Evolution of the bHLH genes involved in stomatal development: implications for the expansion of developmental complexity of stomata in land plants

Beyond stomatal development: SMF transcription factors as versatile toolkits for land plant evolution

As master transcription factors of stomatal development, SPEECHLESS, MUTE, and FAMA, collectively termed SMFs, are primary targets of molecular genetic analyses in the model plant Arabidopsis thaliana. Studies in other model systems identified SMF orthologs as key players in evolutionary developmental biology studies on stomata. However, recent studies on the astomatous liverwort Marchantia polymorpha revealed that the functions of these genes are not limited to the stomatal development, but extend to other types of tissues, namely sporophytic setal and gametophytic epidermal tissues. These studies provide insightful examples of gene-regulatory network co-opting, and highlight SMFs and related transcription factors as general toolkits for novel trait evolution in land plant lineages. Here, we critically review recent literature on the SMF-like gene in M. polymorpha and discuss their implications for plant evolutionary biology.

Investigation of a Perspective Urban Tree Species, Ginkgo biloba L., by Scientific Analysis of Historical Old Specimens

In this study, we examined over 200-year-old Ginkgo biloba L. specimens under different environmental conditions. The overall aim was to explore which factors influence their vitality and general fitness in urban environments and thus their ability to tolerate stressful habitats. In order to determine this, we used a number of different methods, including histological examinations (stomatal density and size) and physiological measurements (peroxidase enzyme activity), as well as assessing the air pollution tolerance index (APTI). The investigation of the genetic relationships between individuals was performed using flow cytometry and miRNA marker methods. The genetic tests revealed that all individuals are diploid, whereas the lus-miR168 and lus-miR408 markers indicated a kinship relation between them. These results show that the effect of different habitat characteristics can be detected through morphological and physiological responses, thus indicating relatively higher stress values for all studied individuals. A significant correlation can be found between the level of adaptability and the relatedness of the examined individuals. These results suggest that Ginkgo biloba L. is well adapted to an environment with increased stress factors and therefore suitable for use in urban areas.

AGAMOUS mediates timing of guard cell formation during gynoecium development

In Arabidopsis thaliana, stomata are composed of two guard cells that control the aperture of a central pore to facilitate gas exchange between the plant and its environment, which is particularly important during photosynthesis. Although leaves are the primary photosynthetic organs of flowering plants, floral organs are also photosynthetically active. In the Brassicaceae, evidence suggests that silique photosynthesis is important for optimal seed oil content. A group of transcription factors containing MADS DNA binding domains is necessary and sufficient to confer floral organ identity. Elegant models, such as the ABCE model of flower development and the floral quartet model, have been instrumental in describing the molecular mechanisms by which these floral organ identity proteins govern flower development. However, we lack a complete understanding of how the floral organ identity genes interact with the underlying leaf development program. Here, we show that the MADS domain transcription factor AGAMOUS (AG) represses stomatal development on the gynoecial valves, so that maturation of stomatal complexes coincides with fertilization. We present evidence that this regulation by AG is mediated by direct transcriptional repression of a master regulator of the stomatal lineage, MUTE, and show data that suggests this interaction is conserved among several members of the Brassicaceae. This work extends our understanding of the mechanisms underlying floral organ formation and provides a framework to decipher the mechanisms that control floral organ photosynthesis.

Experimental validation of the mechanism of stomatal development diversification

Stomata are the structures responsible for gas exchange in plants. The established framework for stomatal development is based on the model plant Arabidopsis, but diverse patterns of stomatal development have been observed in other plant lineages and species. The molecular mechanisms behind these diversified patterns are still poorly understood. We recently proposed a model for the molecular mechanisms of the diversification of stomatal development based on the genus Callitriche (Plantaginaceae), according to which a temporal shift in the expression of key stomatal transcription factors SPEECHLESS and MUTE leads to changes in the behavior of meristemoids (stomatal precursor cells). In the present study, we genetically manipulated Arabidopsis to test this model. By altering the timing of MUTE expression, we successfully generated Arabidopsis plants with early differentiation or prolonged divisions of meristemoids, as predicted by the model. The epidermal morphology of the generated lines resembled that of species with prolonged or no meristemoid divisions. Thus, the evolutionary process can be reproduced by varying the SPEECHLESS to MUTE transition. We also observed unexpected phenotypes, which indicated the participation of additional factors in the evolution of the patterns observed in nature. This study provides novel experimental insights into the diversification of meristemoid behaviors.

Liverwort bHLH transcription factors and the origin of stomata in plants

Stomata are distributed in nearly all major groups of land plants, with the only exception being liverworts. Instead of having stomata on sporophytes, many complex thalloid liverworts possess air pores in their gametophytes. At present, whether stomata in land plants are derived from a common origin remains under debate.^1,2,3 In Arabidopsis thaliana, a core regulatory module for stomatal development comprises members of the bHLH transcription factor (TF) family, including AtSPCH, AtMUTE, and AtFAMA of subfamily Ia and AtSCRM1/2 of subfamily IIIb. Specifically, AtSPCH, AtMUTE, and AtFAMA each successively form heterodimers with AtSCRM1/2, which in turn regulate the entry, division, and differentiation of stomatal lineages.^4,5,6,7 In the moss Physcomitrium patens, two SMF (SPCH, MUTE and FAMA) orthologs have been characterized, one of which is functionally conserved in regulating stomatal development.^8,9 We here provide experimental evidence that orthologous bHLH TFs in the liverwort Marchantia polymorpha affect air pore spacing as well as the development of the epidermis and gametangiophores. We found that the bHLH Ia and IIIb heterodimeric module is highly conserved in plants. Genetic complementation experiments showed that liverwort SCRM and SMF genes weakly restored a stomata phenotype in atscrm1, atmute, and atfama mutant backgrounds in A. thaliana. In addition, homologs of stomatal development regulators FLP and MYB88 also exist in liverworts and weakly rescued the stomatal phenotype of atflp/myb88 double mutant. These results provide evidence not only for a common origin of all stomata in extant plants but also for relatively simple stomata in the ancestral plant.

Different Leaf Anatomical Responses to Water Deficit in Maize and Soybean

The stomata on leaf surfaces control gas exchange and water loss, closing during dry periods to conserve water. The distribution and size of stomatal complexes is determined by epidermal cell differentiation and expansion during leaf growth. Regulation of these processes in response to water deficit may result in stomatal anatomical plasticity as part of the plant acclimation to drought. We quantified the leaf anatomical plasticity under water-deficit conditions in maize and soybean over two experiments. Both species produced smaller leaves in response to the water deficit, partly due to the reductions in the stomata and pavement cell size, although this response was greater in soybean, which also produced thicker leaves under severe stress, whereas the maize leaf thickness did not change. The stomata and pavement cells were smaller with the reduced water availability in both species, resulting in higher stomatal densities. Stomatal development (measured as stomatal index, SI) was suppressed in both species at the lowest water availability, but to a greater extent in maize than in soybean. The result of these responses is that in maize leaves, the stomatal area fraction (f_gc) was consistently reduced in the plants grown under severe but not moderate water deficit, whereas the f_gc did not decrease in the water-stressed soybean leaves. The water deficit resulted in the reduced expression of one of two (maize) or three (soybean) SPEECHLESS orthologs, and the expression patterns were correlated with SI. The vein density (VD) increased in both species in response to the water deficit, although the effect was greater in soybean. This study establishes a mechanism of stomatal development plasticity that can be applied to other species and genotypes to develop or investigate stomatal development plasticity.

Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptations to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptations, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the three main clades that was best explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light- or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and WGDs using phylogenomics.

Genome-wide analysis of potassium transport genes in Gossypium raimondii suggest a role of GrHAK/KUP/KT8, GrAKT2.1 and GrAKT1.1 in response to abiotic stress

Potassium (K⁺) is an important macro-nutrient for plants, which comprises almost 10% of plant's dry mass. It plays a crucial role in the growth of plants as well as other important processes related to metabolism and stress tolerance. Plants have a complex and well-organized potassium distribution system (channels and transporters). Cotton is the most important economic crop, which is the primary source of natural fiber. Soil deficiency in K⁺ can negatively affect yield and fiber quality of cotton. However, potassium transport system in cotton is poorly studied. Current study identified 43 Potassium Transport System (PTS) genes in Gossypium raimondii genome. Based on conserved domains, transmembrane domains, and motif structures, these genes were classified as K⁺ transporters (2 HKTs, 7 KEAs, and 16 KUP/HAK/KTs) and K⁺ channels (11 Shakers and 7 TPKs/KCO). The phylogenetic comparison of GrPTS genes from Arabidopsis thaliana, Glycine max, Oryza sativa, Medicago truncatula and Cicer arietinum revealed variations in PTS gene conservation. Evolutionary analysis predicted that most GrPTS genes were segmentally duplicated. Gene structure analysis showed that the intron/exon organization of these genes was conserved in specific-family. Chromosomal localization demonstrated a random distribution of PTS genes across all the thirteen chromosomes except chromosome six. Many stress responsive cis-regulatory elements were predicted in promoter regions of GrPTS genes. The RNA-seq data analysis followed by qRT-PCR validation demonstrated that PTS genes potentially work in groups against environmental factors. Moreover, a transporter gene (GrHAK/KUP/KT8) and two channel genes (GrAKT2.1 and GrAKT1.1) are important candidate genes for plant stress response. These results provide useful information for further functional characterization of PTS genes with the breeding aim of stress-resistant cultivars.

Chromosome-level genome assembly of Gynostemma pentaphyllum provides insights into gypenoside biosynthesis

Gynostemma pentaphyllum (Thunb.) Makino is an economically valuable medicinal plant belonging to the Cucurbitaceae family that produces the bioactive compound gypenoside. Despite several transcriptomes having been generated for G. pentaphyllum, a reference genome is still unavailable, which has limited the understanding of the gypenoside biosynthesis and regulatory mechanism. Here, we report a high-quality G. pentaphyllum genome with a total length of 582 Mb comprising 1,232 contigs and a scaffold N50 of 50.78 Mb. The G. pentaphyllum genome comprised 59.14% repetitive sequences and 25,285 protein-coding genes. Comparative genome analysis revealed that G. pentaphyllum was related to Siraitia grosvenorii, with an estimated divergence time dating to the Paleogene (∼48 million years ago). By combining transcriptome data from seven tissues, we reconstructed the gypenoside biosynthetic pathway and potential regulatory network using tissue-specific gene co-expression network analysis. Four UDP-glucuronosyltransferases (UGTs), belonging to the UGT85 subfamily and forming a gene cluster, were involved in catalyzing glycosylation in leaf-specific gypenoside biosynthesis. Furthermore, candidate biosynthetic genes and transcription factors involved in the gypenoside regulatory network were identified. The genetic information obtained in this study provides insights into gypenoside biosynthesis and lays the foundation for further exploration of the gypenoside regulatory mechanism.

The diversity of stomatal development regulation in Callitriche is related to the intrageneric diversity in lifestyles

Plant stomata are produced through divisions and differentiation of stem cells, termed meristemoids. During stomatal development, we see diverse patterns of meristemoid behavior among land plant lineages. However, both the ecological significance and the diversification processes of this diversity remain mostly unknown. Here we report that the ecologically diverse genus Callitriche shows unprecedented intrageneric diversity in meristemoid behavior. While meristemoids in terrestrial species of Callitriche undergo a series of asymmetric divisions before differentiation, those in amphibious species skip the divisions and directly differentiate into stomata. The simple shift in the expression times of two key transcription factors underlies these different patterns. This study provides important insights into the evolution and ecological significance of stomatal patterning.

Stomata, the gas exchange structures of plants, are formed by the division and differentiation of stem cells, or meristemoids. Although diverse patterns of meristemoid behavior have been observed among different lineages of land plants, the ecological significance and diversification processes of these different patterns are not well understood. Here we describe an intrageneric diversity in the patterns of meristemoid division within the ecologically diverse genus Callitriche (Plantaginaceae). Meristemoids underwent a series of divisions before differentiating into stomata in the terrestrial species of Callitriche, but these divisions did not occur in amphibious species, which can grow in both air and water, in which meristemoids differentiated directly into stomata. These findings imply the adaptive significance of diversity in meristemoid division. Molecular genetic analyses showed that the different expression times of the stomatal key transcription factors SPEECHLESS and MUTE, which maintain and terminate the meristemoid division, respectively, underlie the different division patterns of meristemoids. Unlike terrestrial species, amphibious species prematurely expressed MUTE immediately after expressing SPEECHLESS, which corresponded to their early termination of stomatal division. By linking morphological, ecological, and genetic elements of stomatal development, this study provides significant insight that should aid ecological evolutionary developmental biology investigations of stomata.

Does Molecular and Structural Evolution Shape the Speedy Grass Stomata?

It has been increasingly important for breeding programs to be aimed at crops that are capable of coping with a changing climate, especially with regards to higher frequency and intensity of drought events. Grass stomatal complex has been proposed as an important factor that may enable grasses to adapt to water stress and variable climate conditions. There are many studies focusing on the stomatal morphology and development in the eudicot model plant Arabidopsis and monocot model plant Brachypodium. However, the comprehensive understanding of the distinction of stomatal structure and development between monocots and eudicots, especially between grasses and eudicots, are still less known at evolutionary and comparative genetic levels. Therefore, we employed the newly released version of the One Thousand Plant Transcriptome (OneKP) database and existing databases of green plant genome assemblies to explore the evolution of gene families that contributed to the formation of the unique structure and development of grass stomata. This review emphasizes the differential stomatal morphology, developmental mechanisms, and guard cell signaling in monocots and eudicots. We provide a summary of useful molecular evidences for the high water use efficiency of grass stomata that may offer new horizons for future success in breeding climate resilient crops.

The Tomato Genome Encodes SPCH, MUTE, and FAMA Candidates That Can Replace the Endogenous Functions of Their Arabidopsis Orthologs

Stomatal abundance determines the maximum potential for gas exchange between the plant and the atmosphere. In Arabidopsis, it is set during organ development through complex genetic networks linking epidermal differentiation programs with environmental response circuits. Three related bHLH transcription factors, SPCH, MUTE, and FAMA, act as positive drivers of stomata differentiation. Mutant alleles of some of these genes sustain different stomatal numbers in the mature organs and have potential to modify plant performance under different environmental conditions. However, knowledge about stomatal genes in dicotyledoneous crops is scarce. In this work, we identified the Solanum lycopersicum putative orthologs of these three master regulators and assessed their functional orthology by their ability to complement Arabidopsis loss-of-function mutants, the epidermal phenotypes elicited by their conditional overexpression, and the expression patterns of their promoter regions in Arabidopsis. Our results indicate that the tomato proteins are functionally equivalent to their Arabidopsis counterparts and that the tomato putative promoter regions display temporal and spatial expression domains similar to those reported for the Arabidopsis genes. In vivo tracking of tomato stomatal lineages in developing cotyledons revealed cell division and differentiation histories similar to those of Arabidopsis. Interestingly, the S. lycopersicum genome harbors a FAMA-like gene, expressed in leaves but functionally distinct from the true FAMA orthologue. Thus, the basic program for stomatal development in S. lycopersicum uses key conserved genetic determinants. This opens the possibility of modifying stomatal abundance in tomato through previously tested Arabidopsis alleles conferring altered stomata abundance phenotypes that correlate with physiological traits related to water status, leaf cooling, or photosynthesis.

Multiple transcriptional factors control stomata development in rice

Grass stomata can balance gas exchange and evaporation effectively in rapidly changing environments via their unique anatomical features. Although the key components of stomatal development in Arabidopsis have been largely elucidated over the past decade, the molecular mechanisms that govern stomatal development in grasses are poorly understood. Via the genome editing system and T-DNA insertion lines, the key transcriptional factors (TFs) regulating stomatal development in rice (Oryza sativa) were knocked out. A combination of genetic and biochemical assays subsequently revealed the functions of these TFs. OsSPCH/OsICE is essential for the initiation of stomatal lineage. OsMUTE/OsICE determines meristemoid to guard mother cell (GMC) transition. OsFAMA/OsICE influences subsidiary mother cell asymmetric division and mature stoma differentiation. OsFLP regulates the orientation of GMC symmetrical division. More importantly, we found that OsSCR/OsSHR controls the initiation of stomatal lineage cells and the formation of subsidiary cells. The transcription of OsSCR is activated by OsSPCH and OsMUTE. This study characterised the functions of master regulatory TFs that control each stomatal developmental stage in rice. Our findings are helpful for elucidating how various species reprogramme the molecular mechanisms to generate different stomatal types during evolution.

Stomatal Development and Perspectives toward Agricultural Improvement

Stomata are small pores on the surface of land plants that facilitate gas exchange-acquiring CO₂ from surrounding atmosphere and releasing water vapor. In adverse conditions, such as drought, stomata close to minimize water loss. The activities of stomata are vital for plant growth and survival. In the last two decades, key players for stomatal development have been discovered thanks to the model plant Arabidopsis thaliana Our knowledge about the formation of stomata and their response to environmental changes are accumulating. In this review, we summarize the genetic and molecular mechanisms of stomatal development, with specific emphasis on recent findings and potential applications toward enhancing the sustainability of agriculture.

Pores for Thought: Can Genetic Manipulation of Stomatal Density Protect Future Rice Yields?

Rice (Oryza sativa L.) contributes to the diets of around 3.5 billion people every day and is consumed more than any other plant. Alarmingly, climate predictions suggest that the frequency of severe drought and high-temperature events will increase, and this is set to threaten the global rice supply. In this review, we consider whether water or heat stresses in crops - especially rice - could be mitigated through alterations to stomata; minute pores on the plant epidermis that permit carbon acquisition and regulate water loss. In the short-term, water loss is controlled via alterations to the degree of stomatal "openness", or, in the longer-term, by altering the number (or density) of stomata that form. A range of molecular components contribute to the regulation of stomatal density, including transcription factors, plasma membrane-associated proteins and intercellular and extracellular signaling molecules. Much of our existing knowledge relating to stomatal development comes from research conducted on the model plant, Arabidopsis thaliana. However, due to the importance of cereal crops to global food supply, studies on grass stomata have expanded in recent years, with molecular-level discoveries underscoring several divergent developmental and morphological features. Cultivation of rice is particularly water-intensive, and there is interest in developing varieties that require less water yet still maintain grain yields. This could be achieved by manipulating stomatal development; a crop with fewer stomata might be more conservative in its water use and therefore more capable of surviving periods of water stress. However, decreasing stomatal density might restrict the rate of CO₂ uptake and reduce the extent of evaporative cooling, potentially leading to detrimental effects on yields. Thus, the extent to which crop yields in the future climate will be affected by increasing or decreasing stomatal density should be determined. Here, our current understanding of the regulation of stomatal development is summarised, focusing particularly on the genetic mechanisms that have recently been described for rice and other grasses. Application of this knowledge toward the creation of "climate-ready" rice is discussed, with attention drawn to the lesser-studied molecular elements whose contributions to the complexity of grass stomatal development must be understood to advance efforts.

Transcriptional networks orchestrating programmed cell death during plant development

Transcriptional gene regulation is a fundamental biological principle in the development of eukaryotes. It does control not only cell proliferation, specification, and differentiation, but also cell death processes as an integral feature of an organism's developmental program. As in animals, developmentally regulated cell death in plants occurs in numerous contexts and is of vital importance for plant vegetative and reproductive development. In comparison with the information available on the molecular regulation of programmed cell death (PCD) in animals, however, our knowledge on plant PCD still remains scarce. Here, we discuss the functions of different classes of transcription factors that have been implicated in the control of developmentally regulated cell death. Though doubtlessly representing but a first layer of PCD regulation, information on PCD-regulating transcription factors and their targets represents a promising strategy to understand the complex machinery that ensures the precise and failsafe execution of PCD processes in plant development.

A2-type cyclin is required for the asymmetric entry division in rice stomatal development

In rice, and other major cereal grass crops, stomata are arranged in linear files parallel to the long growth axis of leaves. Each stomatal unit comprises two dumbbell-shaped guard cells flanked by two subsidiary cells. These morphological and developmental characteristics enable grass stomata to respond to environmental changes more efficiently. Cyclin-dependent kinases (CDKs) and their cyclin partners co-ordinate cell proliferation and differentiation during the development of multicellular organisms. In contrast to animals, plants have many more types and members of cyclins. In Arabidopsis, four A2-type cyclins (CYCA2s) function redundantly in regulating CDKB1 activity to promote the asymmetric division for stomatal initiation and the symmetric division of guard mother cells (GMCs). In this study, we examine the function of the single A2-type cyclin in rice, OsCYCA2;1, as well the single B1-type CDK, OsCDKB1;1. Cross-species complementation tests demonstrated that OsCYCA2;1 and OsCDKB1;1 could complement the defective stomatal phenotypes of Arabidopsis cyca2 and cdkb1 mutants, but also could suppress DNA endoduplication and cell enlargement. The early asymmetric divisions that establish the stomatal lineages are often missing within the stomatal cell files of OsCYCA2;1-RNAi rice transgenic lines, leading to a significantly reduced stomatal production. However, GMC divisions are not disrupted either in OsCYCA2;1-RNAi or in OsCDKB1;1-RNAi rice transgenic lines as expected. Our results demonstrate a conserved but diverged function and behavior of rice A2-type cyclins, which might be associated with the distinct stomatal development pathways between rice and Arabidopsis.

Cell and Developmental Biology of Plant Mitogen-Activated Protein Kinases

Plant mitogen-activated protein kinases (MAPKs) constitute a network of signaling cascades responsible for transducing extracellular stimuli and decoding them to dedicated cellular and developmental responses that shape the plant body. Over the last decade, we have accumulated information about how MAPK modules control the development of reproductive tissues and gametes and the embryogenic and postembryonic development of vegetative organs such as roots, root nodules, shoots, and leaves. Of key importance to understanding how MAPKs participate in developmental and environmental signaling is the characterization of their subcellular localization, their interactions with upstream signal perception mechanisms, and the means by which they target their substrates. In this review, we summarize the roles of MAPK signaling in the regulation of key plant developmental processes, and we survey what is known about the mechanisms guiding the subcellular compartmentalization of MAPK modules.

Reducing Stomatal Density in Barley Improves Drought Tolerance without Impacting on Yield

The epidermal patterning factor (EPF) family of secreted signaling peptides regulate the frequency of stomatal development in model dicot and basal land plant species. Here, we identify and manipulate the expression of a barley (Hordeum vulgare) ortholog and demonstrate that when overexpressed HvEPF1 limits entry to, and progression through, the stomatal development pathway. Despite substantial reductions in leaf gas exchange, barley plants with significantly reduced stomatal density show no reductions in grain yield. In addition, HvEPF1OE barley lines exhibit significantly enhanced water use efficiency, drought tolerance, and soil water conservation properties. Our results demonstrate the potential of manipulating stomatal frequency for the protection and optimization of cereal crop yields under future drier environments.

Origins and Evolution of Stomatal Development

The fossil record suggests stomata-like pores were present on the surfaces of land plants over 400 million years ago. Whether stomata arose once or whether they arose independently across newly evolving land plant lineages has long been a matter of debate. In Arabidopsis, a genetic toolbox has been identified that tightly controls stomatal development and patterning. This includes the basic helix-loop-helix (bHLH) transcription factors SPEECHLESS (SPCH), MUTE, FAMA, and ICE/SCREAMs (SCRMs), which promote stomatal formation. These factors are regulated via a signaling cascade, which includes mobile EPIDERMAL PATTERNING FACTOR (EPF) peptides to enforce stomatal spacing. Mosses and hornworts, the most ancient extant lineages to possess stomata, possess orthologs of these Arabidopsis (Arabidopsis thaliana) stomatal toolbox genes, and manipulation in the model bryophyte Physcomitrella patens has shown that the bHLH and EPF components are also required for moss stomatal development and patterning. This supports an ancient and tightly conserved genetic origin of stomata. Here, we review recent discoveries and, by interrogating newly available plant genomes, we advance the story of stomatal development and patterning across land plant evolution. Furthermore, we identify potential orthologs of the key toolbox genes in a hornwort, further supporting a single ancient genetic origin of stomata in the ancestor to all stomatous land plants.

Stomatal development in time: the past and the future

Stomata have significantly diversified in nature since their first appearance around 400 million years ago. The diversification suggests the active reprogramming of molecular machineries of stomatal development during evolution. This review focuses on recent progress that sheds light on how this rewiring occurred in different organisms. Three specific aspects are discussed in this review: (i) the evolution of the transcriptional complex that governs stomatal state transitions; (ii) the evolution of receptor-ligand pairs that mediate extrinsic signaling; and (iii) the loss of stomatal development genes in an astomatous angiosperm.

PYK10 myrosinase reveals a functional coordination between endoplasmic reticulum bodies and glucosinolates in Arabidopsis thaliana

The endoplasmic reticulum body (ER body) is an organelle derived from the ER that occurs in only three families of the order Brassicales and is suggested to be involved in plant defense. ER bodies in Arabidopsis thaliana contain large amounts of β-glucosidases, but the physiological functions of ER bodies and these enzymes remain largely unclear. Here we show that PYK10, the most abundant β-glucosidase in A. thaliana root ER bodies, hydrolyzes indole glucosinolates (IGs) in addition to the previously reported in vitro substrate scopolin. We found a striking co-expression between ER body-related genes (including PYK10), glucosinolate biosynthetic genes and the genes for so-called specifier proteins affecting the terminal products of myrosinase-mediated glucosinolate metabolism, indicating that these systems have been integrated into a common transcriptional network. Consistent with this, comparative metabolite profiling utilizing a number of A. thaliana relatives within Brassicaceae identified a clear phylogenetic co-occurrence between ER bodies and IGs, but not between ER bodies and scopolin. Collectively, our findings suggest a functional link between ER bodies and glucosinolate metabolism in planta. In addition, in silico three-dimensional modeling, combined with phylogenomic analysis, suggests that PYK10 represents a clade of 16 myrosinases that arose independently from the other well-documented class of six thioglucoside glucohydrolases. These findings provide deeper insights into how glucosinolates are metabolized in cruciferous plants and reveal variation of the myrosinase-glucosinolate system within individual plants.

Origin and function of stomata in the moss Physcomitrella patens

Stomata are microscopic valves on plant surfaces that originated over 400 million years (Myr) ago and facilitated the greening of Earth's continents by permitting efficient shoot-atmosphere gas exchange and plant hydration1. However, the core genetic machinery regulating stomatal development in non-vascular land plants is poorly understood2-4 and their function has remained a matter of debate for a century5. Here, we show that genes encoding the two basic helix-loop-helix proteins PpSMF1 (SPEECH, MUTE and FAMA-like) and PpSCREAM1 (SCRM1) in the moss Physcomitrella patens are orthologous to transcriptional regulators of stomatal development in the flowering plant Arabidopsis thaliana and essential for stomata formation in moss. Targeted P. patens knockout mutants lacking either PpSMF1 or PpSCRM1 develop gametophytes indistinguishable from wild-type plants but mutant sporophytes lack stomata. Protein-protein interaction assays reveal heterodimerization between PpSMF1 and PpSCRM1, which, together with moss-angiosperm gene complementations6, suggests deep functional conservation of the heterodimeric SMF1 and SCRM1 unit is required to activate transcription for moss stomatal development, as in A. thaliana7. Moreover, stomata-less sporophytes of ΔPpSMF1 and ΔPpSCRM1 mutants exhibited delayed dehiscence, implying stomata might have promoted dehiscence in the first complex land-plant sporophytes.

Wheat bHLH-type transcription factor gene TabHLH1 is crucial in mediating osmotic stresses tolerance through modulating largely the ABA-associated pathway

KEY MESSAGE

Wheat bHLH family gene TabHLH1 is responsive to drought and salt stresses, and it acts as one crucial regulator in mediating tolerance to aforementioned stresses largely through an ABA-associated pathway. Osmotic stresses are adverse factors for plant growth and crop productivity. In this study, we characterized TabHLH1, a gene encoding wheat bHLH-type transcription factor (TF) protein, in mediating plant adaptation to osmotic stresses. TabHLH1 protein contains a conserved basic-helix-loop-helix (bHLH) domain shared by its plant counterparts. Upon PEG-simulated drought stress, salt stress, and exogenous abscisic acid (ABA), the TabHLH1 transcripts in roots and leaves were induced. Under PEG-simulated drought stress and salt stress treatments, the tobacco seedlings with TabHLH1 overexpression exhibited improved growth and osmotic stress-associated traits, showing increased biomass and reduced leaf water loss rate (WLR) relative to wild type (WT). The transgenic lines also possessed promoted stomata closure under drought stress, salt stress, and exogenous ABA and increased proline and soluble sugar contents and reduced hydrogen peroxide (H2O2) amount under osmotic stress conditions, indicating that TabHLH1-mediated osmolyte accumulation and cellular ROS homeostasis contributed to the drought stress and salt stress tolerance. NtPYL12 and NtSAPK2;1, the genes encoding ABA receptor and SnRK2 family kinase, respectively, showed up-regulated expression in lines overexpressing TabHLH1 under osmotic stress and exogenous ABA conditions; overexpression of them conferred plants modified stomata movement, leaf WLR, and growth feature under drought and high salinity, suggesting that these ABA-signaling genes are mediated by wheat TabHLH1 gene and involved in regulating plant responses to simulated drought and salt stresses. Our investigation indicates that the TabHLH1 gene plays critical roles in plant tolerance to osmotic stresses largely through an ABA-dependent pathway.

Regulation of plant secondary metabolism and associated specialized cell development by MYBs and bHLHs

Plants are unrivaled in the natural world in both the number and complexity of secondary metabolites they produce, and the ubiquitous phenylpropanoids and the lineage-specific glucosinolates represent two such large and chemically diverse groups. Advances in genome-enabled biochemistry and metabolomic technologies have greatly increased the understanding of their metabolic networks in diverse plant species. There also has been some progress in elucidating the gene regulatory networks that are key to their synthesis, accumulation and function. This review highlights what is currently known about the gene regulatory networks and the stable sub-networks of transcription factors at their cores that regulate the production of these plant secondary metabolites and the differentiation of specialized cell types that are equally important to their defensive function. Remarkably, some of these core components are evolutionarily conserved between secondary metabolism and specialized cell development and across distantly related plant species. These findings suggest that the more ancient gene regulatory networks for the differentiation of fundamental cell types may have been recruited and remodeled for the generation of the vast majority of plant secondary metabolites and their specialized tissues.

Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity

Stomata, epidermal valves facilitating plant-atmosphere gas exchange, represent a powerful model for understanding cell fate and pattern in plants. Core basic helix-loop-helix (bHLH) transcription factors regulating stomatal development were identified in Arabidopsis, but this dicot's developmental pattern and stomatal morphology represent only one of many possibilities in nature. Here, using unbiased forward genetic screens, followed by analysis of reporters and engineered mutants, we show that stomatal initiation in the grass Brachypodium distachyon uses orthologs of stomatal regulators known from Arabidopsis but that the function and behavior of individual genes, the relationships among genes, and the regulation of their protein products have diverged. Our results highlight ways in which a kernel of conserved genes may be alternatively wired to produce diversity in patterning and morphology and suggest that the stomatal transcription factor module is a prime target for breeding or genome modification to improve plant productivity.

Patterning of stomata in the moss Funaria: a simple way to space guard cells

BACKGROUND AND AIMS

Studies on stomatal development and the molecular mechanisms controlling patterning have provided new insights into cell signalling, cell fate determination and the evolution of these processes in plants. To fill a major gap in knowledge of stomatal patterning, this study describes the pattern of cell divisions that give rise to stomata and the underlying anatomical changes that occur during sporophyte development in the moss Funaria.

METHODS

Developing sporophytes at different stages were examined using light, fluorescence and electron microscopy; immunogold labelling was used to investigate the presence of pectin in the newly formed cavities.

KEY RESULTS

Substomatal cavities are liquid-filled when formed and drying of spaces is synchronous with pore opening and capsule expansion. Stomata in mosses do not develop from a self-generating meristemoid as in Arabidopsis, but instead they originate from a protodermal cell that differentiates directly into a guard mother cell. Epidermal cells develop from protodermal or other epidermal cells, i.e. there are no stomatal lineage ground cells.

CONCLUSIONS

Development of stomata in moss occurs by differentiation of guard mother cells arranged in files and spaced away from each other, and epidermal cells that continue to divide after stomata are formed. This research provides evidence for a less elaborated but effective mechanism for stomata spacing in plants, and we hypothesize that this operates by using some of the same core molecular signalling mechanism as angiosperms.

Transcriptional control of cell fate in the stomatal lineage

The Arabidopsis stomatal lineage is a microcosm of development; it undergoes selection of precursor cells, asymmetric and stem cell-like divisions, cell commitment and finally, acquisition of terminal cell fates. Recent transcriptomic approaches revealed major shifts in gene expression accompanying each fate transition, and mechanistic analysis of key bHLH transcription factors, along with mathematical modeling, has begun to unravel how these major shifts are coordinated. In addition, stomatal initiation is proving to be a tractable model for defining the genetic and epigenetic basis of stable cell identities and for understanding the integration of environmental responses into developmental programs.

Down-Regulating the Expression of 53 Soybean Transcription Factor Genes Uncovers a Role for SPEECHLESS in Initiating Stomatal Cell Lineages during Embryo Development

We used an RNA interference screen to assay the function of 53 transcription factor messenger RNAs (mRNAs) that accumulate specifically within soybean (Glycine max) seed regions, subregions, and tissues during development. We show that basic helix-loop-helix (bHLH) transcription factor genes represented by Glyma04g41710 and its paralogs are required for the formation of stoma in leaves and stomatal precursor complexes in mature embryo cotyledons. Phylogenetic analysis indicates that these bHLH transcription factor genes are orthologous to Arabidopsis (Arabidopsis thaliana) SPEECHLESS (SPCH) that initiate asymmetric cell divisions in the leaf protoderm layer and establish stomatal cell lineages. Soybean SPCH (GmSPCH) mRNAs accumulate primarily in embryo, seedling, and leaf epidermal layers. Expression of Glyma04g41710 under the control of the SPCH promoter rescues the Arabidopsis spch mutant, indicating that Glyma04g41710 is a functional ortholog of SPCH. Developing soybean embryos do not form mature stoma, and stomatal differentiation is arrested at the guard mother cell stage. We analyzed the accumulation of GmSPCH mRNAs during soybean seed development and mRNAs orthologous to MUTE, FAMA, and inducer of C-repeat/dehydration responsive element-binding factor expression1/scream2 that are required for stoma formation in Arabidopsis. The mRNA accumulation patterns provide a potential explanation for guard mother cell dormancy in soybean embryos. Our results suggest that variation in the timing of bHLH transcription factor gene expression can explain the diversity of stomatal forms observed during plant development.

The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization

Basic/helix-loop-helix (bHLH) proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum), a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors) maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062) showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus.

Functional specialization of stomatal bHLHs through modification of DNA-binding and phosphoregulation potential

Transcription factor duplication events and subsequent specialization can drive evolution by facilitating biological innovation and developmental complexity. Identification of sequences that confer distinct biochemical function in vivo is an important step in understanding how related factors could refine specific developmental processes over time. Functional analysis of the basic helix-loop-helix (bHLH) protein SPEECHLESS, one of three closely related transcription factors required for stomatal lineage progression in Arabidopsis thaliana, allowed a dissection of motifs associated with specific developmental outputs. Phosphorylated residues, shown previously to quantitatively affect activity, also allow a qualitative shift in function between division and cell fate-promoting activities. Our data also provide surprising evidence that, despite deep sequence conservation in DNA-binding domains, the functional requirement for these domains has diverged, with the three stomatal bHLHs exhibiting absolute, partial, or no requirements for DNA-binding residues for their in vivo activities. Using these data, we build a plausible model describing how the current unique and overlapping roles of these proteins might have evolved from a single ancestral protein.

Patterning and processes: how stomatal development defines physiological potential

Stomata present an excellent opportunity for connecting scientific disciplines: they are governed by complex genetic controls and unique cell biology, while also possessing a large influence over plant productivity and relationships with the environment. For this reason, stomata have engaged scientists for many centuries and continue to be a central interest for many fields of research. Recent technological advances have enabled interdisciplinary studies of stomata that were previously out of reach, and as a result, we are beginning to realize new insights about stomatal biology that place them at the intersection of our changing world. This review is intended to describe these interdisciplinary connections, discuss the relevant scales at which they are having an influence, and highlight ways we can capitalize on such novel approaches. While we incorporate knowledge about molecular advances, this is not intended to be an extensive review of that field, but rather, we focus on how those systems inform plant physiology and are connected to global scales.

FAMA is an essential component for the differentiation of two distinct cell types, myrosin cells and guard cells, in Arabidopsis

Brassicales plants, including Arabidopsis thaliana, have an ingenious two-compartment defense system, which sequesters myrosinase from the substrate glucosinolate and produces a toxic compound when cells are damaged by herbivores. Myrosinase is stored in vacuoles of idioblast myrosin cells. The molecular mechanism that regulates myrosin cell development remains elusive. Here, we identify the basic helix-loop-helix transcription factor FAMA as an essential component for myrosin cell development along Arabidopsis leaf veins. FAMA is known as a regulator of stomatal development. We detected FAMA expression in myrosin cell precursors in leaf primordia in addition to stomatal lineage cells. FAMA deficiency caused defects in myrosin cell development and in the biosynthesis of myrosinases THIOGLUCOSIDE GLUCOHYDROLASE1 (TGG1) and TGG2. Conversely, ectopic FAMA expression conferred myrosin cell characteristics to hypocotyl and root cells, both of which normally lack myrosin cells. The FAMA interactors ICE1/SCREAM and its closest paralog SCREAM2/ICE2 were essential for myrosin cell development. DNA microarray analysis identified 32 candidate genes involved in myrosin cell development under the control of FAMA. This study provides a common regulatory pathway that determines two distinct cell types in leaves: epidermal guard cells and inner-tissue myrosin cells.

The role of brassinosteroids and abscisic acid in stomatal development

Gas exchange with the atmosphere is regulated through the stomata. This process relies on both the degree and duration of stomatal opening, and the number and patterning of these structures in the plant surface. Recent work has revealed that brassinosteroids and abscisic acid (ABA), which control stomatal opening, also repress stomatal development in cotyledons and leaves of at least some plants. It is speculated that, in Arabidopsis, these phytohormones control the same steps of this developmental process, most probably, through the regulation of the same mitogen-activated protein (MAP) kinase module. The conservation, in seeds plants, of components downstream of this module with MAP kinase target domains, suggests that these proteins are also regulated by these cascades, which, in turn, may be regulated by brassinosteroids and/or ABA.

Convergence of stem cell behaviors and genetic regulation between animals and plants: insights from the Arabidopsis thaliana stomatal lineage

Plants and animals are two successful, but vastly different, forms of complex multicellular life. In the 1600 million years since they shared a common unicellular ancestor, representatives of these kingdoms have had ample time to devise unique strategies for building and maintaining themselves, yet they have both developed self-renewing stem cell populations. Using the cellular behaviors and the genetic control of stomatal lineage of Arabidopsis as a focal point, we find current data suggests convergence of stem cell regulation at developmental and molecular levels. Comparative studies between evolutionary distant groups, therefore, have the power to reveal the logic behind stem cell behaviors and benefit both human regenerative medicine and plant biomass production.