Homologs of these diterpene synthase genes have been reported to be involved in the biosynthesis of specialized-metabolic diterpenoids for defense in several plant species, including rice (Oryza sativa). These diterpene synthases consist of three domains, αβγ domains. Active sites of ent-CPS exist at the interface of β and γ domain, while those of KS are located within the α domain. We herein carried out domain-deletion experiments using several KSs and KS like enzymes (KSLs) to obtain insights into the roles of domains other than active-site domains. As previously reported in taxadiene synthase, deletion of γ or βγ domains drastically decreased activities of specialized-metabolic OsKSL5, OsKSL8, OsKSL7 and OsKSL10 in O. sativa. However, unexpectedly, only α domains of several gibberellin-biosynthetic KSs, including OsKS1 in O. sativa, AtKS in Arabidopsis thaliana, TaKS in wheat (Triticum aestivum) and BdKS1 in Brachypodium distachyon, retained their original functions. Additionally, the specialized-metabolic OsKSL4, which is closely related to OsKS1, also functioned without its βγ domains. Domain-swapping experiments showed that replacing βγ domains in OsKSL7 with those from other KS/KSLs retained the OsKSL7 activity. Moreover, deletion of βγ domains of bifunctional PpCPS/KS in moss (Physcomitrella patens) drastically impaired its KS-related activity. Thus, we demonstrate that monofunctional gibberellinbiosynthetic KSs are the unique diterpene synthases that retain their functions without βγ domains. [ABSTRACT FROM AUTHOR]

Zinc-finger homeodomain transcription factors (ZF-HD TFs) are relatively a small gene family in Arabidopsis involved in plant development and stress response. However, the biological functions of ZF-HD TFs remain largely undiscovered. Here, we aimed to elucidate the evolutionary history and functional role of ZF-HD TFs in other species, by performing phylogenic analysis and domain and motif identification studies in Arabidopsis, sorghum (Sorghum bicolor), and moss (Physcomitrella patens). Forty-two ZF-HD TF proteins were classified into two distinct subfamilies based on the conserved ZF Cys/His-rich dimerization and homeodomain (HD) domains. The phylogenetic tree of proteins was further divided into five groups based on the similarity of sequences, and three distinct motifs were defined in the amino acid sequences. Genetic analysis revealed that the moss PpZF-HD1, Pp3c1_15290, gene partially rescued the amiR zf-HD-79 mutant lines at phenotypic and molecular levels. Subcellular localization studies revealed that moss PpZF-HD1 was localized in the cytosol and nuclei. Phylogenetic analysis and genetic complementation revealed that ZF-HD TFs play functional roles in regulating plant architecture, which is conserved in Arabidopsis, sorghum, and moss. Although our study is only a preliminary exploration into ZF-HD TFs, it provides a novel perspective that will help future researchers better understand the biological role of ZF-HD proteins in plants. [ABSTRACT FROM AUTHOR]

SUMMARY: Cells save their energy during nitrogen starvation by selective autophagy of ribosomes and degradation of RNA to ribonucleotides and nucleosides. Nucleosides are hydrolyzed by nucleoside N‐ribohydrolases (nucleosidases, NRHs). Subclass I of NRHs preferentially hydrolyzes the purine ribosides while subclass II is more active towards uridine and xanthosine. Here, we performed a crystallographic and kinetic study to shed light on nucleoside preferences among plant NRHs followed by in vivo metabolomic and phenotyping analyses to reveal the consequences of enhanced nucleoside breakdown. We report the crystal structure of Zea mays NRH2b (subclass II) and NRH3 (subclass I) in complexes with the substrate analog forodesine. Purine and pyrimidine catabolism are inseparable because nucleobase binding in the active site of ZmNRH is mediated via a water network and is thus unspecific. Dexamethasone‐inducible ZmNRH overexpressor lines of Arabidopsis thaliana, as well as double nrh knockout lines of moss Physcomitrium patents, reveal a fine control of adenosine in contrast to other ribosides. ZmNRH overexpressor lines display an accelerated early vegetative phase including faster root and rosette growth upon nitrogen starvation or osmotic stress. Moreover, the lines enter the bolting and flowering phase much earlier. We observe changes in the pathways related to nitrogen‐containing compounds such as β‐alanine and several polyamines, which allow plants to reprogram their metabolism to escape stress. Taken together, crop plant breeding targeting enhanced NRH‐mediated nitrogen recycling could therefore be a strategy to enhance plant growth tolerance and productivity under adverse growth conditions. [ABSTRACT FROM AUTHOR]

The moss Physcomitrium patens (P. patens), formerly known as Physcomitrella patens, has ascended to prominence as a pivotal model organism in plant biology. Its simplicity in structure and life cycle, coupled with genetic amenability, has rendered it indispensable in unraveling the complexities of land plant evolution and responses to environmental stimuli. As an evolutionary bridge between algae and vascular plants, P. patens offers a unique perspective on early terrestrial adaptation. This research involved the biotechnological cultivation of P. patens, followed by a deep phytochemical investigation of two extracts covering a large polarity range together using an NMR-based dereplication approach combined with GC/MS analyses. Subsequently, a multidisciplinary approach combining bioinformatics, in-silico techniques, and traditional methods was adopted to uncover intriguing molecules such as the diterpene ceruchinol and its potential receptor interactions for future cosmetic applications. The kaurene diterpene ceruchinol, representing up to 50% of the supercritical CO2 extract and also identified in the hydroalcoholic extract, was selected for the molecular docking study, which highlighted several biological targets as CAR, AKR1D1, and 17β-HSD1 for potential cosmetic use. These findings offer valuable insights for novel uses of this plant biomass in the future. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

MutS homolog 1 (MSH1) is involved in the recombining and repairing of organelle genomes and is essential for maintaining their stability. Previous studies indicated that the length of the gene varied greatly among species and detected species-specific partial gene duplications in Physcomitrella patens. However, there are critical gaps in the understanding of the gene size expansion, and the extent of the partial gene duplication of MSH1 remains unclear. Here, we screened MSH1 genes in 85 selected species with genome sequences representing the main clades of green plants (Viridiplantae). We identified the MSH1 gene in all lineages of green plants, except for nine incomplete species, for bioinformatics analysis. The gene is a singleton gene in most of the selected species with conserved amino acids and protein domains. Gene length varies greatly among the species, ranging from 3234 bp in Ostreococcus tauri to 805,861 bp in Cycas panzhihuaensis. The expansion of MSH1 repeatedly occurred in multiple clades, especially in Gymnosperms, Orchidaceae, and Chloranthus spicatus. MSH1 has exceptionally long introns in certain species due to the gene length expansion, and the longest intron even reaches 101,025 bp. And the gene length is positively correlated with the proportion of the transposable elements (TEs) in the introns. In addition, gene structure analysis indicated that the MSH1 of green plants had undergone parallel intron gains and losses in all major lineages. However, the intron number of seed plants (gymnosperm and angiosperm) is relatively stable. All the selected gymnosperms contain 22 introns except for Gnetum montanum and Welwitschia mirabilis, while all the selected angiosperm species preserve 21 introns except for the ANA grade. Notably, the coding region of MSH1 in algae presents an exceptionally high GC content (47.7% to 75.5%). Moreover, over one-third of the selected species contain species-specific partial gene duplications of MSH1, except for the conserved mosses-specific partial gene duplication. Additionally, we found conserved alternatively spliced MSH1 transcripts in five species. The study of MSH1 sheds light on the evolution of the long genes of green plants. [ABSTRACT FROM AUTHOR]

There exists an obvious gap in our knowledge of the nuclear DNA amount of bryophytes, not only in terms of the low number of species represented, but also in systematic and geographic representation. In order to increase our knowledge of nuclear DNA amounts and variation patterns in bryophytes, and their potential phylogenetic significances and influences on phenotypes, we used flow cytometry to determine the DNA 1C values of 209 bryophyte accessions, which belong to 145 mosses and 18 liverworts collected from China, by using Physcomitrella patens as a standard. We quantified the differences in DNA 1C values among different orders and families and constructed a phylogenetic tree of 112 mosses with four gene sequences (nad5, rbcL, trnL-F, and 18S-ITS1-5.8S-ITS2-26S). DNA 1C values were mapped onto the phylogenetic tree to test a potential phylogenetic signal. We also evaluated the correlations of the DNA 1C value with the sizes of individuals, leaves, cells, and spores by using a phylogenetically controlled analysis. New estimates of nuclear DNA amounts were reported for 145 species. The DNA 1C values of 209 bryophyte accessions ranged from 0.422 pg to 0.860 pg, with an average value of 0.561 pg, and a 2.04-fold variation covered the extremes of all the accessions. Although the values are not significantly different (p = 0.355) between mosses (0.528 pg) and liverworts (0.542 pg), there are variations to varying extents between some families and orders. The DNA 1C value size exerts a positive effect on the sizes of plants, leaves, and cells, but a negative effect on spore size. A weak phylogenetic signal is detected across most moss species. Phylogenetic signals are comparatively strong for some lineages. Our findings show that bryophytes have very small and highly constrained nuclear DNA amounts. There are nucleotype effects of nuclear DNA amounts for bryophytes at the individual, organ, and cell levels. We speculate that smaller nuclear DNA amounts are advantageous for bryophytes in dry environments. Significant differences in the DNA 1C values among some moss families and orders, as well as phylogenetic signals for some lineages, imply that nuclear DNA amount evolution in mosses seems to be unidirectional. [ABSTRACT FROM AUTHOR]

Syntrichia caninervis can survive under 80–90% protoplasmic water losses, and it is a model plant in desiccation tolerance research. A previous study has revealed that S. caninervis would accumulate ABA under dehydration stress, while the ABA biosynthesis genes in S. caninervis are still unknown. This study identified one ScABA1, two ScABA4s, five ScNCEDs, twenty-nine ScABA2s, one ScABA3, and four ScAAOs genes, indicating that the ABA biosynthesis genes were complete in S. caninervis. Gene location analysis showed that the ABA biosynthesis genes were evenly distributed in chromosomes but were not allocated to sex chromosomes. Collinear analysis revealed that ScABA1, ScNCED, and ScABA2 had homologous genes in Physcomitrella patens. RT-qPCR detection found that all of the ABA biosynthesis genes responded to abiotic stress; it further indicated that ABA plays an important role in S. caninervis. Moreover, the ABA biosynthesis genes in 19 representative plants were compared to study their phylogenetic and conserved motifs; the results suggested that the ABA biosynthesis genes were closely associated with plant taxa, but these genes had the same conserved domain in each plant. In contrast, there is a huge variation in the exon number between different plant taxa; it revealed that ABA biosynthesis gene structures are closely related to plant taxa. Above all, this study provides strong evidence demonstrating that ABA biosynthesis genes were conserved in the plant kingdom and deepens our understanding of the evolution of the phytohormone ABA. [ABSTRACT FROM AUTHOR]

The vast diversity of traits exhibited by horticultural crops largely depends upon variation in gene expression regulation. The uppermost layer of gene expression regulation is chromatin compaction. In plants, the LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is a member of the Polycomb Repressive Complex 1 (PRC1) that controls the spreading of the H3K27me3 mark throughout the genome to regulate gene expression. Much of the epigenetic control exerted by LHP1 has been deeply explored on the model species Arabidopsis thaliana. Recent advances in melon, tomato, and soybean highlight the relevance of LHP1 in controlling the development and physiology of a plethora of traits in crops. However, whether LHP1 exerts its diverse roles through similar mechanisms and through modulating the same target genes has been overlooked. In this review, we gather a wealth of knowledge about the LHP1 mode of action, which involves a tight connection with histone marks and long noncoding RNAs to modulate gene expression. Strikingly, we found that LHP1 may be linked to H3K27me3 regulation across the plant lineage, yet, through epigenetic regulation of a distinct set of target genes. This is supported by subtle differences in subcellular LHP1 localization between species found here. In addition, we summarize the variety of developmental outputs modulated by LHP1 across land plants pinpointing its importance for plant breeding. Hence, LHP1 has probably been co-opted in different lineages to modulate diverse traits contributing to crop diversification. [ABSTRACT FROM AUTHOR]

Plant oxylipins are a class of lipid-derived signaling molecules being involved in the regulation of various biotic and abiotic stress responses. A major class of oxylipins are the circular derivatives to which 12-oxo-phytodienoic acid (OPDA) and its metabolite jasmonic acid (JA) belong. While OPDA and its shorter chain homologue dinor-OPDA (dnOPDA) seem to be ubiquitously found in land plants ranging from bryophytes to angiosperms, the occurrence of JA and its derivatives is still under discussion. The bryophyte Physcomitrium patens has received increased scientific interest as a nonvascular plant model organism over the last decade. Therefore, we followed the metabolism upon wounding by metabolite fingerprinting with the aim to identify jasmonates as well as novel oxylipins in P. patens. A non-targeted metabolomics approach was used to reconstruct the metabolic pathways for the synthesis of oxylipins, derived from roughanic, linoleic, a-linolenic, and arachidonic acid in wild type, the oxylipin-deficient mutants of Ppaos1 and Ppaos2, the mutants of Ppdes being deficient in all fatty acids harboring a D6- double bond and the C20-fatty acid-deficient mutants of Ppelo. Beside of OPDA, iso-OPDA, dnOPDA, and iso-dnOPDA, three additional C18- compounds and a metabolite being isobaric to JA were identified to accumulate after wounding. These findings can now serve as foundation for future research in determining, which compound(s) will serve as native ligand(s) for the oxylipin-receptor COI1 in P. patens. [ABSTRACT FROM AUTHOR]

Plant cells form microtubule arrays, called 'cortical microtubules', beneath the plasma membrane which are critical for cell‐wall organization and directional cell growth. Cortical microtubules are nucleated independently of centrosomes. Spiral2 is a land‐plant‐specific microtubule minus‐end‐targeting protein that stabilizes the minus ends by inhibiting depolymerization of the filament. Spiral2 possesses an N‐terminal microtubule‐binding domain and a conserved C‐terminal domain whose function is unknown. In this study, the crystal structure of the conserved C‐terminal domain of Spiral2 was determined using the single‐wavelength anomalous dispersion method. Refinement of the model to a resolution of 2.2 Å revealed a helix–turn–helix fold with seven α‐helices. The protein crystallized as a dimer, but SEC‐MALS analysis showed the protein to be monomeric. A structural homology search revealed that the protein has similarity to the C‐terminal domain of the katanin regulatory subunit p80. The structure presented here suggests that the C‐terminal domain of Spiral2 represents a new class of microtubule dynamics modulator across the kingdom. [ABSTRACT FROM AUTHOR]

A study published in the journal Plant Cell explores the role of SUPPRESSOR OF MAX2 (SMAX)1-LIKE (SMXL) proteins in regulating growth in the moss Physcomitrium patens. The researchers found that SMXL proteins act as negative growth regulators in the moss, functioning downstream of MAX2 in the KL signaling pathway. They also discovered that SMXL proteins do not act as repressors in the strigolactone (SL) pathway. The study provides insights into the molecular mechanisms of moss growth regulation and suggests a possible interplay between SL and KL signaling pathways in moss development. [Extracted from the article]

Plant oxylipins are a class of lipid-derived signaling molecules being involved in the regulation of various biotic and abiotic stress responses. A major class of oxylipins are the circular derivatives to which 12-oxo-phytodienoic acid (OPDA) and its metabolite jasmonic acid (JA) belong. While OPDA and its shorter chain homologue dinor-OPDA (dnOPDA) seem to be ubiquitously found in land plants ranging from bryophytes to angiosperms, the occurrence of JA and its derivatives is still under discussion. The bryophyte Physcomitrium patens has received increased scientific interest as a non-vascular plant model organism over the last decade. Therefore, we followed the metabolism upon wounding by metabolite fingerprinting with the aim to identify jasmonates as well as novel oxylipins in P. patens. A non-targeted metabolomics approach was used to reconstruct the metabolic pathways for the synthesis of oxylipins, derived from roughanic, linoleic, α-linolenic, and arachidonic acid in wild type, the oxylipin-deficient mutants of Ppaos1 and Ppaos2, the mutants of Ppdes being deficient in all fatty acids harboring a Δ6-double bond and the C20-fatty acid-deficient mutants of Ppelo. Beside of OPDA, iso-OPDA, dnOPDA, and iso-dnOPDA, three additional C18-compounds and a metabolite being isobaric to JA were identified to accumulate after wounding. These findings can now serve as foundation for future research in determining, which compound(s) will serve as native ligand(s) for the oxylipin-receptor COI1 in P. patens.

Plant phospholipase D (PLD) exerts important roles in various biological processes, such as intracellular signaling and morphological development. Our knowledge about early land plant PLDs is still underdeveloped. In this study, we identified 84 PLD genes in six mosses, i.e., Physcomitrella patens, Ceratodon purpureus, Fontinalis antipyretica, Pleurozium schreberi, Sphagnum magellanicum, and Sphagnum fallax. These PLDs were classified into four clades (I-IV). We showed that PLD underwent rapid expansion in mosses. A total of six conserved domains and two core HKD motifs were detected. Structure analysis uncovered that the moss PLDs from within a clade generally exhibited similar exon-intron organization. Cis-elements prediction and expression analyses indicated that P. patens PLDs had key roles in stress responsiveness and plant development. Particularly, about half of the P. patens PLDs (e.g., PpPLD1, PpPLD2, and PpPLD5) were differentially expressed under biotic and abiotic stresses. We also determined the expression pattern of P. patens PLD genes in various tissues and at different stages of development. Although the moss, clubmoss, liverwort, and fern PLDs evolved largely under functional constraints, we found episodic positive selection in the moss PLDs, e.g., C. purpureus PLD2 and P. patens PLD11. We infer that the evolutionary force acting on the PLDs may have facilitated moss colonization of land. Our work provides valuable insights into the diversification of moss PLD genes, and can be used for future studies of their functions. [ABSTRACT FROM AUTHOR]

High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages - protonema, gametophore and sporophyte - allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories.

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.

Plant cell wall proteins (CWPs) play critical roles during plant development and in response to stresses. Proteomics has revealed their great diversity. With nearly 1000 identified CWPs, the Arabidopsis thaliana cell wall proteome is the best described to date and it covers the main plant organs and cell suspension cultures. Other monocot and dicot plants have been studied as well as bryophytes, such as Physcomitrella patens and Marchantia polymorpha. Although these proteomes were obtained using various flowcharts, they can be searched for the presence of members of a given protein family. Thereby, a core cell wall proteome which does not pretend to be exhaustive, yet could be defined. It comprises: (i) glycoside hydrolases and pectin methyl esterases, (ii) class III peroxidases, (iii) Asp, Ser and Cys proteases, (iv) non-specific lipid transfer proteins, (v) fasciclin arabinogalactan proteins, (vi) purple acid phosphatases and (vii) thaumatins. All the conserved CWP families could represent a set of house-keeping CWPs critical for either the maintenance of the basic cell wall functions, allowing immediate response to environmental stresses or both. Besides, the presence of non-canonical proteins devoid of a predicted signal peptide in cell wall proteomes is discussed in relation to the possible existence of alternative secretion pathways. [ABSTRACT FROM AUTHOR]

Genome-wide identification of the EIN3 / EIL gene family in Ginkgo biloba and functional study of a GbEIL in the ethylene signaling pathway. [Display omitted] • Five GbEIL s are differentially expressed with high, low, and moderate levels. • A GbEIL (Gb_03292) modulates the expression of a GbERF by binding to its promoter. • Gb_03292 rescues the defect of triple response to ethylene in ein3eil1 Arabidopsis. • Gb_03292 has the evolutionary conservation in ethylene signaling. ETHYLENE-INSENSITIVE3 (EIN3) or EIN3-Like (EIL) proteins, play critical roles in integrating ethylene signaling and physiological regulation in plants by modulating the expression of various downstream genes, such as ethylene-response factors (ERFs). However, little is known about the characteristics of EIN3/EILs in the gymnosperm Ginkgo biloba. In the present study, a genome-wide comparative analysis of Ginkgo EIN3 / EIL gene family was performed with those from an array of species, including bryophytes (Physcomitrella patens), gymnosperms (Cycas panzhihuaensis), and angiosperms (Arabidopsis thaliana , Gossypium raimondii , Gossypium hirsutum , Oryza sativa , and Brachypodium distachyon). Within the constructed phylogenetic tree for the 53 EIN3/EILs identified, 5 GbEILs from G. biloba , 2 PpEILs from P. patens , and 3 CpEILs from C. panzhihuaensis were assigned to one cluster, suggesting that their derivation occurred after the split of their ancestors and angiosperms. Although considerable divergence accumulated in amino acid sequences along with the evolutionary process, the specific EIN3_DNA-binding domains were evolutionarily conserved among the 53 EIN3/EILs. Collinearity analysis indicated that whole-genome or segmental duplication and subsequent purifying selection might have prompted the generation and evolution of EIN3 / EIL multigene families. Based on the expression patterns of five GbEIL s at the four developmental stages of Ginkgo ovules, one GbEIL gene (Gb_03292) was further investigated for its role in mediating ethylene signaling. The functional activity of Gb_03292 was closely related to ethylene signaling, as it complemented the triple response via ectopic expression in ein3eil1 double mutant Arabidopsis. Additionally, GbEIL likely modulates the expression of a Ginkgo ERF (Gb_15517) by directly binding to its promoter. These results demonstrated that the GbEIL gene could have participated in mediating ethylene signal transduction during ovule development in G. biloba. The present study also provides insights into the conservation of ethylene signaling across the gymnosperm G. biloba and angiosperm species. [ABSTRACT FROM AUTHOR]

The vast diversity of traits exhibited by horticultural crops largely depends upon variation in gene expression regulation. The uppermost layer of gene expression regulation is chromatin compaction. In plants, the LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is a member of the Polycomb Repressive Complex 1 (PRC1) that controls the spreading of the H3K27me3 mark throughout the genome to regulate gene expression. Much of the epigenetic control exerted by LHP1 has been deeply explored on the model species Arabidopsis thaliana. Recent advances in melon, tomato, and soybean highlight the relevance of LHP1 in controlling the development and physiology of a plethora of traits in crops. However, whether LHP1 exerts its diverse roles through similar mechanisms and through modulating the same target genes has been overlooked. In this review, we gather a wealth of knowledge about the LHP1 mode of action, which involves a tight connection with histone marks and long noncoding RNAs to modulate gene expression. Strikingly, we found that LHP1 may be linked to H3K27me3 regulation across the plant lineage, yet, through epigenetic regulation of a distinct set of target genes. This is supported by subtle differences in subcellular LHP1 localization between species found here. In addition, we summarize the variety of developmental outputs modulated by LHP1 across land plants pinpointing its importance for plant breeding. Hence, LHP1 has probably been co-opted in different lineages to modulate diverse traits contributing to crop diversification.

The purpose of this study was to explore the structural and expression characteristics of LEA2 genes from Brachymenium exile. BeLEA2 gene was firstly isolated and analyzed by polymerase chain reaction(PCR). The results were as follows:(1)Gene structure analysis showed that BeLEA2 gene contained 2 exons and 1 intron and contained an open reading frame(ORF)of 456 bp encoding a protein of 151 amino acids, and its molecular mass was predicted to be 16 515.96 Da.(2)The phylogenetic analysis of LEA2 with other LEA2 in different plants revealed that BeLEA2 from B. exile and LEA2 from Physcomitrella patens belonged to the same branch of evolutionary distance.(3)The promoter sequence of the BeLEA2 gene of 1 072 bp was isolated from Brachymenium exile by high-efficiency hermal asymmetric interlaced polymerase chain reaction (HiTail-PCR) and analyzed by PlantCARE, the results showed that it had TATA-box, CAAT-box, ABRE, MYB, MYC, MYB binding site and other cis-acting elements.(4)Quantitative real-time PCR analysis indicated that BeLEA2 expressed in different stages and tissues of B. exile, and BeLEA2 responded to dehydration stress. These results lay a foundation for further study on the function of LEA2 gene in bryophytes. [ABSTRACT FROM AUTHOR]

As a transcription factor first found in plants, WRKY plays an important role in plant growth and development. However, it has not been studied in Physcomitrella patens. By using the WRKY gene family data(accession number is PF03106) in Pfam database, this paper studied the basic information of WRKY in P. patens, which included physicochemical properties, protein secondary structure prediction, chromosome localization, exon and intron distribution and phylogenetic relationship. The results were as follows:(1)The WRKY gene family in P. patens consisted of 38 members which were divided into two major categories ─Ⅰ and Ⅱ, and the conserved domains of some WRKY genes had mutated.(2)The amino acid length of WRKY protein was 216-775 aa and the relative molecular mass was 24.5-82.8 kDa; Subcellular location showed that the proteins of WRKY gene family were distributed in the nucleus.(3)The secondary structure of WRKY protein was composed of four constituent elements: α-helix, extended strand, β-turn, and random coil; Except for PpWRKY11(α-helix dominated), the proportion of random coil was up to 70%.(4)The phylogenetic relationship with Arabidopsis showed that the number of the WRKY family members and the way of their revolution had changed in the process of plants' evolution, the number of exons of WRKY gene family members were 3-7.(5)The members of WRKY gene were randomly dispersed on 21 chromosomes without forming a gene cluster. This study analyzed the basic structure and properties of the WRKY gene family, and it was found that the WRKY gene family of Physcomitrella patens has evolutionary diversity and unique variability in conserved domains, laying the foundation for subsequent research. [ABSTRACT FROM AUTHOR]

Plant viruses are important pathogens able to overcome plant defense mechanisms using their viral suppressors of RNA silencing (VSR). Small RNA pathways of bryophytes and vascular plants have significant similarities, but little is known about how viruses interact with mosses. This study elucidated the responses of Physcomitrella patens to two different VSRs. We transformed P. patens plants to express VSR P19 from tomato bushy stunt virus and VSR 2b from cucumber mosaic virus, respectively. RNA sequencing and quantitative PCR were used to detect the effects of VSRs on gene expression. Small RNA (sRNA) sequencing was used to estimate the influences of VSRs on the sRNA pool of P. patens. Expression of either VSR‐encoding gene caused developmental disorders in P. patens. The transcripts of four different transcription factors (AP2/erf, EREB‐11 and two MYBs) accumulated in the P19 lines. sRNA sequencing revealed that VSR P19 significantly changed the microRNA pool in P. patens. Our results suggest that VSR P19 is functional in P. patens and affects the abundance of specific microRNAs interfering with gene expression. The results open new opportunities for using Physcomitrella as an alternative system to study plant–virus interactions. Expression of VSRs caused developmental disorders in P. patens. P. patens expressing P19 showed accumulation of four transcription factors and significant changes in the microRNA pool indicating that VSR P19 affects the abundance of specific microRNAs in P. patens. [ABSTRACT FROM AUTHOR]

Mosses (Bryophyta) are a key group occupying an important phylogenetic position in land plant (embryophyte) evolution. The class Bryopsida represents the most diversified lineage, containing more than 95% of modern mosses, whereas other classes are species‐poor. Two branches with large numbers of gene duplications were elucidated by phylogenomic analyses, one in the ancestry of all mosses and another before the separation of the Bryopsida, Polytrichopsida, and Tetraphidopsida. The analysis of the phylogenetic progression of duplicated paralogs retained on genomic syntenic regions in the Physcomitrella patens genome confirmed that the whole‐genome duplication events WGD1 and WGD2 were re‐recognized as the ψ event and the Funarioideae duplication event, respectively. The ψ polyploidy event was tightly associated with the early diversification of Bryopsida, in the ancestor of Bryidae, Dicranidae, Timmiidae, and Funariidae. Together, four branches with large numbers of gene duplications were unveiled in the evolutionary past of P. patens. Gene retention patterns following the four large‐scale duplications in different moss lineages were analyzed and discussed. Recurrent significant retention of stress‐related genes may have contributed to their adaption to distinct ecological environments and the evolutionary success of this early‐diverging land plant lineage. [ABSTRACT FROM AUTHOR]

Photosynthetic organisms have evolved photoprotective mechanisms to acclimate to light intensity fluctuations in their natural growth environments. Photosystem (PS) II subunit S (PsbS) and light-harvesting complex (LHC) stress-related proteins (LhcSR) are essential for triggering photoprotection in vascular plants and green algae, respectively. The activity of both proteins is strongly enhanced in the moss Physcomitrella patens under high-light conditions. However, their role in regulating photosynthesis acclimation in P. patens under fluctuating light (FL) conditions is still unknown. Here, we compare the responses of wild-type (WT) P. patens and mutants lacking PsbS (psbs KO) or LhcSR1 and 2 (lhcsr KO) to FL conditions in which the low-light phases were periodically interrupted with high-light pulses. lhcsr KO mutant showed a strong reduction in growth with respect to WT and psbs KO under FL conditions. The lack of LhcSR not only decreased the level of non-photochemical quenching, resulting in an over-reduced plastoquinone pool, but also significantly increased the PSI acceptor limitation values with respect to WT and psbs KO under FL conditions. Moreover, in lhcsr KO mutant, the abundance of PSI core and PSI–LHCI complex decreased greatly under FL conditions compared with the WT and psbs KO. We proposed that LhcSR in P. patens play a crucial role in moss acclimation to dynamic light changes. [ABSTRACT FROM AUTHOR]

Plants have developed complex defense mechanisms to cope with microbial pathogens. Pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) are perceived by pattern recognition receptors (PRRs), leading to the activation of defense. While substantial progress has been made in understanding the activation of plant defense by PAMPs and DAMPs recognition in tracheophytes, far less information exists on related processes in early divergent plants like mosses. The aim of this study was to identify genes that were induced in P. patens in response to elicitors of Pectobacterium carotovorum subsp. carotovorum, using a cDNA suppression subtractive hybridization (SSH) method. A total of 239 unigenes were identified, including genes involved in defense responses related to the shikimate, phenylpropanoid, and oxylipin pathways. The expression levels of selected genes related to these pathways were analyzed using quantitative RT-PCR, confirming their rapid induction by P.c. carotovorum derived elicitors. In addition, P. patens induced cell wall reinforcement after elicitor treatment by incorporation of phenolic compounds, callose deposition, and elevated expression of Dirigent-like encoding genes. Small molecule defense markers and phytohormones such as cinnamic acid, 12-oxo-phytodienoic acid, and auxin levels all increased in elicitor-treated moss tissues. In contrast, salicylic acid levels decreased while abscisic acid levels remained unchanged. P. patens reporter lines harboring an auxin-inducible promoter fused to β-glucuronidase revealed GUS activity in protonemal and gametophores tissues treated with elicitors of P.c. carotovorum, consistent with a localized activation of auxin signaling. These results indicate that P. patens activates the shikimate, phenylpropanoid, oxylipins, and auxin pathways upon treatment with P.c. carotovorum derived elicitors.

Summary: In the last few years, next‐generation sequencing techniques have started to be used to identify new viruses infecting plants. This has allowed to rapidly increase our knowledge on viruses other than those causing symptoms in economically important crops. Here we used this approach to identify a virus infecting Physcomitrium patens that has the typical structure of the double‐stranded RNA endogenous viruses of the Amalgaviridae family, which we named Physcomitrium patens amalgavirus 1, or PHPAV1. PHPAV1 is present only in certain accessions of P. patens, where its RNA can be detected throughout the cell cycle of the plant. Our analysis demonstrates that PHPAV1 can be vertically transmitted through both paternal and maternal germlines, in crosses between accessions that contain the virus with accessions that do not contain it. This work suggests that PHPAV1 can replicate in genomic backgrounds different from those that actually contain the virus and opens the door for future studies on virus–host coevolution. Significance Statement: We describe here Physcomitrium patens amalgavirus 1 (PHPAV1), the first virus associated with P. patens. PHPAV1 is a double‐stranded RNA endogenous virus of the Amalgaviridae family present in only certain accessions of P. patens and can be transmitted vertically through both paternal and maternal germlines. [ABSTRACT FROM AUTHOR]

Key message: Homologous genes for the peptidoglycan precursor flippase MurJ, and peptidoglycan hydrolases: lytic transglycosylase MltB, and dd-carboxypeptidase VanY are required for chloroplast division in the moss Physcomitrella patens. The moss Physcomitrella patens is used as a model plant to study plastid peptidoglycan biosynthesis. In bacteria, MurJ flippase transports peptidoglycan precursors from the cytoplasm to the periplasm. In this study, we identified a MurJ homolog (PpMurJ) in the P. patens genome. Bacteria employ peptidoglycan degradation and recycling pathways for cell division. We also searched the P. patens genome for genes homologous to bacterial peptidoglycan hydrolases and identified genes homologous for the lytic transglycosylase mltB, N-acetylglucosaminidase nagZ, and ld-carboxypeptidase ldcA in addition to a putative dd-carboxypeptidase vanY reported previously. Moreover, we found a ß-lactamase-like gene (Pplactamase). GFP fusion proteins with either PpMltB or PpVanY were detected in the chloroplasts, whereas fusion proteins with PpNagZ, PpLdcA, or Pplactamase localized in the cytoplasm. Experiments seeking PpMurJ-GFP fusion proteins failed. PpMurJ gene disruption in P. patens resulted in the appearance of macrochloroplasts in protonemal cells. Compared with the numbers of chloroplasts in wild-type plants (38.9 ± 4.9), PpMltB knockout and PpVanY knockout had lower numbers of chloroplasts (14.3 ± 6.7 and 28.1 ± 5.9, respectively). No differences in chloroplast numbers were observed after PpNagZ, PpLdcA, or Pplactamase single-knockout. Chloroplast numbers in PpMltB/PpVanY double-knockout cells were similar to those in PpMltB single-knockout cells. Zymogram analysis of the recombinant PpMltB protein revealed its peptidoglycan hydrolase activity. Our results imply that PpMurJ, PpMltB and PpVanY play a critical role in chloroplast division in the moss P. patens. [ABSTRACT FROM AUTHOR]

The moss Physcomitrium (Physcomitrella) patens is a bryophyte that provides genetic information about the adaptation to the life on land by early Embryophytes and is a reference organism for comparative evolutionary studies in plants. Copper is an essential micronutrient for every living organism, its transport across the plasma membrane is achieved by the copper transport protein family COPT/CTR. Two genes related to the COPT family were identified in Physcomitrella patens , Ppa COPT1 and Ppa COPT2. Homology modelling of both proteins showed the presence of three putative transmembrane domains (TMD) and the Mx 3 M motif, constituting a potential Cu + selectivity filter present in other members of this family. Functional characterization of Ppa COPT1 and Ppa COPT2 in the yeast mutant ctr1Δctr3Δ restored its growth on medium with non-fermentable carbon sources at micromolar Cu concentrations, providing support that these two moss proteins function as high affinity Cu + transporters. Localization of Ppa COPT1 and Ppa COPT2 in yeast cells was observed at the tonoplast and plasma membrane, respectively. The heterologous expression of Ppa COPT2 in tobacco epidermal cells co-localized with the plasma membrane marker. Finally, only Ppa COPT1 was expressed in seven-day old protonema and was influenced by extracellular copper levels. This evidence suggests different roles of Ppa COPT1 and Ppa COPT2 in copper homeostasis in Physcomitrella patens. Created with BioRender.com. [Display omitted] • Ppa COPT1 and Ppa COPT2 are phylogenetic related to the COPT family. • Ppa COPT1 and Ppa COPT2 possess three transmembrane domains and methionine motives important for copper selectivity. • Ppa COPT1 and Ppa COPT2 function as copper transporters according to functional complementation of the yeast mutant ctr1Δctr3Δ. • PpaCOPT1 and PpaCOPT2 are differentially localized to the tonoplast and plasma membrane, respectively. • Ppa COPT1 transcript is modulated by extracellular Cu concentrations probably contributing to Cu homeostasis in the moss. [ABSTRACT FROM AUTHOR]

Bryophytes inhabit all ecosystems on the Earth except seas. Thus, it is commonly accepted to ask are there real halophytes among bryophytes? However, some species do inhabit salty grassland or even brackish waters. Not much research has been done on the physiological reaction of moss species to salt stress. In order to study these responses, we selected three moss species, two of which are considered to be halophytes−Entosthodon hungaricus (Funariaceae), Hennediella heimii (Pottiaceae) and the non-halophytic model moss Physcomitrella patens (Funariaceae) and tested salt effects on them in controlled conditions. The idea was to show if there is tolerance to salt in the selected moss species and to document it if there is a difference in salt tolerance among them. Established in vitro moss cultures of gametophores were used to test various developmental parameters for the selected moss species. Morpho-developmental parameters (secondary protonema diameter and the index of multiplication) and biochemical parameters (pigment content and antioxidative capacity) were analysed in relation to salt concentration and time of exposure. All of the tested moss species tolerated salt stress to some extent and during some time of exposure to it. Recovery after salt stress depended both on the concentration of salt and duration of the stress. The three tested moss species did not show similar patterns of response to salt stress.

Targeted gene knockout is particularly useful for analyzing gene functions in plant growth, signaling, and development. By transforming knockout cassettes consisting of homologous sequences of the target gene into protoplasts, the classical gene targeting method aims to obtain targeted gene replacement, allowing for the characterization of gene functions in vivo. The moss Physcomitrella patens is a known model organism for a high frequency of homologous recombination and thus harbors a remarkable rate of gene targeting. Other moss features, including easy to culture, dominant haploidy phase, and sequenced genome, make gene targeting prevalent in Physcomitrella patens. However, even gene targeting was powerful to generate knockouts, researchers using this method still experienced technical challenges. For example, obtaining a good number of targeted knockouts after protoplast transformation and regeneration disturbed the users. Off-target mutations such as illegitimate random integration mediated by nonhomologous end joining and targeted insertion wherein one junction on-target but the other end off-target is commonly present in the knockouts. Protoplast fusion during transformation and regeneration was also a problem. This review will discuss the advantages and technical challenges of gene targeting. Recently, CRISPR-Cas9 is a revolutionary technology and becoming a hot topic in plant gene editing. In the second part of this review, CRISPR-Cas9 technology will be focused on and compared to gene targeting regarding the practical use in Physcomitrella patens. This review presents an updated perspective of the gene targeting and CRISPR-Cas9 techniques to plant biologists who may consider studying gene functions in the model organism Physcomitrella patens.

Transcriptional reprogramming is critical for plant immunity. Several calmodulin (CaM)-binding protein 60 (CBP60) family transcription factors (TFs) in Arabidopsis (Arabidopsis thaliana), including CBP60g, Systemic Acquired Resistance Deficient 1 (SARD1), CBP60a, and CBP60b, are critical for and show distinct roles in immunity. However, there are additional CBP60 members whose function is unclear. We report here that Arabidopsis CBP60c-f, four uncharacterized CBP60 members, play redundant roles with CBP60b in the transcriptional regulation of immunity responses, whose pCBP60b-driven expression compensates the loss of CBP60b. By contrast, neither CBP60g nor SARD1 is inter-changeable with CBP60b, suggesting clade-specific functionalization. We further show that function of CBP60b clade TFs relies on DNA-binding domains (DBDs) and CaM-binding domains, suggesting that they are downstream components of calcium signaling. Importantly, we demonstrate that CBP60s encoded in earliest land plant lineage Physcomitrium patens and Selaginella moellendorffii, are functionally homologous to Arabidopsis CBP60b, suggesting that the CBP60b clade contains the prototype TFs of the CBP60 family. Furthermore, tomato and cucumber CBP60b-like genes rescue the defects of Arabidopsis cbp60b and activate the expression of tomato and cucumber SALICYLIC ACID INDUCTION DEFICIIENT2 (SID2) and ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1) genes, suggesting that immune response pathways centered on CBP60b are also evolutionarily conserved. Together, these findings suggest CBP60b clade transcription factors are functionally conserved in evolution and positively mediate immunity., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Specialized photosynthetic organs have appeared several times independently during the evolution of land plants. Phyllids, the leaf-like organs of bryophytes such as mosses or leafy liverworts, display a simple morphology, with a small number of cells and cell types and lack typical vascular tissue which contrasts greatly with flowering plants. Despite this, the leaf structures of these two plant types share many morphological characteristics. In this review, we summarize the current understanding of leaf morphogenesis in the model moss Physcomitrium patens , focusing on the underlying cellular patterns and molecular regulatory mechanisms. We discuss this knowledge in an evolutionary context and identify parallels between moss and flowering plant leaf development. Finally, we propose potential research directions that may help to answer fundamental questions in plant development using moss leaves as a model system. [ABSTRACT FROM AUTHOR]

Plant cell walls are highly dynamic structures that are composed predominately of polysaccharides. As such, endogenous carbohydrate active enzymes (CAZymes) are central to the synthesis and subsequent modification of plant cells during morphogenesis. The endo-glucanase 16 (EG16) members constitute a distinct group of plant CAZymes, angiosperm orthologs of which were recently shown to have dual β-glucan/xyloglucan hydrolase activity. Molecular phylogeny indicates that EG16 members comprise a sister clade with a deep evolutionary relationship to the widely studied apoplastic xyloglucan endotransglycosylases/hydrolases (XTH). A cross-genome survey indicated that EG16 members occur as a single ortholog across species and are widespread in early diverging plants, including the non-vascular bryophytes, for which functional data were previously lacking. Remarkably, enzymological characterization of an EG16 ortholog from the model moss Physcomitrella patens (PpEG16) revealed that EG16 activity and sequence/structure are highly conserved across 500 million years of plant evolution, vis-à-vis orthologs from grapevine and poplar. Ex vivo biomechanical assays demonstrated that the application of EG16 gene products caused abrupt breakage of etiolated hypocotyls rather than slow extension, thereby indicating a mode-of-action distinct from endogenous expansins and microbial endo-glucanases. The biochemical data presented here will inform future genomic, genetic, and physiological studies of EG16 enzymes. [ABSTRACT FROM AUTHOR]

Gravity is a critical environmental factor regulating directional growth and morphogenesis in plants, and gravitropism is the process by which plants perceive and respond to the gravity vector. The cytoskeleton is proposed to play important roles in gravitropism, but the underlying mechanisms are obscure. Here we use genetic screening in Physcomitrella patens, to identify a locus GTRC, that when mutated, reverses the direction of protonemal gravitropism. GTRC encodes a processive minus-end-directed KCHb kinesin, and its N-terminal, C-terminal and motor domains are all essential for transducing the gravity signal. Chimeric analysis between GTRC/KCHb and KCHa reveal a unique role for the N-terminus of GTRC in gravitropism. Further study shows that gravity-triggered normal asymmetric distribution of actin filaments in the tip of protonema is dependent on GTRC. Thus, our work identifies a microtubule-based cellular motor that determines the direction of plant gravitropism via mediating the asymmetric distribution of actin filaments. Gravitropism is the process by which plants perceive and respond to gravity. Here the authors identify a minus-end-directed kinesin required for gravity-triggered actin filament rearrangement and negative gravitropic response in the moss Physcomitrella patens, thus linking a microtubule-based cellular motor to gravitropism via actin. [ABSTRACT FROM AUTHOR]

Sphingolipids have roles as membrane structural components and as bioactive molecules in plants. In Physcomitrella patens, 4‐hydroxysphinganine (phytosphingosine, t18:0) is the predominant sphingolipid long‐chain base (LCB). To assess the functional significance of t18:0, CRISPR‐Cas9 mutagenesis was used to generate mutant lines lacking the sole SPHINGOID BASE HYDROXYLASE (SBH) gene encoding the hydroxylase responsible for converting sphinganine (d18:0) to t18:0. Total sphingolipid content in sbh protonemata was 2.4‐fold higher than in wild‐type. Modest changes in glycosyl inositolphosphorylceramide (GIPC) glycosylation patterns occurred. Sphingolipidomic analyses of mutants lacking t18:0 indicated modest alterations in acyl‐chain pairing with d18:0 in GIPCs and ceramides, but dramatic alterations in acyl‐chain pairing in glucosylceramides, in which 4,8‐sphingadienine (d18:2) was the principal LCB. A striking accumulation of free and phosphorylated LCBs accompanied loss of the hydroxylase. The sbh lines exhibited altered morphology, including smaller chloronemal cell size, irregular cell shape, reduced gametophore size, and increased pigmentation. In the presence of the synthetic trihydroxy LCB t17:0, the endogenous sphingolipid content of sbh lines decreased to wild‐type levels, and the mutants exhibited phenotypes more similar to wild‐type plants. These results demonstrate the importance of sphingolipid content and composition to Physcomitrella growth. They also illuminate similarities in regulating sphingolipid content but differences in regulating sphingolipid species composition between the bryophyte P. patens and angiosperm A. thaliana. [ABSTRACT FROM AUTHOR]

Dynamic reorganization of photosystems I and II is suggested to occur in chloroplast thylakoid membranes to maintain the efficiency of photosynthesis under fluctuating light conditions. To directly observe the process in action, live-cell imaging techniques are necessary. Using live-cell imaging, we have shown that the fine thylakoid structures in the moss Physcomitrella patens are flexible in time. However, the spatiotemporal resolution of a conventional confocal microscopy limits more precise visualization of entire thylakoid structures and understanding of the structural dynamics. Here, we discuss the issues related to observing chlorophyll fluorescence at multiple spatiotemporal scales in vivo and in vitro.

Specialized photosynthetic organs have appeared several times independently during the evolution of land plants. Phyllids, the leaf-like organs of bryophytes such as mosses or leafy liverworts, display a simple morphology, with a small number of cells and cell types and lack typical vascular tissue which contrasts greatly with flowering plants. Despite this, the leaf structures of these two plant types share many morphological characteristics. In this review, we summarize the current understanding of leaf morphogenesis in the model moss Physcomitrium patens, focusing on the underlying cellular patterns and molecular regulatory mechanisms. We discuss this knowledge in an evolutionary context and identify parallels between moss and flowering plant leaf development. Finally, we propose potential research directions that may help to answer fundamental questions in plant development using moss leaves as a model system.

Whilst the biosorption of metal ions by phototrophic (micro)organisms has been demonstrated in earlier and more recent research, the isolation of rare earth elements (REEs) from highly dilute aqueous solutions with this type of biomass remains largely unexplored. Therefore, the selective binding abilities of two microalgae (Calothrix brevissima, Chlorella kessleri) and one moss (Physcomitrella patens) were examined using Neodym and Europium as examples. The biomass of P. patens showed the highest sorption capacities for both REEs (Nd3+: 0.74 ± 0.05 mmol*g−1; Eu3+: 0.48 ± 0.05 mmol*g−1). A comparison with the sorption of precious metals (Au3+, Pt4+) and typical metal ions contained in wastewaters (Pb2+, Fe2+, Cu2+, Ni2+), which might compete for binding sites, revealed that the sorption capacities for Au3+ (1.59 ± 0.07 mmol*g−1) and Pb2+ (0.83 ± 0.02 mmol*g−1) are even higher. Although different patterns of maximum sorption capacities for the tested metal ions were observed for the microalgae, they too showed the highest affinities for Au3+, Pb2+, and Nd3+. Nd-sorption experiments in the pH range from 1 to 6 and the recorded adsorption isotherms for this element showed that the biomass of P. patens has favourable properties as biosorbent compared to the microalgae investigated here. Whilst the cultivation mode did not influence the sorption capacities for the target elements of the two algal species, it had a great impact on the properties of the moss. Thus, further studies are necessary to develop effective biosorption processes for the recovery of REEs from alternative and so far unexploited sources. Key points: • The highest binding capacity for selected REEs was registered for P. patens. • The highest biosorption was found for Au and the biomass of the examined moss. • Biosorption capacities of P. patens seem to depend on the cultivation mode. [ABSTRACT FROM AUTHOR]

Plant lysin motif receptor-like kinase(LYKs)are an important type of RLK found in plants. They have a non-negligible role in plant growth and development, resistance to adversity stress, etc. It is a gene function in plants research hotspots. In order to better understand the LYK gene in Physcomitrella patens, we identified and analyzed members of the LysM-type receptor kinase gene family of P. patens, using bioinformatics and preliminarily discussed the relationship between LYK gene structure, evolution and function by analyzing the basic physical information, gene structure, chromosomal location and phylogenetic relationship of the LYK family members. The results were as follows:(1)There were 21 LYK genes in the moss, the amino acid sequence size ranged from 625 to 755 aa, the molecular weight ranges from 69.54 to 82.02 kDa, and the isoelectric point ranged from 5.98 to 7.78.(2)A phylogenetic tree was constructed by combining all the LYK proteins of P. patens with the LYK proteins of three typical model plants(Rice, Arabidopsis, and Medicago truncatula). All LYK proteins were divided into four subgroups(LYK-I, LYK- II, LYR-I and LYR-II). The genetic structure and conserved domain characteristics of the members in each subgroup of P. patens showed relatively similar characteristics, and it was speculated that they might have the same or similar functions.(3)Chromosome mapping found that 21 LYK genes were concentrated on four chromosomes and there were small gene clusters, which may also be related to gene function. This article analyzed the basic information of the LysM receptor-like protein kinase gene family of P. patens, which can lay the foundation for the in-depth study of the physiological and biochemical functions of its LYK gene family members. [ABSTRACT FROM AUTHOR]

Destabilization of organelle genomes causes organelle dysfunction that appears as abnormal growth in plants and diseases in human. In plants, loss of the bacterial-type homologous recombination repair (HRR) factors RECA and RECG induces organelle genome instability. In this study, we show the landscape of organelle genome instability in Physcomitrella patens HRR knockout mutants by deep sequencing in combination with informatics approaches. Genome-wide maps of rearrangement positions in the organelle genomes, which exhibited prominent mutant-specific patterns, were highly biased in terms of direction and location and often associated with dramatic variation in read depth. The rearrangements were location-dependent and mostly derived from the asymmetric products of microhomology-mediated recombination. Our results provide an overall picture of organelle-specific gross genomic rearrangements in the HRR mutants, and suggest that chloroplasts and mitochondria share common mechanisms for replication-related rearrangements. Masaki Odahara and Kensuke Nakamura et al. use deep paired-end sequencing to examine organellar genome recombination when homologous recombination repair genes are individually knocked out in the moss, Physcomitrella patens. Their results suggest that chloroplasts and mitochondria share a common mechanism for replication-related rearrangements. [ABSTRACT FROM AUTHOR]

Summary: CRISPR‐Cas9 has proven to be highly valuable for genome editing in plants, including the model plant Physcomitrium patens. However, the fact that most of the editing events produced using the native Cas9 nuclease correspond to small insertions and deletions is a limitation.CRISPR‐Cas9 base editors enable targeted mutation of single nucleotides in eukaryotic genomes and therefore overcome this limitation. Here, we report two programmable base‐editing systems to induce precise cytosine or adenine conversions in P. patens.Using cytosine or adenine base editors, site‐specific single‐base mutations can be achieved with an efficiency up to 55%, without off‐target mutations. Using the APT gene as a reporter of editing, we could show that both base editors can be used in simplex or multiplex, allowing for the production of protein variants with multiple amino‐acid changes. Finally, we set up a co‐editing selection system, named selecting modification of APRT to report gene targeting (SMART), allowing up to 90% efficiency site‐specific base editing in P. patens.These two base editors will facilitate gene functional analysis in P. patens, allowing for site‐specific editing of a given base through single sgRNA base editing or for in planta evolution of a given gene through the production of randomly mutagenised variants using multiple sgRNA base editing. [ABSTRACT FROM AUTHOR]

One of the most defining moments in history was the colonization of land by plants approximately 470 million years ago. The transition from water to land was accompanied by significant changes in the plant body plan, from those than resembled filamentous representatives of the charophytes, the sister group to land plants, to those that were morphologically complex and capable of colonizing harsher habitats. The moss Physcomitrium patens (also known as Physcomitrella patens) is an extant representative of the bryophytes, the earliest land plant lineage. The protonema of P. patens emerges from spores from a chloronemal initial cell, which can divide to self‐renew to produce filaments of chloronemal cells. A chloronemal initial cell can differentiate into a caulonemal initial cell, which can divide and self‐renew to produce filaments of caulonemal cells, which branch extensively and give rise to three‐dimensional shoots. The process by which a chloronemal initial cell differentiates into a caulonemal initial cell is tightly regulated by auxin‐induced remodeling of the actin cytoskeleton. Studies have revealed that the genetic mechanisms underpinning this transition also regulate tip growth and differentiation in diverse plant taxa. This review summarizes the known cellular and molecular mechanisms underpinning the chloronema to caulonema transition in P. patens. [ABSTRACT FROM AUTHOR]

Natural products from plants have served mankind in a wide range of applications, such as medicines, perfumes, or flavoring agents. For this reason, synthesis, regulation and function of plant-derived chemicals, as well as the evolution of metabolic diversity, has attracted researchers all around the world. In particular, vascular plants have been subject to such analyses due to prevalent characteristics such as appearance, fragrance, and ecological settings. In contrast, bryophytes, constituting the second largest group of plants in terms of species number, have been mostly overlooked in this regard, potentially due to their seemingly tiny, simple and obscure nature. However, the identification of highly interesting chemicals from bryophytes with potential for biotechnological exploitation is changing this perception. Bryophytes offer a high degree of biochemical complexity, as a consequence of their ecological and genetic diversification, which enable them to prosper in various, often very harsh habitats. The number of bioactive compounds isolated from bryophytes is growing rapidly. The rapidly increasing wealth of bryophyte genetics opens doors to functional and comparative genomics approaches, including disentangling of the biosynthesis of potentially interesting chemicals, mining for novel gene families and tracing the evolutionary history of metabolic pathways. Throughout the last decades, the moss Physcomitrella (Physcomitrium patens) has moved from being a model plant together with Marchantia polymorpha in fundamental biology into an attractive host for the production of biotechnologically relevant compounds such as biopharmaceuticals. In the future, bryophytes like the moss P. patens might also be attractive candidates for the production of novel bryophyte-derived chemicals of commercial interest. This review provides a comprehensive overview of natural product research in bryophytes from different perspectives together with biotechnological advances throughout the last decade. [ABSTRACT FROM AUTHOR]

Plants utilize a plethora of peptide signals to regulate their immune response. Peptide ligands and their cognate receptors involved in immune signaling share common motifs among many species of vascular plants. However, the origin and evolution of immune peptides is still poorly understood. Here, we searched for genes encoding small secreted peptides in the genomes of three bryophyte lineages—mosses, liverworts and hornworts—that occupy a critical position in the study of land plant evolution. We found that bryophytes shared common predicted small secreted peptides (SSPs) with vascular plants. The number of SSPs is higher in the genomes of mosses than in both the liverwort Marchantia polymorpha and the hornwort Anthoceros sp. The synthetic peptide elicitors—AtPEP and StPEP—specific for vascular plants, triggered ROS production in the protonema of the moss Physcomitrella patens, suggesting the possibility of recognizing peptide ligands from angiosperms by moss receptors. Mass spectrometry analysis of the moss Physcomitrella patens, both the wild type and the Δcerk mutant secretomes, revealed peptides that specifically responded to chitosan treatment, suggesting their role in immune signaling. [ABSTRACT FROM AUTHOR]