Homologues of the Arabidopsis thaliana SHI/STY/LRP1 genes control auxin biosynthesis and affect growth and development in the moss Physcomitrella patens

Arabidopsis hydathodes are sites of auxin accumulation and nutrient scavenging

Hydathodes are small organs found on the leaf margins of vascular plants which release excess xylem sap through a process called guttation. While previous studies have hinted at additional functions of hydathode in metabolite transport or auxin metabolism, experimental support is limited. We conducted comprehensive transcriptomic, metabolomic and physiological analyses of mature Arabidopsis hydathodes. This study identified 1460 genes differentially expressed in hydathodes compared to leaf blades, indicating higher expression of most genes associated with auxin metabolism, metabolite transport, stress response, DNA, RNA or microRNA processes, plant cell wall dynamics and wax metabolism. Notably, we observed differential expression of genes encoding auxin-related transcriptional regulators, biosynthetic processes, transport and vacuolar storage supported by the measured accumulation of free and conjugated auxin in hydathodes. We also showed that 78% of the total content of 52 xylem metabolites was removed from guttation fluid at hydathodes. We demonstrate that NRT2.1 and PHT1;4 transporters capture nitrate and inorganic phosphate in guttation fluid, respectively, thus limiting the loss of nutrients during this process. Our transcriptomic and metabolomic analyses unveil an organ with its specific physiological and biological identity.

Cell death in bryophytes: emerging models to study core regulatory modules and conserved pathways

This review summarizes recent progress in our current understanding of the mechanisms underlying the cell death pathways in bryophytes, focusing on conserved pathways and particularities in comparison to angiosperms. Regulated cell death (RCD) plays key roles during essential processes along the plant life cycle. It is part of specific developmental programmes and maintains homeostasis of the organism in response to unfavourable environments. Bryophytes could provide valuable models to study developmental RCD processes as well as those triggered by biotic and abiotic stresses. Some pathways analogous to those present in angiosperms occur in the gametophytic haploid generation of bryophytes, allowing direct genetic studies. In this review, we focus on such RCD programmes, identifying core conserved mechanisms and raising new key questions to analyse RCD from an evolutionary perspective.

Ethylene controls three-dimensional growth involving reduced auxin levels in the moss Physcomitrium patens

The conquest of land by plants was concomitant with, and possibly enabled by, the evolution of three-dimensional (3D) growth. The moss Physcomitrium patens provides a model system for elucidating molecular mechanisms in the initiation of 3D growth. Here, we investigate whether the phytohormone ethylene, which is believed to have been a signal before land plant emergence, plays a role in 3D growth regulation in P. patens. We report ethylene controls 3D gametophore formation, based on results from exogenously applied ethylene and genetic manipulation of PpEIN2, which is a central component in the ethylene signaling pathway. Overexpression (OE) of PpEIN2 activates ethylene responses and leads to earlier formation of gametophores with fewer gametophores produced thereafter, phenocopying ethylene-treated wild-type. Conversely, Ppein2 knockout mutants, which are ethylene insensitive, show initially delayed gametophore formation with more gametophores produced later. Furthermore, pharmacological and biochemical analyses reveal auxin levels are decreased in the OE lines but increased in the knockout mutants. Our results suggest that evolutionarily, ethylene and auxin molecular networks were recruited to build the plant body plan in ancestral land plants. This might have played a role in enabling ancient plants to acclimate to the continental surfaces of the planet.

The genetic control of herkogamy

Herkogamy is the spatial separation of anthers and stigmas within complete flowers, and is a key floral trait that promotes outcrossing in many angiosperms. The degree of separation between pollen-producing anthers and receptive stigmas has been shown to influence rates of self-pollination amongst plants, with a reduction in herkogamy increasing rates of successful selfing in self-compatible species. Self-pollination is becoming a critical issue in horticultural crops grown in environments where biotic pollinators are limited, absent, or difficult to utilise. In these cases, poor pollination results in reduced yield and misshapen fruit. Whilst there is a growing body of work elucidating the genetic basis of floral organ development, the genetic and environmental control points regulating herkogamy are poorly understood. A better understanding of the developmental and regulatory pathways involved in establishing varying degrees of herkogamy is needed to provide insights into the production of flowers more adept at selfing to produce consistent, high-quality fruit. This review presents our current understanding of herkogamy from a genetics and hormonal perspective.

Physcomitrium patens PpRIC, an ancestral CRIB-domain ROP effector, inhibits auxin-induced differentiation of apical initial cells

RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.

The SAH7 Homologue of the Allergen Ole e 1 Interacts with the Putative Stress Sensor SBP1 (Selenium-Binding Protein 1) in Arabidopsis thaliana

In this study, we focused on a member of the Ole e 1 domain-containing family, AtSAH7, in Arabidopsis thaliana. Our lab reports for the first time on this protein, AtSAH7, that was found to interact with Selenium-binding protein 1 (AtSBP1). We studied by GUS assisted promoter deletion analysis the expression pattern of AtSAH7 and determined that the sequence 1420 bp upstream of the transcription start can act as a minimal promoter inducing expression in vasculature tissues. Moreover, mRNA levels of AtSAH7 were acutely increased under selenite treatment in response to oxidative stress. We confirmed the aforementioned interaction in vivo, in silico and in planta. Following a bimolecular fluorescent complementation approach, we determined that the subcellular localization of the AtSAH7 and the AtSAH7/AtSBP1 interaction occur in the ER. Our results indicate the participation of AtSAH7 in a biochemical network regulated by selenite, possibly associated with responses to ROS production.

Exogenously Applied Cytokinin Altered the Bacterial Release and Subsequent Stages of Nodule Development in Pea Ipd3/Cyclops Mutant

Regulation of plant hormonal status is one of the major targets of symbiotic signaling during nodule formation in legume plants. However, the genetic and hormonal networks that regulate transition to differentiation of nodules are not well-characterized in legume plants. Analysis of plant mutants forming nodules impaired in rhizobial infection allowed us to identify some regulators involved in the control of the later stages of nodule development. In the current work, we extend our earlier studies on the influence of exogenously applied cytokinin on the later stages of nodule morphogenesis using pea sym33 (ipd3/cyclops) mutants impaired in the gene encoding IPD3/CYCLOPS transcription factor. One of the noticeable effects of the influence of exogenously applied cytokinin on nodules in the sym33-3 mutant was an increasing size of these structures. Cytokinin treatment was shown to stimulate bacterial release and increase the percentage of infected cells in nodules. To explore the role of possible regulators of nodule differentiation, we performed searching in pea transcriptome. The transcriptome study in pea P. sativum revealed the importance of the CCS52 regulator, EFD transcription factor, SYMREM regulator, RSD, the MADS-domain/AGL, and SHORT INTERNODE/STYLISH gene families encoding transcription factors in the control of nodule differentiation. Analysis of the expression patterns was verified by real-time PCR in response to exogenously applied cytokinin treatment.

Organ Patterning at the Shoot Apical Meristem (SAM): The Potential Role of the Vascular System

Auxin, which is transported in the outermost cell layer, is one of the major players involved in plant organ initiation and positioning at the shoot apical meristem (SAM). However, recent studies have recognized the role of putative internal signals as an important factor collaborating with the well-described superficial pathway of organogenesis regulation. Different internal signals have been proposed; however, their nature and transport route have not been precisely determined. Therefore, in this mini-review, we aimed to summarize the current knowledge regarding the auxin-dependent regulation of organ positioning at the SAM and to discuss the vascular system as a potential route for internal signals. In addition, as regular organ patterning is a universal phenomenon, we focus on the role of the vasculature in this process in the major lineages of land plants, i.e., bryophytes, lycophytes, ferns, gymnosperms, and angiosperms.

Genome-Wide Identification and Expression Profiling of the SRS Gene Family in Melilotus albus Reveals Functions in Various Stress Conditions

The plant-specific SHI-related sequence (SRS) family of transcription factors plays a vital role in growth regulation, plant development, phytohormone biosynthesis, and stress response. However, the genome-wide identification and role in the abiotic stress-related functions of the SRS gene family were not reported in white sweet clover (Melilotus albus). In this study, nine M. albus SRS genes (named MaSRS01-MaSRS09) were identified via a genome-wide search method. All nine genes were located on six out of eight chromosomes in the genome of M. albus and duplication analysis indicated eight segmentally duplicated genes in the MaSRS family. These MaSRS genes were classified into six groups based on their phylogenetic relationships. The gene structure and motif composition results indicated that MaSRS members in the same group contained analogous intron/exon and motif organizations. Further, promoter region analysis of MaSRS genes uncovered various growth, development, and stress-responsive cis-acting elements. Protein interaction networks showed that each gene has both functions of interacting with other genes and members within the family. Moreover, real-time quantitative PCR was also performed to verify the expression patterns of nine MaSRS genes in the leaves of M. albus. The results showed that nine MaSRSs were up- and down-regulated at different time points after various stress treatments, such as salinity, low-temperature, salicylic acid (SA), and methyl jasmonate (MeJA). This is the first systematic study of the M. albus SRS gene family, and it can serve as a strong foundation for further elucidation of the stress response and physiological improvement of the growth functions in M. albus.

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.

Apical dominance control by TAR-YUC-mediated auxin biosynthesis is a deep homology of land plants

A key aim in biology is to identify which genetic changes contributed to the evolution of form through time. Apical dominance, the inhibitory effect exerted by shoot apices on the initiation or outgrowth of distant lateral buds, is a major regulatory mechanism of plant form.¹ Nearly a century of studies in the sporophyte of flowering plants have established the phytohormone auxin as a front-runner in the search for key factors controlling apical dominance,^2,3 identifying critical roles for long-range polar auxin transport and local auxin biosynthesis in modulating shoot branching.^4-10 A capacity for lateral branching evolved by convergence in the gametophytic shoot of mosses and primed its diversification;¹¹ however, polar auxin transport is relatively unimportant in this developmental process,¹² the contribution of auxin biosynthesis genes has not been assessed, and more generally, the extent of conservation in apical dominance regulation within the land plants remains largely unknown. To fill this knowledge gap, we sought to identify genetic determinants of apical dominance in the moss Physcomitrium patens. Here, we show that leafy shoot apex decapitation releases apical dominance through massive and rapid transcriptional reprogramming of auxin-responsive genes and altering auxin biosynthesis gene activity. We pinpoint a subset of P. patens TRYPTOPHAN AMINO-TRANSFERASE (TAR) and YUCCA FLAVIN MONOOXYGENASE-LIKE (YUC) auxin biosynthesis genes expressed in the main and lateral shoot apices and show that they are essential for coordinating branch initiation and outgrowth. Our results demonstrate that local auxin biosynthesis acts as a pivotal regulator of apical dominance in moss and constitutes a shared mechanism underpinning shoot architecture control in land plants.

Regulation of the Later Stages of Nodulation Stimulated by IPD3/CYCLOPS Transcription Factor and Cytokinin in Pea Pisum sativum L

The IPD3/CYCLOPS transcription factor was shown to be involved in the regulation of nodule primordia development and subsequent stages of nodule differentiation. In contrast to early stages, the stages related to nodule differentiation remain less studied. Recently, we have shown that the accumulation of cytokinin at later stages may significantly impact nodule development. This conclusion was based on a comparative analysis of cytokinin localization between pea wild type and ipd3/cyclops mutants. However, the role of cytokinin at these later stages of nodulation is still far from understood. To determine a set of genes involved in the regulation of later stages of nodule development connected with infection progress, intracellular accommodation, as well as plant tissue and bacteroid differentiation, the RNA-seq analysis of pea mutant SGEFix--2 (sym33) nodules impaired in these processes compared to wild type SGE nodules was performed. To verify cytokinin's influence on late nodule development stages, the comparative RNA-seq analysis of SGEFix--2 (sym33) mutant plants treated with cytokinin was also conducted. Findings suggest a significant role of cytokinin in the regulation of later stages of nodule development.

Genome-Wide Identification and Expression Analysis of the SRS Gene Family in Medicago sativa

SHI-related sequence (SRS) transcription factors, specific to plants, act as crucial regulators of plant organ growth and development. Here, we examined the Medicago sativa (alfalfa) SRS gene family (MsSRSs) to analyze the structure and function of MsSRSs using bioinformatics methods, and verify their abiotic stress responses through growth experiments. Twenty-seven MsSRS genes were identified from the genome-wide data of nontransgenic alfalfa. MsSRSs were distributed on 16 chromosomes and classified into seven different subfamilies by phylogenetic analysis. Forty-five cis-regulatory elements related to stress and phytohormone responsiveness, and tissue-specific expression occurred in the promoter sequences of MsSRSs. Ks values and Ka/Ks ratios of duplicate gene pairs showed that purifying selection affected most duplicate genes during their evolutionary history, while rapid recent positive selection strongly influenced MsSRS25 and MsSRS01. Real-time fluorescence quantitative PCR results showed that MsSRS genes could be induced by cold and salt stress. Within 12 h of salt stress exposure, the expression levels of seven and nine MsSRSs showed significant upregulation and downregulation, respectively. Within 12 h of cold stress exposure, the expression levels of the 3 and 13 selected MsSRSs showed significant upregulation and downregulation, respectively. Thus, this study provides novel comprehensive information on the MsSRS gene family, helpful for the study of SRS-mediated tolerance in alfalfa and the functional characteristics of SRS genes in other plants.

Biosorption effect of Aspergillus niger and Penicillium chrysosporium for Cd- and Pb-contaminated soil and their physiological effects on Vicia faba L

Phytoremediation is an important solution to soil pollution management. The goal of this study is to determine the biosorption ability of the two selected fungi (Aspergillus niger and Penicillium chrysosporium) under heavy metal stress on faba bean plants. The fungal strains produced phytohormones, siderophore, ACC deaminase, and secondary metabolites. The biosorption capacity of A. niger and P. chrysosporium was 0.09 and 0.06 mg g^-1 and 0.5 and 0.4 mg g^-1 in media containing Cd and Pb, respectively. Fourier transform infrared spectroscopy of the fungal cell wall show primary functional groups like hydroxyl, amide, carboxyl, phosphoryl, sulfhydryl, and nitro. Therefore, A. niger and P. chrysosporium were inoculated to soils, and then the faba bean seeds were sown. After 21 days of sowing, the plants were irrigated with water to severe as control, with 100 mg L^-1 of Cd and 200 mg L^-1 of Pb. The results show that Cd and Pb caused a significant reduction in morphological characteristics, auxin, gibberellins, photosynthetic pigments, minerals content, and antioxidant enzymes as compared to control plants but caused a substantial boost in abscisic acid, ethylene, electrolyte leakage, lipid peroxidation, glutathione, proline, superoxide dismutase, secondary metabolites, and antioxidant capacity. In inoculated plants, metal-induced oxidative stress was modulated by inhibiting the transport of metal and decreased electrolyte leakage and lipid peroxidation. Finally, the inoculation of endophytic fungi contributed actively to the absorption of heavy metals and decreased their content in soil and plants. This could be utilized as an excellent technique in the fields of heavy metal-contaminated sustainable agriculture.

Phytohormone biosynthesis and signaling pathways of mosses

Most known phytohormones regulate moss development. We present a comprehensive view of the synthesis and signaling pathways for the most investigated of these compounds in mosses, focusing on the model Physcomitrium patens. The last 50 years of research have shown that most of the known phytohormones are synthesized by the model moss Physcomitrium patens (formerly Physcomitrella patens) and regulate its development, in interaction with responses to biotic and abiotic stresses. Biosynthesis and signaling pathways are best described in P. patens for the three classical hormones auxins, cytokinins and abscisic acid. Furthermore, their roles in almost all steps of development, from early filament growth to gametophore development and sexual reproduction, have been the focus of much research effort over the years. Evidence of hormonal roles exist for ethylene and for CLE signaling peptides, as well as for salicylic acid, although their possible effects on development remain unclear. Production of brassinosteroids by P. patens is still debated, and modes of action for these compounds are even less known. Gibberellin biosynthesis and signaling may have been lost in P. patens, while gibberellin precursors such as ent-kaurene derivatives could be used as signals in a yet to discover pathway. As for jasmonic acid, it is not used per se as a hormone in P. patens, but its precursor OPDA appears to play a corresponding role in defense against abiotic stress. We have tried to gather a comprehensive view of the biosynthesis and signaling pathways for all these compounds in mosses, without forgetting strigolactones, the last class of plant hormones to be reported. Study of the strigolactone response in P. patens points to a novel signaling compound, the KAI2-ligand, which was likely employed as a hormone prior to land plant emergence.

PpEBB1 directly binds to the GCC box-like element of auxin biosynthesis related genes

EARLY BUD-BREAK 1 (EBB1) can promote bud break, and this function is likely conserved in woody plants. To get a more comprehensive understand of its function, peach (Prunus persica var. nectarina cultivar Zhongyou 4) PpEBB1 was overexpressed in Arabidopsis; the resultant phenotypes, including curved leaves, abnormal development of floral organs and low seed set, were similar to those of DORNRÖSCHEN-LIKE (DRNL) overexpression, indicating that PpEBB1 was a putative ortholog of AtDRNL. PpEBB1 bound to the GCC box-like element in the STYLISH1/SHI RELATED SEQUENCE5 (STY1/SRS5) promoter of peach, which has been proposed to occur in Arabidopsis as well. A GCC box-like element was also found in the YUCCA1 (YUC1) promoter, and PpEBB1 could bind to this element and activate the expression of YUC1. In addition to the elevated auxin content in the PpEBB1-oe plants as observed in our previous study, these results suggest that PpEBB1 can regulate auxin biosynthesis by directly activating related genes. Besides, we screened a zinc finger RING-finger protein, MYB30-INTERACTING E3 LIGASE 1 (PpMIEL1), showing interaction with PpEBB1, suggesting that the stability of PpEBB1 might be influenced by PpMIEL1 through ubiquitination.

A fundamental developmental transition in Physcomitrium patens is regulated by evolutionarily conserved mechanisms

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.

The production of auxin by dying cells

In this review, I discuss the possibility that dying cells produce much of the auxin in vascular plants. The natural auxin, indole-3-acetic acid (IAA), is derived from tryptophan by a two-step pathway via indole pyruvic acid. The first enzymes in the pathway, tryptophan aminotransferases, have a low affinity for tryptophan and break it down only when tryptophan levels rise far above normal intracellular concentrations. Such increases occur when tryptophan is released from proteins by hydrolytic enzymes as cells autolyse and die. Many sites of auxin production are in and around dying cells: in differentiating tracheary elements; in root cap cells; in nutritive tissues that break down in developing flowers and seeds; in senescent leaves; and in wounds. Living cells also produce auxin, such as those transformed genetically by the crown gall pathogen. IAA may first have served as an exogenous indicator of the presence of nutrient-rich decomposing organic matter, stimulating the production of rhizoids in bryophytes. As cell death was internalized in bryophytes and in vascular plants, IAA may have taken on a new role as an endogenous hormone.

Auxin Biology in Bryophyta: A Simple Platform with Versatile Functions

Bryophytes, including liverworts, mosses, and hornworts, are gametophyte-dominant land plants that are derived from a common ancestor and underwent independent evolution from the sporophyte-dominant vascular plants since their divergence. The plant hormone auxin has been shown to play pleiotropic roles in the haploid bodies of bryophytes. Pharmacological and chemical studies identified conserved auxin molecules, their inactivated forms, and auxin transport in bryophyte tissues. Recent genomic and molecular biological studies show deep conservation of components and their functions in auxin biosynthesis, inactivation, transport, and signaling in land plants. Low genetic redundancy in model bryophytes enable unique assays, which are elucidating the design principles of the auxin signaling pathway. In this article, the physiological roles of auxin and regulatory mechanisms of gene expression and development by auxin in Bryophyta are reviewed.

Lotus japonicus Nuclear Factor YA1, a nodule emergence stage-specific regulator of auxin signalling

Organogenesis of legume root nodules begins with the nodulation factor-dependent stimulation of compatible root cells to initiate divisions, signifying an early nodule primordium formation event. This is followed by cellular differentiation, including cell expansion and vascular bundle formation, and we previously showed that Lotus japonicus NF-YA1 is essential for this process, presumably by regulating three members of the SHORT INTERNODES/STYLISH (STY) transcription factor gene family. In this study, we used combined genetics, genomics and cell biology approaches to characterize the role of STY genes during root nodule formation and to test a hypothesis that they mediate nodule development by stimulating auxin signalling. We show here that L. japonicus STYs are required for nodule emergence. This is attributed to the NF-YA1-dependent regulatory cascade, comprising STY genes and their downstream targets, YUCCA1 and YUCCA11, involved in a local auxin biosynthesis at the post-initial cell division stage. An analogous NF-YA1/STY regulatory module seems to operate in Medicago truncatula in association with the indeterminate nodule patterning. Our data define L. japonicus and M. truncatula NF-YA1 genes as important nodule emergence stage-specific regulators of auxin signalling while indicating that the inductive stage and subsequent formation of early nodule primordia are mediated through an independent mechanism(s).

Light- and hormone-mediated development in non-flowering plants: An overview

Light, hormones and their interaction regulate different aspects of development in non-flowering plants. They might have played a role in the evolution of different plant groups by conferring specific adaptive evolutionary changes. Plants are sessile organisms. Unlike animals, they lack the opportunity to abandon their habitat in unfavorable conditions. They respond to different environmental cues and adapt accordingly to control their growth and developmental pattern. While phytohormones are known to be internal regulators of plant development, light is a major environmental signal that shapes plant processes. It is plausible that light-hormone crosstalk might have played an important role in plant evolution. But how the crosstalk between light and phytohormone signaling pathways might have shaped the plant evolution is unclear. One of the possible reasons is that flowering plants have been studied extensively in context of plant development, which cannot serve the purpose of evolutionary comparisons. In order to elucidate the role of light, hormone and their crosstalk in the evolutionary adaptation in plant kingdom, one needs to understand various light- and hormone-mediated processes in diverse non-flowering plants. This review is an attempt to outline major light- and phytohormone-mediated responses in non-flowering plant groups such as algae, bryophytes, pteridophytes and gymnosperms.

Evolution of NIN and NIN-like Genes in Relation to Nodule Symbiosis

Legumes and actinorhizal plants are capable of forming root nodules symbiosis with rhizobia and Frankia bacteria. All these nodulating species belong to the nitrogen fixation clade. Most likely, nodulation evolved once in the last common ancestor of this clade. NIN (NODULE INCEPTION) is a transcription factor that is essential for nodulation in all studied species. Therefore, it seems probable that it was recruited at the start when nodulation evolved. NIN is the founding member of the NIN-like protein (NLP) family. It arose by duplication, and this occurred before nodulation evolved. Therefore, several plant species outside the nitrogen fixation clade have NLP(s), which is orthologous to NIN. In this review, we discuss how NIN has diverged from the ancestral NLP, what minimal changes would have been essential for it to become a key transcription controlling nodulation, and which adaptations might have evolved later.

Minimal auxin sensing levels in vegetative moss stem cells revealed by a ratiometric reporter

Efforts to reveal ancestral functions of auxin, a key regulator of plant growth and development, and its importance for evolution have been hampered by a fragmented picture of auxin response domains in early-diverging land plants. We report the mapping of auxin sensing and responses during vegetative moss development using novel reporters. We established a moss-specific ratiometric reporter (PpR2D2) for Auxin Response Element- and AUXIN RESPONSE FACTOR-independent auxin sensing in Physcomitrella patens, and its readout during vegetative development was compared with new promoter-based GmGH3::GFPGUS and DR5revV2::GFPGUS auxin response reporters. The ratiometric reporter responds rapidly to auxin in a time-, dose- and TRANSPORT INHIBITOR RESISTANT1/AUXIN F-BOX-dependent manner and marks known, anticipated and novel auxin sensing domains. It reveals proximal auxin sensing maxima in filamentous tissues and sensing minima in all five vegetative gametophytic stem cell types as well as dividing cells. PpR2D2 readout is compliant with an ancestral function of auxin as a positive regulator of differentiation vs proliferation in stem cell regions. The PpR2D2 reporter is a sensitive tool for high-resolution mapping of auxin sensing, which can increase our knowledge of auxin function in early-diverging land plants substantially, thereby advancing our understanding of its importance for plant evolution.

Gynoecium development: networks in Arabidopsis and beyond

Life has always found a way to preserve itself. One strategy that has been developed for this purpose is sexual reproduction. In land plants, the gynoecium is considered to be at the top of evolutionary innovation, since it has been a key factor in the success of the angiosperms. The gynoecium is composed of carpels with different tissues that need to develop and differentiate in the correct way. In order to control and guide gynoecium development, plants have adapted elements of pre-existing gene regulatory networks (GRNs) but new ones have also evolved. The GRNs can interact with internal factors (e.g. hormones and other metabolites) and external factors (e.g. mechanical signals and temperature) at different levels, giving robustness and flexibility to gynoecium development. Here, we review recent findings regarding the role of cytokinin-auxin crosstalk and the genes that connect these hormonal pathways during early gynoecium development. We also discuss some examples of internal and external factors that can modify GRNs. Finally, we make a journey through the flowering plant lineage to determine how conserved are these GRNs that regulate gynoecium and fruit development.

Homologs of the STYLISH gene family control nectary development in Aquilegia

Floral nectaries are an interesting example of a convergent trait in flowering plants, and are associated with the diversification of numerous angiosperm lineages, including the adaptive radiation of the New World Aquilegia species. However, we know very little as to what genes contribute to nectary development and evolution, particularly in noncore eudicot taxa. We analyzed expression patterns and used RNAi-based methods to investigate the functions of homologs from the STYLISH (STY) family in nectar spur development in Aquilegia coerulea. We found that AqSTY1 exhibits concentrated expression in the presumptive nectary of the growing spur tip, and triple gene silencing of the three STY-like genes revealed that they function in style and nectary development. Strong expression of STY homologs was also detected in the nectary-bearing petals of Delphinium and Epimedium. Our results suggest that the novel recruitment of STY homologs to control nectary development is likely to have occurred before the diversification of the Ranunculaceae and Berberidaceae. To date, the STY homologs of the Ranunculales are the only alternative loci for the control of nectary development in flowering plants, providing a critical data point in understanding the evolutionary origin and developmental basis of nectaries.

Chiral events in developing gametophores of Physcomitrella patens and other moss species are driven by an unknown, universal direction-sensing mechanism

PREMISE OF THE STUDY

We used the model species Physcomitrella patens to examine chirality in moss gametophores. Chirality is manifested in the direction of consecutive apical cell divisions, cell plate configurations, and deviations of leaf connecting lines from the vertical course. However, the frequencies of chiral configurations of all these processes as well as their mutual dependence-especially in the case of gametophore branching-are not known. Other moss species were checked to determine the universality of our findings.

METHODS

The gametophore structure of Physcomitrella patens grown in the laboratory under controlled conditions was investigated using light microscopy and compared with that of other moss species collected from their natural stands.

KEY RESULTS

In all investigated moss species, the tetrahedral apical cell exhibits either clockwise or counterclockwise consecutive divisions, and selection of this directionality in the primary axis is random. It is, however, related to cell plate configuration. If the plate is skewed, leaf-producing segments arising from the apical cell cleavage exhibit circumferential rotation. Three parallel lines connecting the leaves deviate from a vertical course, but always in the same direction as that of leaf initiation; thus, the angular distance between consecutive leaves increases to >120°. Lateral branches are exclusively antidromous.

CONCLUSIONS

Gametophore chiral configuration appears to be useful in resolving problems of moss modular growth and branching. Morphological and anatomical evidence strongly suggests that an unknown direction-sensing mechanism controls the development of moss axial organs. We propose that leaves are responsible for a horizontal gradient of sugar signals that develops along the gametophore circumference, thus influencing branching-unit chirality.

Mutational studies of the Aux/IAA proteins in Physcomitrella reveal novel insights into their function

The plant hormone auxin regulates many aspects of plant growth and development. Auxin signaling involves hormone perception by the TRANSPORT INHIBITOR RESPONSE/AUXIN F-BOX (TIR1/AFB)-Aux/IAA co-receptor system, and the subsequent degradation of the Aux/IAA transcriptional repressors by the ubiquitin proteasome pathway. This leads to the activation of downstream gene expression and diverse physiological responses. Here, we investigate how the structural elements in the Aux/IAAs determine their function in Auxin perception and transcriptional repression. We took advantage of the facile genetics of the moss Physcomitrella patens to determine the activity of wild-type and mutant PpIAA1a proteins in a Δaux/iaa null background. In this way, Aux/IAA function was characterized at the molecular and physiological levels without the interference of genetic redundancy. We identified and characterized degron variants in Aux/IAAs that affect their stability and Auxin response. We also demonstrated that neither the Aux/IAA EAR motif nor Aux/IAA oligomerization is essential for the repressive function of Aux/IAA. Our study demonstrates how key elements within the Aux/IAA proteins fine tune stability and repressor activity, as well as the long-term developmental outcome.

Auxin-mediated developmental control in the moss Physcomitrella patens

The signalling molecule auxin regulates many fundamental aspects of growth and development in plants. We review and discuss what is known about auxin-regulated development in mosses, with special emphasis on the model species Physcomitrella patens. It is well established that mosses and other early diverging plants produce and respond to auxin. By sequencing the P. patens genome, it became clear that it encodes many core proteins important for auxin homeostasis, perception, and signalling, which have also been identified in flowering plants. This suggests that the auxin molecular network was present in the last common ancestor of flowering plants and mosses. Despite fundamental differences in their life cycles, key processes such as organ initiation and outgrowth, branching, tropic responses, as well as cell differentiation, division, and expansion appear to be regulated by auxin in the two lineages. This knowledge paves the way for studies aimed at a better understanding of the origin and evolution of auxin function and how auxin may have contributed to the evolution of land plants.

Co-expression and Transcriptome Analysis of Marchantia polymorpha Transcription Factors Supports Class C ARFs as Independent Actors of an Ancient Auxin Regulatory Module

We performed differential gene expression (DGE) and co-expression analyses with genes encoding components of hormonal signaling pathways and the ∼400 annotated transcription factors (TFs) of M. polymorpha across multiple developmental stages of the life cycle. We identify a putative auxin-related co-expression module that has significant overlap with transcripts induced in auxin-treated tissues. Consistent with phylogenetic and functional studies, the class C ARF, MpARF3, is not part of the auxin-related co-expression module and instead is associated with transcripts enriched in gamete-producing gametangiophores. We analyze the Mparf3 and MpmiR160 mutant transcriptomes in the context of coexpression to suggest that MpARF3 may antagonize the reproductive transition via activating the MpMIR11671 and MpMIR529c precursors whose encoded microRNAs target SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcripts of MpSPL1 and MpSPL2. Both MpSPL genes are part of the MpARF3 co-expression group corroborating their functional significance. We provide evidence of the independence of MpARF3 from the auxin-signaling module and provide new testable hypotheses on the role of auxin-related genes in patterning meristems and differentiation events in liverworts.

The Physcomitrella patens exocyst subunit EXO70.3d has distinct roles in growth and development, and is essential for completion of the moss life cycle

The exocyst, an evolutionarily conserved secretory vesicle-tethering complex, spatially controls exocytosis and membrane turnover in fungi, metazoans and plants. The exocyst subunit EXO70 exists in multiple paralogs in land plants, forming three conserved clades with assumed distinct roles. Here we report functional analysis of the first moss exocyst subunit to be studied, Physcomitrella patens PpEXO70.3d (Pp1s97_91V6), from the, as yet, poorly characterized EXO70.3 clade. Following phylogenetic analysis to confirm the presence of three ancestral land plant EXO70 clades outside angiosperms, we prepared and phenotypically characterized loss-of-function Ppexo70.3d mutants and localized PpEXO70.3d in vivo using green fluorescent protein-tagged protein expression. Disruption of PpEXO70.3d caused pleiotropic cell elongation and differentiation defects in protonemata, altered response towards exogenous auxin, increased endogenous IAA concentrations, along with defects in bud and gametophore development. During mid-archegonia development, an abnormal egg cell is formed and subsequently collapses, resulting in mutant sterility. Mutants exhibited altered cell wall and cuticle deposition, as well as compromised cytokinesis, consistent with the protein localization to the cell plate. Despite some functional redundancy allowing survival of moss lacking PpEXO70.3d, this subunit has an essential role in the moss life cycle, indicating sub-functionalization within the moss EXO70 family.

How hormones regulate floral architecture in barley

A defining characteristic of grasses, including major cereal crops, is the way in which flowers are arranged on an inflorescence. A new study finds that regulation of hormone levels during development is crucial for determining the arrangement of flowers on a barley inflorescence, opening new doors for increasing grain yield.

An Evolutionary Framework for Carpel Developmental Control Genes

Carpels are the female reproductive organs of flowering plants (angiosperms), enclose the ovules, and develop into fruits. The presence of carpels unites angiosperms, and they are suggested to be the most important autapomorphy of the angiosperms, e.g., they prevent inbreeding and allow efficient seed dispersal. Many transcriptional regulators and coregulators essential for carpel development are encoded by diverse gene families and well characterized in Arabidopsis thaliana. Among these regulators are AGAMOUS (AG), ETTIN (ETT), LEUNIG (LUG), SEUSS (SEU), SHORT INTERNODE/STYLISH (SHI/STY), and SEPALLATA1, 2, 3, 4 (SEP1, 2, 3, 4). However, the timing of the origin and their subsequent molecular evolution of these carpel developmental regulators are largely unknown. Here, we have sampled homologs of these carpel developmental regulators from the sequenced genomes of a wide taxonomic sampling of the land plants, such as Physcomitrella patens, Selaginella moellendorfii, Picea abies, and several angiosperms. Careful phylogenetic analyses were carried out that provide a phylogenetic background for the different gene families and provide minimal estimates for the ages of these developmental regulators. Our analyses and published work show that LUG-, SEU-, and SHI/STY-like genes were already present in the Most Recent Common Ancestor (MRCA) of all land plants, AG- and SEP-like genes were present in the MRCA of seed plants and their origin may coincide with the ξ Whole Genome Duplication. Our work shows that the carpel development regulatory network was, in part, recruited from preexisting network components that were present in the MRCA of angiosperms and modified to regulate gynoecium development.

ABSCISIC ACID INSENSITIVE3 Is Involved in Cold Response and Freezing Tolerance Regulation in Physcomitrella patens

 Synopsis This work demonstrates that PpABI3 contributes to freezing tolerance regulation in Physcomitrella patens. Transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3) is known to play a major role in regulating seed dormancy, germination, seedling development as well as stress responses. ABI3 is conserved among land plants; however, its roles in non-seed plants under stress conditions have not been well characterized. In this study, we report that ABI3 is involved in freezing tolerance regulation during cold acclimation at least in part through ABA signaling pathway in moss Physcomitrella patens (P. patens). Deletion of PpABI3 (Δabi3-1) compromises the induction of genes related to cold response and antioxidative protection, resulting in reduced accumulation of cryoprotectants and antioxidants. In addition, photosystem II (PSII) activity is repressed in Δabi3-1 during cold acclimation partially due to alternations of photosynthetic protein complexes compositions. The gametophyte of Δabi3-1 displays severe growth inhibition and developmental deficiency under low temperature condition, while two independent complementary lines display phenotypes similar to that of wild-type P. patens (WT). Furthermore, the freezing tolerance of Δabi3-1 was significantly affected by deletion of PpABI3. These data revealed that PpABI3 plays an important role in low temperature response and freezing tolerance in P. patens.

The Role of SHI/STY/SRS Genes in Organ Growth and Carpel Development Is Conserved in the Distant Eudicot Species Arabidopsis thaliana and Nicotiana benthamiana

Carpels are a distinctive feature of angiosperms, the ovule-bearing female reproductive organs that endow them with multiple selective advantages likely linked to the evolutionary success of flowering plants. Gene regulatory networks directing the development of carpel specialized tissues and patterning have been proposed based on genetic and molecular studies carried out in Arabidopsis thaliana. However, studies on the conservation/diversification of the elements and the topology of this network are still scarce. In this work, we have studied the functional conservation of transcription factors belonging to the SHI/STY/SRS family in two distant species within the eudicots, Eschscholzia californica and Nicotiana benthamiana. We have found that the expression patterns of EcSRS-L and NbSRS-L genes during flower development are similar to each other and to those reported for Arabidopsis SHI/STY/SRS genes. We have also characterized the phenotypic effects of NbSRS-L gene inactivation and overexpression in Nicotiana. Our results support the widely conserved role of SHI/STY/SRS genes at the top of the regulatory network directing style and stigma development, specialized tissues specific to the angiosperm carpels, at least within core eudicots, providing new insights on the possible evolutionary origin of the carpels.

Lotus japonicus NF-YA1 Plays an Essential Role During Nodule Differentiation and Targets Members of the SHI/STY Gene Family

Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation. However, the exact mechanism by which these transcriptional factors exert their symbiotic functions has remained elusive. By carrying out detailed functional analyses of Lotus japonicus mutants, we demonstrate that LjNF-YA1 becomes indispensable downstream from the initial cortical cell divisions but prior to nodule differentiation, including cell enlargement and vascular bundle formation. Three affiliates of the SHORT INTERNODES/STYLISH transcription factor gene family, called STY1, STY2, and STY3, are demonstrated to be among likely direct targets of LjNF-YA1, and our results point to their involvement in nodule formation.

VRS2 regulates hormone-mediated inflorescence patterning in barley

Plant architecture has clear agronomic and economic implications for crops such as wheat and barley, as it is a critical factor for determining grain yield. Despite this, only limited molecular information is available about how grain-bearing inflorescences, called spikes, are formed and maintain their regular, distichous pattern. Here we elucidate the molecular and hormonal role of Six-rowed spike 2 (Vrs2), which encodes a SHORT INTERNODES (SHI) transcriptional regulator during barley inflorescence and shoot development. We show that Vrs2 is specifically involved in floral organ patterning and phase duration by maintaining hormonal homeostasis and gradients during normal spike development and similarly influences plant stature traits. Furthermore, we establish a link between the SHI protein family and sucrose metabolism during organ growth and development that may have implications for deeper molecular insights into inflorescence and plant architecture in crops.

Multi-Scale Characean Experimental System: From Electrophysiology of Membrane Transporters to Cell-to-Cell Connectivity, Cytoplasmic Streaming and Auxin Metabolism

The morphology of characean algae could be mistaken for a higher plant: stem-like axes with leaf-like branchlets anchored in the soil by root-like rhizoids. However, all of these structures are made up of giant multinucleate cells separated by multicellular nodal complexes. The excised internodal cells survive long enough for the nodes to give rise to new thallus. The size of the internodes and their thick cytoplasmic layer minimize impalement injury and allow specific micro-electrode placement. The cell structure can be manipulated by centrifugation, perfusion of cell contents or creation of cytoplasmic droplets, allowing access to both vacuolar and cytoplasmic compartments and both sides of the cell membranes. Thousands of electrical measurements on intact or altered cells and cytoplasmic droplets laid down basis to modern plant electrophysiology. Furthermore, the giant internodal cells and whole thalli facilitate research into many other plant properties. As nutrients have to be transported from rhizoids to growing parts of the thallus and hormonal signals need to pass from cell to cell, Characeae possess very fast cytoplasmic streaming. The mechanism was resolved in the characean model. Plasmodesmata between the internodal cells and nodal complexes facilitate transport of ions, nutrients and photosynthates across the nodes. The internal structure was found to be similar to those of higher plants. Recent experiments suggest a strong circadian influence on metabolic pathways producing indole-3-acetic acid (IAA) and serotonin/melatonin. The review will discuss the impact of the characean models arising from fragments of cells, single cells, cell-to-cell transport or whole thalli on understanding of plant evolution and physiology.

Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins

The coordinated action of the auxin-sensitive Aux/IAA transcriptional repressors and ARF transcription factors produces complex gene-regulatory networks in plants. Despite their importance, our knowledge of these two protein families is largely based on analysis of stabilized forms of the Aux/IAAs, and studies of a subgroup of ARFs that function as transcriptional activators. To understand how auxin regulates gene expression we generated a Physcomitrella patens line that completely lacks Aux/IAAs. Loss of the repressors causes massive changes in transcription with misregulation of over a third of the annotated genes. Further, we find that the aux/iaa mutant is blind to auxin indicating that auxin regulation of transcription occurs exclusively through Aux/IAA function. We used the aux/iaa mutant as a simplified platform for studies of ARF function and demonstrate that repressing ARFs regulate auxin-induced genes and fine-tune their expression. Further the repressing ARFs coordinate gene induction jointly with activating ARFs and the Aux/IAAs.

Diversification of fruit shape in the Brassicaceae family

Diversity in fruit shape. Angiosperms (flowering plants) evolved during the Cretaceous Period more than 100 million years ago and quickly colonized all terrestrial habitats on the planet. A major reason for their success was the formation of fruits that would protect and nurture the developing seeds. Moreover, a massive range of diversity in fruit shape occurred during a relatively short time, which allowed for the development of ingenious ways of fertilization as well as strategies for efficient seed dispersal. The Brassicaceae family more than any exemplifies the diversity in fruit morphologies, thus providing an ideal group of plants to study how specific shapes are established. Although many genes controlling fruit patterning in the model plant Arabidopsis thaliana have been identified, the processes of carpel and fruit morphogenesis are still poorly understood. Moreover, Arabidopsis fruits are relatively simple in their structure and are therefore not ideally suited for analyzing processes of morphology determination without comparison to species with differently shaped fruits. Here, we review the diversity of fruit shape within the Brassicaceae family. As an example we describe the close relative of Arabidopsis, Capsella rubella that develops flat, heart-shaped fruits showing and highlighting its potential as a model system for research into organ shape. Recent progress in genomics including fast and cheap genome sequencing and annotation as well as development of mutant populations has opened entirely new and exciting possibilities of studying the mechanisms and processes underlying fruit formation in angiosperms.

RSL Class I Genes Controlled the Development of Epidermal Structures in the Common Ancestor of Land Plants

The colonization of the land by plants, sometime before 470 million years ago, was accompanied by the evolution tissue systems [1-3]. Specialized structures with diverse functions-from nutrient acquisition to reproduction-derived from single cells in the outermost layer (epidermis) were important sources of morphological innovation at this time [2, 4, 5]. In extant plants, these structures may be unicellular extensions, such as root hairs or rhizoids [6-9], or multicellular structures, such as asexual propagules or secretory hairs (papillae) [10-12]. Here, we show that a ROOTHAIR DEFECTIVE SIX-LIKE (RSL) class I basic helix-loop-helix transcription factor positively regulates the development of the unicellular and multicellular structures that develop from individual cells that expand out of the epidermal plane of the liverwort Marchantia polymorpha; mutants that lack MpRSL1 function do not develop rhizoids, slime papillae, mucilage papillae, or gemmae. Furthermore, we discovered that RSL class I genes are also required for the development of multicellular axillary hairs on the gametophyte of the moss Physcomitrella patens. Because class I RSL proteins also control the development of rhizoids in mosses and root hairs in angiosperms [13, 14], these data demonstrate that the function of RSL class I genes was to control the development of structures derived from single epidermal cells in the common ancestor of the land plants. Class I RSL genes therefore controlled the generation of adaptive morphological diversity as plants colonized the land from the water.

Transgenic poplar expressing Arabidopsis YUCCA6 exhibits auxin-overproduction phenotypes and increased tolerance to abiotic stress

YUCCA6, a member of the YUCCA family of flavin monooxygenase-like proteins, is involved in the tryptophan-dependent IAA biosynthesis pathway and responses to environmental cues in Arabidopsis. However, little is known about the role of the YUCCA pathway in auxin biosynthesis in poplar. Here, we generated transgenic poplar (Populus alba × P. glandulosa) expressing the Arabidopsis YUCCA6 gene under the control of the oxidative stress-inducible SWPA2 promoter (referred to as SY plants). Three SY lines (SY7, SY12 and SY20) were selected based on the levels of AtYUCCA6 transcript. SY plants displayed auxin-overproduction morphological phenotypes, such as rapid shoot growth and retarded main root development with increased root hair formation. In addition, SY plants had higher levels of free IAA and early auxin-response gene transcripts. SY plants exhibited tolerance to drought stress, which was associated with reduced levels of reactive oxygen species. Furthermore, SY plants showed delayed hormone- and dark-induced senescence in detached leaves due to higher photosystem II efficiency and less membrane permeability. These results suggest that the conserved IAA biosynthesis pathway mediated by YUCCA family members exists in poplar.

Conserved regulatory mechanism controls the development of cells with rooting functions in land plants

Land plants develop filamentous cells-root hairs, rhizoids, and caulonemata-at the interface with the soil. Members of the group XI basic helix-loop-helix (bHLH) transcription factors encoded by LOTUS JAPONICUS ROOTHAIRLESS1-LIKE (LRL) genes positively regulate the development of root hairs in the angiosperms Lotus japonicus, Arabidopsis thaliana, and rice (Oryza sativa). Here we show that auxin promotes rhizoid and caulonema development by positively regulating the expression of PpLRL1 and PpLRL2, the two LRL genes in the Physcomitrella patens genome. Although the group VIII bHLH proteins, AtROOT HAIR DEFECTIVE6 and AtROOT HAIR DEFECTIVE SIX-LIKE1, promote root-hair development by positively regulating the expression of AtLRL3 in A. thaliana, LRL genes promote rhizoid development independently of PpROOT HAIR DEFECTIVE SIX-LIKE1 and PpROOT HAIR DEFECITVE SIX-LIKE2 (PpRSL1 and PpRSL2) gene function in P. patens. Together, these data demonstrate that both LRL and RSL genes are components of an ancient auxin-regulated gene network that controls the development of tip-growing cells with rooting functions among most extant land plants. Although this network has diverged in the moss and the angiosperm lineages, our data demonstrate that the core network acted in the last common ancestor of the mosses and angiosperms that existed sometime before 420 million years ago.

LATERAL ROOT PRIMORDIA 1 of maize acts as a transcriptional activator in auxin signalling downstream of the Aux/IAA gene rootless with undetectable meristem 1

Only little is known about target genes of auxin signalling downstream of the Aux/IAA-ARF module. In the present study, it has been demonstrated that maize lateral root primordia 1 (lrp1) encodes a transcriptional activator that is directly regulated by the Aux/IAA protein ROOTLESS WITH UNDETECTABLE MERISTEM 1 (RUM1). Expression of lrp1 is confined to early root primordia and meristems and is auxin-inducible. Based on its primary protein structure, LRP1 is predicted to be a transcription factor. This notion is supported by exclusive LRP1 localization in the nucleus and its ability to activate downstream gene activity. Based on the observation that lrp1 transcription is completely repressed in the semi-dominant gain of function mutant rum1, it was demonstrated that the lrp1 promoter is a direct target of RUM1 proteins. Subsequently, promoter activation assays indicated that RUM1 represses the expression of a GFP reporter fused to the native promoter of lrp1. Constitutive repression of lrp1 in rum1 mutants is a consequence of the stability of mutated rum1 proteins which cannot be degraded by the proteasome and thus constitutively bind to the lrp1 promoter and repress transcription. Taken together, the repression of the transcriptional activator lrp1 by direct binding of RUM1 to its promoter, together with specific expression of lrp1 in root meristems, suggests a function in maize root development via the RUM1-dependent auxin signalling pathway.

A Simple Auxin Transcriptional Response System Regulates Multiple Morphogenetic Processes in the Liverwort Marchantia polymorpha

In land plants comparative genomics has revealed that members of basal lineages share a common set of transcription factors with the derived flowering plants, despite sharing few homologous structures. The plant hormone auxin has been implicated in many facets of development in both basal and derived lineages of land plants. We functionally characterized the auxin transcriptional response machinery in the liverwort Marchantia polymorpha, a member of the basal lineage of extant land plants. All components known from flowering plant systems are present in M. polymorpha, but they exist as single orthologs: a single MpTOPLESS (TPL) corepressor, a single MpTRANSPORT inhibitor response 1 auxin receptor, single orthologs of each class of auxin response factor (ARF; MpARF1, MpARF2, MpARF3), and a single negative regulator auxin/indole-3-acetic acid (MpIAA). Phylogenetic analyses suggest this simple system is the ancestral condition for land plants. We experimentally demonstrate that these genes act in an auxin response pathway--chimeric fusions of the MpTPL corepressor with heterodimerization domains of MpARF1, MpARF2, or their negative regulator, MpIAA, generate auxin insensitive plants that lack the capacity to pattern and transition into mature stages of development. Our results indicate auxin mediated transcriptional regulation acts as a facilitator of branching, differentiation and growth, rather than acting to determine or specify tissues during the haploid stage of the M. polymorpha life cycle. We hypothesize that the ancestral role of auxin is to modulate a balance of differentiated and pluri- or totipotent cell states, whose fates are determined by interactions with combinations of unrelated transcription factors.

Three ancient hormonal cues co-ordinate shoot branching in a moss

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

DOI:http://dx.doi.org/10.7554/eLife.06808.001

Most land plants have shoots that form branches and plants can regulate when and where they grow these branches to best exploit their environment. Plants with flowers and the more ancient mosses both have branching shoots, but these two groups of plants evolved to grow in this way independently of each other. Most studies on shoot branching have focused on flowering plants and so it is less clear how branching works in mosses.

Three plant hormones—called auxin, cytokinin and strigolactone—control shoot branching in flowering plants. Auxin moves down the main shoot of the plant to prevent new branches from forming. This movement is controlled by the PIN proteins and several other families of proteins. On the other hand, cytokinin promotes the growth of new branches; and strigolactone can either promote or inhibit shoot branching depending on how the auxin is travelling around the plant.

Coudert, Palubicki et al. studied shoot branching in a species of moss called Physcomitrella patens. The experiments show that cells on the outer surface of the main shoot are essentially reprogrammed to become so-called ‘branch initials’, which will then develop into new branches. Next, Coudert, Palubicki et al. made a computational model that was able to simulate the pattern of shoot branching in the moss.

Further experiments supported the predictions made by the model. Coudert, Palubicki et al. found that, as in flowering plants, auxin from the tip of the main shoot suppresses branching in the moss, and cytokinin promotes branching. The experiments also showed that strigolactone inhibits shoot branching, but its role is restricted to the base of the shoots. The model predicts that, unlike in flowering plants, auxin must flow in both directions in moss shoots to produce the observed patterns of shoot branching. Also, the experiments suggest that the PIN proteins and another group of proteins that control the movement of auxin do not regulate shoot branching in moss. Instead, it appears that auxin may move through microscopic channels that link one moss cell to the next.

Coudert, Palubicki et al.'s findings suggest that both flowering plants and mosses have evolved to use the same three hormones to control shoot branching, but that these hormones interact in different ways. One key next step will be to find out how auxin is transported during shoot branching in moss by manipulating the opening of the channels between the cells. A further challenge will be to find out the precise details of how the hormones control the activity of the branch initial cells.

DOI:http://dx.doi.org/10.7554/eLife.06808.002

Three ancient hormonal cues co-ordinate shoot branching in a moss

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

Copper mediates auxin signalling to control cell differentiation in the copper moss Scopelophila cataractae

The copper (Cu) moss Scopelophila cataractae (Mitt.) Broth. is often found in Cu-enriched environments, but it cannot flourish under normal conditions in nature. Excess Cu is toxic to almost all plants, and therefore how this moss species thrives in regions with high Cu concentration remains unknown. In this study, we investigated the effect of Cu on gemma germination and protonemal development in S. cataractae. A high concentration of Cu (up to 800 µM) did not affect gemma germination. In the protonemal stage, a low concentration of Cu promoted protonemal gemma formation, which is the main strategy adopted by S. cataractae to expand its habitat to new locations. Cu-rich conditions promoted auxin accumulation and induced differentiation of chloronema into caulonema cells, whereas it repressed protonemal gemma formation. Under low-Cu conditions, auxin treatment mimicked the effects of high-Cu conditions. Furthermore, Cu-induced caulonema differentiation was severely inhibited in the presence of the auxin antagonist α-(phenylethyl-2-one)-indole-3-acetic acid, or the auxin biosynthesis inhibitor l-kynurenine. These results suggest that S. cataractae flourishes in Cu-rich environments via auxin-regulated cell differentiation. The copper moss might have acquired this mechanism during the evolutionary process to benefit from its advantageous Cu-tolerance ability.

The Physcomitrella patens unique alpha-dioxygenase participates in both developmental processes and defense responses

BACKGROUND

Plant α-dioxygenases catalyze the incorporation of molecular oxygen into polyunsaturated fatty acids leading to the formation of oxylipins. In flowering plants, two main groups of α-DOXs have been described. While the α-DOX1 isoforms are mainly involved in defense responses against microbial infection and herbivores, the α-DOX2 isoforms are mostly related to development. To gain insight into the roles played by these enzymes during land plant evolution, we performed biochemical, genetic and molecular analyses to examine the function of the single copy moss Physcomitrella patens α-DOX (Ppα-DOX) in development and defense against pathogens.

RESULTS

Recombinant Ppα-DOX protein catalyzed the conversion of fatty acids into 2-hydroperoxy derivatives with a substrate preference for α-linolenic, linoleic and palmitic acids. Ppα-DOX is expressed during development in tips of young protonemal filaments with maximum expression levels in mitotically active undifferentiated apical cells. In leafy gametophores, Ppα-DOX is expressed in auxin producing tissues, including rhizoid and axillary hairs. Ppα-DOX transcript levels and Ppα-DOX activity increased in moss tissues infected with Botrytis cinerea or treated with Pectobacterium carotovorum elicitors. In B. cinerea infected leaves, Ppα-DOX-GUS proteins accumulated in cells surrounding infected cells, suggesting a protective mechanism. Targeted disruption of Ppα-DOX did not cause a visible developmental alteration and did not compromise the defense response. However, overexpressing Ppα-DOX, or incubating wild-type tissues with Ppα-DOX-derived oxylipins, principally the aldehyde heptadecatrienal, resulted in smaller moss colonies with less protonemal tissues, due to a reduction of caulonemal filament growth and a reduction of chloronemal cell size compared with normal tissues. In addition, Ppα-DOX overexpression and treatments with Ppα-DOX-derived oxylipins reduced cellular damage caused by elicitors of P. carotovorum.

CONCLUSIONS

Our study shows that the unique α-DOX of the primitive land plant P. patens, although apparently not crucial, participates both in development and in the defense response against pathogens, suggesting that α-DOXs from flowering plants could have originated by duplication and successive functional diversification after the divergence from bryophytes.