A conserved regulatory mechanism mediates the convergent evolution of plant shoot lateral organs

Lignin synthesis plays an essential role in the adaptation of Haloxylon ammodendron to adverse environments

Haloxylon ammodendron is a desert shrub exhibiting remarkable tolerance to adverse environments, making it an excellent model for studying the mechanisms by which plants adapt to harsh environmental conditions. Lignin, a crucial component of plants, has been shown to play an important role in the adaptation of H. ammodendron to osmotic and salt stress. Therefore, this study was focused on the role of lignin synthesis by H. ammodendron in its adaptation to osmotic and salt stress (imposed by 0.4 % sorbitol and 350 mM NaCl, respectively). We investigated lignin deposition, the polymerization of lignin monomers, water content and adjustment of osmotic potential in assimilating branches of H. ammodendron, as well as gene expression and small molecules related to lignin biosynthesis. The results indicated that osmotic and salt stress induced the activity of peroxidase (POD) and laccase (LAC), while H2O2 concentration also increased. The genes encoding functions associated with lignin biosynthesis in both shoots and roots were upregulated and lignin accumulation in H. ammodendron increased, thereby maintaining osmotic potential and shoot water content under stress. These results showed that osmotic and salt stresses significantly increased lignin production in H. ammodendron, polymerization of lignin monomers, and the expression of genes encoding functions correlated to lignin synthesis. In addition, under osmotic stress, phenylalanine and p-coumaric acid increased in the shoots and roots, as did coniferyl alcohol and sinapyl alcohol. Overall, this study confirmed the role of lignin biosynthesis in the stress resistance of H. ammodendron, providing further insights into its adaptive strategies to adversity, and suggesting new ideas for improving the resistance of cultivated plants.

Characterization and Expression Analysis of the ALOG Gene Family in Rice (Oryza sativa L.)

ALOG (Arabidopsis LSH1 and Oryza G1) proteins constitute a plant-specific family of transcription factors that play crucial roles in lateral organ development across land plants. Initially identified through forward genetic studies of Arabidopsis LSH1 and rice G1 proteins, ALOG family members have since been functionally characterized in various plant species. However, research focusing on the characteristics and expression patterns of all ALOG family members in rice remains relatively limited. In this study, we systematically characterized OsALOG family genes in rice. Compared to other genes in rice and Arabidopsis, the ALOG family genes have a relatively simple structure. The alignment of OsALOG amino acid sequences and analysis of disorder predictions reveal that all members possess conserved ALOG domains, while the conservation of intrinsically disordered regions (IDRs) is relatively low. Four amino acids-alanine, glycine, proline, and serine-are significantly enriched in the IDRs of each ALOG protein. Synteny analysis indicates that most OsALOG genes have undergone considerable divergence compared to their counterparts in Arabidopsis. Bioinformatic analysis of cis-regulatory elements predicts that OsALOG family genes contain elements responsive to ABA, light, and methyl jasmonate, although the abundance and composition of these elements vary among different members. The expression patterns associated with the rice floral development of OsALOG genes can be broadly categorized into two types; however, even within the same type, differences in expression levels, as well as the initiation time and duration of expression, were observed. These results provide a comprehensive understanding of the structural characteristics and expression patterns of OsALOG members in rice.

ALOG/LSHs: a novel class of transcription factors that regulate plant growth and development

The ARABIDOPSIS LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and rice G1/LIGHT-DEPENDENT SHORT HYPOCOTYLS (ALOG/LSH) group proteins are highly conserved across plant lineages from moss to higher flowering plants, suggesting their crucial role in the evolution and adaptation of land plants. The role of ALOG/LSH proteins is highly conserved in various developmental responses, such as vegetative and reproductive developmental programs. Their role in meristem identity, cotyledon development, seedling photomorphogenesis, and leaf and shoot development has been relatively well established. Moreover, several key pieces of evidence suggest their role in inflorescence architecture and flower development, including male and female reproductive organs and flower colouration. Recent research has started to explore their role in stress response. Functionally, ALOG/LSH proteins have been demonstrated to act as transcriptional regulators and are considered a newly emerging class of transcription factors in plants that regulate diverse developmental and physiological processes. This review aims to stimulate discussion about their role in plant development and as transcription factors. It also seeks to further unravel the underlying molecular mechanism by which they regulate growth and development throughout the plant lineage.

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.

Non-cell-autonomous signaling associated with barley ALOG1 specifies spikelet meristem determinacy

Inflorescence architecture and crop productivity are often tightly coupled in our major cereal crops. However, the underlying genetic mechanisms controlling cereal inflorescence development remain poorly understood. Here, we identified recessive alleles of barley (Hordeum vulgare L.) HvALOG1 (Arabidopsis thaliana LSH1 and Oryza G1) that produce non-canonical extra spikelets and fused glumes abaxially to the central spikelet from the upper-mid portion until the tip of the inflorescence. Notably, we found that HvALOG1 exhibits a boundary-specific expression pattern that specifically excludes reproductive meristems, implying the involvement of previously proposed localized signaling centers for branch regulation. Importantly, during early spikelet formation, non-cell-autonomous signals associated with HvALOG1 expression may specify spikelet meristem determinacy, while boundary formation of floret organs appears to be coordinated in a cell-autonomous manner. Moreover, barley ALOG family members synergistically modulate inflorescence morphology, with HvALOG1 predominantly governing meristem maintenance and floral organ development. We further propose that spatiotemporal redundancies of expressed HvALOG members specifically in the basal inflorescence may be accountable for proper patterning of spikelet formation in mutant plants. Our research offers new perspectives on regulatory signaling roles of ALOG transcription factors during the development of reproductive meristems in cereal inflorescences.

Transcriptional convergence after repeated duplication of an amino acid transporter gene leads to the independent emergence of the black husk/pericarp trait in barley and rice

The repeated emergence of the same trait (convergent evolution) in distinct species is an interesting phenomenon and manifests visibly the power of natural selection. The underlying genetic mechanisms have important implications to understand how the genome evolves under environmental challenges. In cereal crops, both rice and barley can develop black-coloured husk/pericarp due to melanin accumulation. However, it is unclear if this trait shares a common origin. Here, we fine-mapped the barley HvBlp gene controlling the black husk/pericarp trait and confirmed its function by gene silencing. The result was further supported by a yellow husk/pericarp mutant with deletion of the HvBlp gene, derived from gamma ray radiation of the wild-type W1. HvBlp encodes a putative tyrosine transporter homologous to the black husk gene OsBh4 in rice. Surprisingly, synteny and phylogenetic analyses showed that HvBlp and OsBh4 belonged to different lineages resulted from dispersed and tandem duplications, respectively, suggesting that the black husk/pericarp trait has emerged independently. The dispersed duplication (dated at 21.23 MYA) yielding HvBlp occurred exclusively in the common ancestor of Triticeae. HvBlp and OsBh4 displayed converged transcription in husk/pericarp tissues, contributing to the black husk/pericarp trait. Further transcriptome and metabolome data identified critical candidate genes and metabolites related to melanin production in barley. Taken together, our study described a compelling case of convergent evolution resulted from transcriptional convergence after repeated gene duplication, providing valuable genetic insights into phenotypic evolution. The identification of the black husk/pericarp genes in barley also has great potential in breeding for stress-resilient varieties with higher nutritional values.

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.

The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development

The ALOG (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 (LSH1) and Oryza G1) proteins are conserved plant-specific Transcription Factors (TFs). They play critical roles in the development of various plant organs (meristems, inflorescences, floral organs, and nodules) from bryophytes to higher flowering plants. Despite the fact that the first members of this family were originally discovered in Arabidopsis, their role in this model plant has remained poorly characterized. Moreover, how these transcriptional regulators work at the molecular level is unknown. Here, we study the redundant function of the ALOG proteins LSH1,3,4 from Arabidopsis. We uncover their role in the repression of bract development and position them within a gene regulatory network controlling this process and involving the floral regulators LEAFY, BLADE-ON-PETIOLE, and PUCHI. Next, using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from evolutionarily distant species (the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato, and rice). Resolution of the crystallographic structure of the ALOG DNA-binding domain in complex with DNA revealed the domain is a four-helix bundle with a disordered NLS and a zinc ribbon insertion between helices 2 and 3. The majority of DNA interactions are mediated by specific contacts made by the third alpha helix and the NLS. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in Arabidopsis flower development.

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.

Control of stem cell behavior by CLE-JINGASA signaling in the shoot apical meristem in Marchantia polymorpha

Land plants undergo indeterminate growth by the activity of meristems in both gametophyte (haploid) and sporophyte (diploid) generations. In the sporophyte of the flowering plant Arabidopsis thaliana, the apical meristems are located at the shoot and root tips in which a number of regulatory gene homologs are shared for their development, implying deep evolutionary origins. However, little is known about their functional conservation with gametophytic meristems in distantly related land plants such as bryophytes, even though genomic studies have revealed that the subfamily-level diversity of regulatory genes is mostly conserved throughout land plants. Here, we show that a NAM/ATAF/CUC (NAC) domain transcription factor, JINGASA (MpJIN), acts downstream of CLAVATA3 (CLV3)/ESR-related (CLE) peptide signaling and controls stem cell behavior in the gametophytic shoot apical meristem of the liverwort Marchantia polymorpha. In the meristem, strong MpJIN expression was associated with the periclinal cell division at the periphery of the stem cell zone (SCZ), whereas faint MpJIN expression was found at the center of the SCZ. Time course observation indicates that the MpJIN-negative cells are lost from the SCZ and respecified de novo at two separate positions during the dichotomous branching event. Consistently, the induction of MpJIN results in ectopic periclinal cell division in the SCZ and meristem termination. Based on the comparative expression data, we speculate that the function of JIN/FEZ subfamily genes was shared among the shoot apical meristems in the gametophyte and sporophyte generations in early land plants but was lost in certain lineages, including the flowering plant A. thaliana.

Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae

The ALOG gene family, which was named after its earliest identified members ( Arabidopsis LSH1 and Oryza G1), encodes a class of transcription factors (TF) characterized by the presence of a highly conserved ALOG domain. These proteins are found in various plant species playing regulatory roles in plant growth, development, and morphological diversification of inflorescence. The functional characterization of these genes in some plant species has demonstrated their involvement in floral architecture. In this study, we used a genome-wide and phylogenetic approach to gain insights into plants' origin, diversification, and functional aspects of the ALOG gene family. In total, 648 ALOG homologous genes were identified in 77 Viridiplantae species, and their evolutionary relationships were inferred using maximum likelihood phylogenetic analyses. Our results suggested that the ALOG gene family underwent several rounds of gene duplication and diversification during angiosperm evolution. Furthermore, we found three functional orthologous groups in Solanaceae species. The study provides insights into the evolutionary history and functional diversification of the ALOG gene family, which could aid in understanding the mechanisms underlying floral architecture in angiosperms.

The renaissance and enlightenment of Marchantia as a model system

The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.

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.

DOMINANT AWN INHIBITOR Encodes the ALOG Protein Originating from Gene Duplication and Inhibits AWN Elongation by Suppressing Cell Proliferation and Elongation in Sorghum

The awn, a needle-like structure extending from the tip of the lemma in grass species, plays a role in environmental adaptation and fitness. In some crops, awns appear to have been eliminated during domestication. Although numerous genes involved in awn development have been identified, several dominant genes that eliminate awns are also known to exist. For example, in sorghum (Sorghum bicolor), the dominant awn-inhibiting gene has been known since 1921; however, its molecular features remain uncharacterized. In this study, we conducted quantitative trait locus analysis and a genome-wide association study of awn-related traits in sorghum and identified DOMINANT AWN INHIBITOR (DAI), which encodes the ALOG family protein on chromosome 3. DAI appeared to be present in most awnless sorghum cultivars, likely because of its effectiveness. Detailed analysis of the ALOG protein family in cereals revealed that DAI originated from a duplication of its twin paralog (DAIori) on chromosome 10. Observations of immature awns in near-isogenic lines revealed that DAI inhibits awn elongation by suppressing both cell proliferation and elongation. We also found that only DAI gained a novel function to inhibit awn elongation through an awn-specific expression pattern distinct from that of DAIori. Interestingly, heterologous expression of DAI with its own promoter in rice inhibited awn elongation in the awned cultivar Kasalath. We found that DAI originated from gene duplication, providing an interesting example of gain-of-function that occurs only in sorghum but shares its functionality with rice and sorghum.

The liverwort Marchantia polymorpha, a model for all ages

The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.

A glycogen synthase kinase 3-like kinase MpGSK regulates cell differentiation in Marchantia polymorpha

Plants precisely coordinate the balance between cell proliferation and differentiation to ensure the continuous development. In Arabidopsis thaliana, members of glycogen synthase kinase 3 (GSK3) family, which are highly conserved serine/threonine protein kinases among eukaryotes, play important roles in regulating cell proliferation and differentiation during various developmental processes. However, functional roles of GSK3s in the plant lineages except angiosperms remain to be elucidated. Here, we utilized a model liverwort, Marchantia polymorpha, for studies of GSK3, because it has a single GSK3-like kinase, MpGSK. When M. polymorpha was treated with a chemical compound, bikinin, which is known as a specific inhibitor for GSK3-like kinases, growth and morphologies were altered with an expansion of the meristematic region. Similarly, Mpgsk loss-of-function mutants accumulated undifferentiated cell mass with no differentiated tissues. By contrast, overexpression of MpGSK reduced the size of the meristem region. These results suggest that MpGSK plays important roles as a regulator for the balance between cell differentiation and proliferation in M. polymorpha.

Heterotypic transcriptional condensates formed by prion-like paralogous proteins canalize flowering transition in tomato

BACKGROUND

Paralogs that arise from gene duplications during genome evolution enable genetic redundancy and phenotypic robustness. Variation in the coding or regulatory sequence of paralogous transcriptional regulators diversifies their functions and relationships, which provides developmental robustness against genetic or environmental perturbation. The fate transition of plant shoot stem cells for flowering and reproductive success requires a robust transcriptional control. However, how paralogs function and interact to achieve such robustness is unknown.

RESULTS

Here, we explore the genetic relationship and protein behavior of ALOG family transcriptional factors with diverse transcriptional abundance in shoot meristems. A mutant spectrum covers single and higher-order mutant combinations of five ALOG paralogs and creates a continuum of flowering transition defects, showing gradually enhanced precocious flowering, along with inflorescence simplification from wild-type-like to progressively fewer flowers until solitary flower with sterile floral organs. Therefore, these paralogs play unequal roles and act together to achieve a robust genetic canalization. All five proteins contain prion-like intrinsically disordered regions (IDRs) and undergo phase separation. Accumulated mutations following gene duplications lead to IDR variations among ALOG paralogs, resulting in divergent phase separation and transcriptional regulation capabilities. Remarkably, they retain the ancestral abilities to assemble into a heterotypic condensate that prevents precocious activation of the floral identity gene ANANTHA.

CONCLUSIONS

Our study reveals a novel genetic canalization mechanism enabled by heterotypic transcriptional condensates formed by paralogous protein interactions and phase separation, uncovering the molecular link between gene duplication caused IDR variation and robust transcriptional control of stem cell fate transition.

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.

Normal oil body formation in Marchantia polymorpha requires functional coat protein complex I proteins

Eukaryotic cells possess endomembrane organelles equipped with specific sets of proteins, lipids, and polysaccharides that are fundamental for realizing each organelle's specific function and shape. A tightly regulated membrane trafficking system mediates the transportation and localization of these substances. Generally, the secretory/exocytic pathway is responsible for transporting cargo to the plasma membrane and/or the extracellular space. However, in the case of oil body cells in the liverwort Marchantia polymorpha, the oil body, a liverwort-unique organelle, is thought to be formed by secretory vesicle fusion through redirection of the secretory pathway inside the cell. Although their formation mechanism remains largely unclear, oil bodies exhibit a complex and bumpy surface structure. In this study, we isolated a mutant with spherical oil bodies through visual screening of mutants with abnormally shaped oil bodies. This mutant harbored a mutation in a coat protein complex I (COPI) subunit MpSEC28, and a similar effect on oil body morphology was also detected in knockdown mutants of other COPI subunits. Fluorescently tagged MpSEC28 was localized to the periphery of the Golgi apparatus together with other subunits, suggesting that it is involved in retrograde transport from and/or in the Golgi apparatus as a component of the COPI coat. The Mpsec28 mutants also exhibited weakened stiffness of the thalli, suggesting impaired cell-cell adhesion and cell wall integrity. These findings suggest that the mechanism of cell wall biosynthesis is also involved in shaping the oil body in M. polymorpha, supporting the redirection of the secretory pathway inward the cell during oil body formation.

Fundamental mechanisms of the stem cell regulation in land plants: lesson from shoot apical cells in bryophytes

This review compares the molecular mechanisms of stem cell control in the shoot apical meristems of mosses and angiosperms and reveals the conserved features and evolution of plant stem cells. The establishment and maintenance of pluripotent stem cells in the shoot apical meristem (SAM) are key developmental processes in land plants including the most basal, bryophytes. Bryophytes, such as Physcomitrium (Physcomitrella) patens and Marchantia polymorpha, are emerging as attractive model species to study the conserved features and evolutionary processes in the mechanisms controlling stem cells. Recent studies using these model bryophyte species have started to uncover the similarities and differences in stem cell regulation between bryophytes and angiosperms. In this review, we summarize findings on stem cell function and its regulation focusing on different aspects including hormonal, genetic, and epigenetic control. Stem cell regulation through auxin, cytokinin, CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) signaling and chromatin modification by Polycomb Repressive Complex 2 (PRC2) and PRC1 is well conserved. Several transcription factors crucial for SAM regulation in angiosperms are not involved in the regulation of the SAM in mosses, but similarities also exist. These findings provide insights into the evolutionary trajectory of the SAM and the fundamental mechanisms involved in stem cell regulation that are conserved across land plants.

A plant-specific DYRK kinase DYRKP coordinates cell morphology in Marchantia polymorpha

Dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs) are activated via the auto-phosphorylation of conserved tyrosine residues in their activation loop during protein translation, and they then phosphorylate serine/threonine residues on substrates. The DYRK family is widely conserved in eukaryotes and is composed of six subgroups. In plant lineages, DYRK homologs are classified into four subgroups, DYRK2s, yet another kinase1s, pre-mRNA processing factor 4 kinases, and DYRKPs. Only the DYRKP subgroup is plant-specific and has been identified in a wide array of plant lineages, including land plants and green algae. It has been suggested that in Arabidopsis thaliana DYRKPs are involved in the regulation of centripetal nuclear positioning induced by dark light conditions. However, the molecular functions, such as kinase activity and the developmental and physiological roles of DYRKPs are poorly understood. Here, we focused on a sole DYRKP ortholog in the model bryophyte, Marchantia polymorpha, MpDYRKP. MpDYRKP has a highly conserved kinase domain located in the C-terminal region and shares common sequence motifs in the N-terminal region with other DYRKP members. To identify the roles of MpDYRKP in M. polymorpha, we generated loss-of-function Mpdyrkp mutants via genome editing. Mpdyrkp mutants exhibited abnormal, shrunken morphologies with less flattening in their vegetative plant bodies, thalli, and male reproductive organs, antheridial receptacles. The surfaces of the thalli in the Mpdyrkp mutants appeared uneven and disordered. Moreover, their epidermal cells were drastically altered to a narrower shape when compared to the wild type. These results suggest that MpDYRKP acts as a morphological regulator, which contributes to orderly tissue morphogenesis via the regulation of cell shape.

Major components of the KARRIKIN INSENSITIVE2-dependent signaling pathway are conserved in the liverwort Marchantia polymorpha

KARRIKIN INSENSITIVE2 (KAI2) was first identified as a receptor of karrikins, smoke-derived germination stimulants. KAI2 is also considered a receptor of an unidentified endogenous molecule called the KAI2 ligand. Upon KAI2 activation, signals are transmitted through the degradation of D53/SMXL proteins via MAX2-dependent ubiquitination. Although components in the KAI2-dependent signaling pathway, namely MpKAI2A and MpKAI2B, MpMAX2, and MpSMXL, exist in the genome of the liverwort Marchantia polymorpha, their functions remain unknown. Here, we show that early thallus growth is retarded and gemma dormancy in the dark is suppressed in Mpkai2a and Mpmax2 loss-of-function mutants. These defects are counteracted in Mpkai2a Mpsmxl and Mpmax2 Mpsmxl double mutants indicating that MpKAI2A, MpMAX2, and MpSMXL act in the same genetic pathway. Introduction of MpSMXLd53, in which a domain required for degradation is mutated, into wild-type plants mimicks Mpkai2a and Mpmax2 plants. In addition, the detection of citrine fluorescence in Nicotiana benthamiana cells transiently expressing a SMXL-Citrine fusion protein requires treatment with MG132, a proteasome inhibitor. These findings imply that MpSMXL is subjected to degradation, and that the degradation of MpSMXL is crucial for MpKAI2A-dependent signaling in M. polymorpha. Therefore, we claim that the basic mechanisms in the KAI2-dependent signaling pathway are conserved in M. polymorpha.

Development and Molecular Genetics of Marchantia polymorpha

Bryophytes occupy a basal position in the monophyletic evolution of land plants and have a life cycle in which the gametophyte generation dominates over the sporophyte generation, offering a significant advantage in conducting genetics. Owing to its low genetic redundancy and the availability of an array of versatile molecular tools, including efficient genome editing, the liverwort Marchantia polymorpha has become a model organism of choice that provides clues to the mechanisms underlying eco-evo-devo biology in plants. Recent analyses of developmental mutants have revealed that key genes in developmental processes are functionally well conserved in plants, despite their morphological differences, and that lineage-specific evolution occurred by neo/subfunctionalization of common ancestral genes. We suggest that M. polymorpha is an excellent platform to uncover the conserved and diversified mechanisms underlying land plant development.

Molecular mechanisms involved in functional macroevolution of plant transcription factors

Transcription factors (TFs) are key components of the transcriptional regulation machinery. In plants, they accompanied the evolution from unicellular aquatic algae to complex flowering plants that dominate the land environment. The adaptations of the body plan and physiological responses required changes in the biological functions of TFs. Some ancestral gene regulatory networks are highly conserved, while others evolved more recently and only exist in particular lineages. The recent emergence of novel model organisms provided the opportunity for comparative studies, producing new insights to infer these evolutionary trajectories. In this review, we comprehensively revisit the recent literature on TFs of nonseed plants and algae, focusing on the molecular mechanisms driving their functional evolution. We discuss the particular contribution of changes in DNA-binding specificity, protein-protein interactions and cis-regulatory elements to gene regulatory networks. Current advances have shown that these evolutionary processes were shaped by changes in TF expression pattern, not through great innovation in TF protein sequences. We propose that the role of TFs associated with environmental and developmental regulation was unevenly conserved during land plant evolution.

ROS regulated reversible protein phase separation synchronizes plant flowering

How aerobic organisms exploit inevitably generated but potentially dangerous reactive oxygen species (ROS) to benefit normal life is a fundamental biological question. Locally accumulated ROS have been reported to prime stem cell differentiation. However, the underlying molecular mechanism is unclear. Here, we reveal that developmentally produced H₂O₂ in plant shoot apical meristem (SAM) triggers reversible protein phase separation of TERMINATING FLOWER (TMF), a transcription factor that times flowering transition in the tomato by repressing pre-maturation of SAM. Cysteine residues within TMF sense cellular redox to form disulfide bonds that concatenate multiple TMF molecules and elevate the amount of intrinsically disordered regions to drive phase separation. Oxidation triggered phase separation enables TMF to bind and sequester the promoter of a floral identity gene ANANTHA to repress its expression. The reversible transcriptional condensation via redox-regulated phase separation endows aerobic organisms with the flexibility of gene control in dealing with developmental cues.

Lonely at the top? Regulation of shoot apical meristem activity by intrinsic and extrinsic factors

All the above-ground organs of a plant are derived from stem cells that reside in shoot apical meristems (SAM). Over the past 25 years, the genetic pathways that control the proliferation of stem cells within the SAM, and the differentiation of their progenitors into lateral organs, have been described in great detail. However, longstanding questions regarding the importance of communication between cells within the SAM and lateral organs have, until recently, remained unanswered. In this review, we describe recent investigations into the extent, nature and significance of signaling both to and from the SAM.

Ancestral function of the phytochelatin synthase C-terminal domain in inhibition of heavy metal-mediated enzyme overactivation

Phytochelatin synthases (PCSs) play essential roles in detoxification of a broad range of heavy metals in plants and other organisms. Until now, however, no PCS gene from liverworts, the earliest branch of land plants and possibly the first one to acquire a PCS with a C-terminal domain, has been characterized. In this study, we isolated and functionally characterized the first PCS gene from a liverwort, Marchantia polymorpha (MpPCS). MpPCS is constitutively expressed in all organs examined, with stronger expression in thallus midrib. The gene expression is repressed by Cd2+ and Zn2+. The ability of MpPCS to increase heavy metal resistance in yeast and to complement cad1-3 (the null mutant of the Arabidopsis ortholog AtPCS1) proves its function as the only PCS from M. polymorpha. Site-directed mutagenesis of the most conserved cysteines of the C-terminus of the enzyme further uncovered that two twin-cysteine motifs repress, to different extents, enzyme activation by heavy metal exposure. These results highlight an ancestral function of the PCS elusive C-terminus as a regulatory domain inhibiting enzyme overactivation by essential and non-essential heavy metals. The latter finding may be relevant for obtaining crops with decreased root to shoot mobility of cadmium, thus preventing its accumulation in the food chain.

The origin and evolution of the ALOG proteins, members of a plant-specific transcription factor family, in land plants

The Arabidopsis LSH1 and Oryza G1 (ALOG) protein is a family of plant-specific transcription factors that regulate reproductive growth in angiosperms. Despite their importance in plant development, little research has been conducted on ALOG proteins in basal land plants and the processes involved in their evolution remain largely unknown. Here, we studied the molecular evolution of ALOG family proteins. We found that ALOG proteins are absent in green algae but exist in all land plants analyzed as well as in some Charophycean algae, closest relatives of land plants. Multiple sequence alignments identified the high sequence conservation of ALOG domains in divergent plant lineages. Phylogenetic analyses also identified a distinct clade of ALOG protein member of lycophytes and bryophytes, including two of Marchantia polymorpha LATERAL ORGAN SUPPRESOR (MpLOS1 and MpLOS2) with a long branch length in MpLOS2. Consistent with this, the function of MpLOS1 was replaceable by Phycomitrella patens ALOG proteins, whereas MpLOS2 failed to replace the molecular function of MpLOS1. Moreover, the rice ALOG proteins, OsTAW1 and OsG1, were not able to replace the molecular function of MpLOS1 although we previously found that the function of OsG1 was replaceable by MpLOS1. Altogether, these findings suggest that ALOG proteins emerged before the evolution of land plants and that they exhibit functional conservation and diversification during the evolution of land plants. The finding that MpLOS1 is able to complement rice ALOG mutants but not vice versa also suggest the existence of conserved and the partly divergent functions of ALOG proteins in bryophytes and angiosperms.