Pluripotency of a founding field: rebranding developmental biology

The field of developmental biology has declined in prominence in recent decades, with off-shoots from the field becoming more fashionable and highly funded. This has created inequity in discovery and opportunity, partly due to the perception that the field is antiquated or not cutting edge. A 'think tank' of scientists from multiple developmental biology-related disciplines came together to define specific challenges in the field that may have inhibited innovation, and to provide tangible solutions to some of the issues facing developmental biology. The community suggestions include a call to the community to help 'rebrand' the field, alongside proposals for additional funding apparatuses, frameworks for interdisciplinary innovative collaborations, pedagogical access, improved science communication, increased diversity and inclusion, and equity of resources to provide maximal impact to the community.

Distinct ADP-ribosylation factor-GTP exchange factors govern the opposite polarity of 2 receptor kinases

Polarity of plasma membrane proteins is essential for cell morphogenesis and control of cell division and, thus, influences organ and whole plant development. In Arabidopsis (Arabidopsis thaliana) root endodermal cells, 2 transmembrane kinases, INFLORESCENCE AND ROOT APICES RECEPTOR KINASE (IRK) and KINASE ON THE INSIDE (KOIN), accumulate at opposite lateral domains. Their polarization is tightly linked to their activities regulating cell division and ground tissue patterning. The polarization of IRK and KOIN relies solely on the secretion of newly synthesized protein. However, the secretion machinery by which their opposite, lateral polarity is achieved remains largely unknown. Here, we show that different sets of ADP-ribosylation factor (ARF)-guanine-nucleotide exchange factors (ARF-GEFs) mediate their secretion. ARF-GEF GNOM-like-1 (GNL1) regulates KOIN secretion to the inner polar domain, thereby directing KOIN sorting early in the secretion pathway. For IRK, combined chemical and genetic analyses showed that the ARG-GEF GNL1, GNOM, and the BREFELDIN A-INHIBITED-GUANINE NUCLEOTIDE-EXCHANGE FACTORs 1 to 4 (BIG1-BIG4) collectively regulate its polar secretion. The ARF-GEF-dependent mechanisms guiding IRK or KOIN lateral polarity were active across different root cell types and functioned regardless of the protein's inner/outer polarity in those cells. Therefore, we propose that specific polar trafficking of IRK and KOIN occurs via distinct mechanisms that are not constrained by cell identity or polar axis and likely rely on individual protein recognition.

A G-type lectin receptor kinase negatively regulates Arabidopsis immunity against root-knot nematodes

Root-knot nematodes (Meloidogyne spp., RKN) are responsible for extensive crop losses worldwide. During infection, they penetrate plant roots, migrate between plant cells, and establish feeding sites, known as giant cells, near the root vasculature. Previously, we found that nematode perception and early responses in plants were similar to those of microbial pathogens and required the BRI1-ASSOCIATED KINASE1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE3 (BAK1/SERK3) coreceptor in Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum). Here, we implemented a reverse genetic screen for resistance or sensitivity to RKN using Arabidopsis T-DNA alleles of genes encoding transmembrane receptor-like kinases to identify additional receptors involved in this process. This screen identified a pair of allelic mutations with enhanced resistance to RKN in a gene we named ENHANCED RESISTANCE TO NEMATODES1 (ERN1). ERN1 encodes a G-type lectin receptor kinase (G-LecRK) with a single-pass transmembrane domain. Further characterization showed that ern1 mutants displayed stronger activation of MAP kinases, elevated levels of the defense marker MYB51, and enhanced H2O2 accumulation in roots upon RKN elicitor treatments. Elevated MYB51 expression and ROS bursts were also observed in leaves of ern1 mutants upon flg22 treatment. Complementation of ern1.1 with 35S- or native promoter-driven ERN1 rescued the RKN infection and enhanced defense phenotypes. Our results indicate that ERN1 is an important negative regulator of immunity.

Membrane nanodomains: Dynamic nanobuilding blocks of polarized cell growth

Cell polarity is intimately linked to numerous biological processes, such as oriented plant cell division, particular asymmetric division, cell differentiation, cell and tissue morphogenesis, and transport of hormones and nutrients. Cell polarity is typically initiated by a polarizing cue that regulates the spatiotemporal dynamic of polarity molecules, leading to the establishment and maintenance of polar domains at the plasma membrane. Despite considerable progress in identifying key polarity regulators in plants, the molecular and cellular mechanisms underlying cell polarity formation have yet to be fully elucidated. Recent work suggests a critical role for membrane protein/lipid nanodomains in polarized morphogenesis in plants. One outstanding question is how the spatiotemporal dynamics of signaling nanodomains are controlled to achieve robust cell polarization. In this review, we first summarize the current state of knowledge on potential regulatory mechanisms of nanodomain dynamics, with a special focus on Rho-like GTPases from plants. We then discuss the pavement cell system as an example of how cells may integrate multiple signals and nanodomain-involved feedback mechanisms to achieve robust polarity. A mechanistic understanding of nanodomains' roles in plant cell polarity is still in the early stages and will remain an exciting area for future investigations.

Girl power: NORTIA polarization seals pollen tube fate

How protein dynamics contribute to developmental processes is a critical biological question. In this issue of Developmental Cell, Ju et al. show that subcellular localization of NORTIA in the female gametophyte is required for pollen reception. NORTIA redistribution boosts cues that drive pollen tube bursting, thus promoting male gamete release and fertilization.

Confocal Analysis of Arabidopsis Root Cell Divisions in 3D: A Focus on the Endodermis

The development of multicellular organisms requires coordinated cell divisions for the production of diverse cell types and body plan elaboration and growth. There are two main types of cell divisions: proliferative or symmetric divisions, which produce more cells of a given type, and formative or asymmetric divisions, which produce cells of different types. Because plant cells are surrounded by cell walls, the orientation of plant cell divisions is particularly important in cell fate specification and tissue or organ morphology. The cellular organization of the Arabidopsis thaliana root makes an excellent tool to study how oriented cell division contributes to tissue patterning during organ development. To understand how division plane orientation in a specific genotype or growth condition may impact organ or tissue development, a detailed characterization of cell division orientation is required. Here we describe a confocal microscopy-based, live imaging method for Arabidopsis root tips to examine the 3D orientations of cell division planes and quantify formative, proliferative, and atypical endodermal cell divisions.

A Course-Based Undergraduate Research Experience in CRISPR-Cas9 Experimental Design to Support Reverse Genetic Studies in Arabidopsis thaliana

Gene-editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene-editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a 5-week period. In the remote-learning version, students performed homology searches, designed guide RNAs (gRNAs) and primers, and learned the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as during closures that have occurred in response to the COVID-19 pandemic. In person, students designed gRNAs, cloned CRISPR-Cas9 constructs, and performed genetic transformation of Arabidopsis thaliana. Students learned how to design effective gRNA pairs targeting their assigned gene with an 86% success rate. Final exams tested students' ability to apply knowledge of an unfamiliar genome database to characterize gene structure and to properly design gRNAs. Average final exam scores of ∼73% and ∼84% for in-person and remote-learning CUREs, respectively, indicated that students met learning outcomes. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of sections. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be adapted readily to other organisms or projects that employ gene editing.

Membrane receptor-mediated mechano-transduction maintains cell integrity during pollen tube growth within the pistil

Invasive or penetrative growth is critical for developmental and reproductive processes (e.g., pollen tube penetration of pistils) and disease progression (e.g., cancer metastasis and fungal hyphae invasion). The invading or penetrating cells experience drastic changes in mechanical pressure from the surroundings and must balance growth with cell integrity. Here, we show that Arabidopsis pollen tubes sense and/or respond to mechanical changes via a cell-surface receptor kinase Buddha's Paper Seal 1 (BUPS1) while emerging from compressing female tissues. BUPS1-defective pollen tubes fail to maintain cell integrity after emergence from these tissues. The mechano-transduction function of BUPS1 is established by using a microfluidic channel device mimicking the mechanical features of the in vivo growth path. BUPS1-based mechano-transduction activates Rho-like GTPase from Plant 1 (ROP1) GTPase to promote exocytosis that facilitates secretion of BUPS1's ligands for mechanical signal amplification and cell wall rigidification in pollen tubes. These findings uncover a membrane receptor-based mechano-transduction system for cells to cope with the physical challenges during invasive or penetrative growth.

A series of dual-reporter vectors for ratiometric analysis of protein abundance in plants

Ratiometric reporter systems enable comparisons of the abundance of a protein of interest, or "target," relative to a reference protein. Both proteins are encoded on a single transcript but are separated during translation. This arrangement bypasses the potential for discordant expression that can arise when the target and reference proteins are encoded by separate genes. We generated a set of 18 Gateway-compatible vectors termed pRATIO that combine a variety of promoters, fluorescent, and bioluminescent reporters, and 2A "self-cleaving" peptides. These constructs are easily modified to produce additional combinations or introduce new reporter proteins. We found that mScarlet-I provides the best signal-to-noise ratio among several fluorescent reporter proteins during transient expression experiments in Nicotiana benthamiana. Firefly and Gaussia luciferase also produce high signal-to-noise in N. benthamiana. As proof of concept, we used this system to investigate whether degradation of the receptor KAI2 after karrikin treatment is influenced by its subcellular localization. KAI2 is normally found in the cytoplasm and the nucleus of plant cells. In N. benthamiana, karrikin-induced degradation of KAI2 was only observed when it was retained in the nucleus. These vectors are tools to easily monitor in vivo the abundance of a protein that is transiently expressed in plants, and will be particularly useful for investigating protein turnover in response to different stimuli.

Asymmetry and cell polarity in root development

Within living systems, striking juxtapositions in symmetry and asymmetry can be observed and the superficial appearance of symmetric organization often gives way to cellular asymmetries at higher resolution. It is frequently asymmetry and polarity that fascinate and challenge developmental biologists. In multicellular eukaryotes, cell polarity and asymmetry are essential for diverse cellular, tissue, and organismal level function and physiology and are particularly crucial for developmental processes. In plants, where cells are surrounded by rigid cell walls, asymmetric cell divisions are the foundation of pattern formation and differential cell fate specification. Thus, cellular asymmetry is a key feature of plant biology and in the plant root the consequences of these asymmetries are elegantly displayed. Yet despite the frequency of asymmetric (formative) cell divisions, cell/tissue polarity and the proposed roles for directional signaling in these processes, polarly localized proteins, beyond those involved in auxin or nutrient transport, are exceedingly rare. Indeed, although half of the asymmetric cell divisions in root patterning are oriented parallel to the axis of growth, laterally localized proteins directly involved in patterning are largely missing in action. Here, various asymmetric cell divisions and cellular and structural polarities observed in roots are highlighted and discussed in the context of the proposed roles for positional and/or directional signaling in these processes. The importance of directional signaling and the weight given to polarity in the root-shoot axis is contrasted with how little we currently understand about laterally oriented asymmetry and polarity in the root.

Root system patterning: auxin synthesis at the root periphery

Plasticity in plant form is achieved through differential elaboration of developmental pre-patterns during postembryonic organ development. A new report links the output of the root clock, an oscillatory transcriptional pre-patterning mechanism, with cell-type-specific production of the plant hormone auxin, and identifies a downstream component required for elaboration of the pre-pattern.

Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

In plants, continuous formation of lateral roots (LRs) facilitates efficient exploration of the soil environment. Roots can maximize developmental capacity in variable environmental conditions through establishment of sites competent to form LRs. This LR prepattern is established by a periodic oscillation in gene expression near the root tip. The spatial distribution of competent (prebranch) sites results from the interplay between this periodic process and primary root growth; yet, much about this oscillatory process and the formation of prebranch sites remains unknown. We find that disruption of carotenoid biosynthesis results in seedlings with very few LRs. Carotenoids are further required for the output of the LR clock because inhibition of carotenoid synthesis also results in fewer sites competent to form LRs. Genetic analyses and a carotenoid cleavage inhibitor indicate that an apocarotenoid, distinct from abscisic acid or strigolactone, is specifically required for LR formation. Expression of a key carotenoid biosynthesis gene occurs in a spatially specific pattern along the root's axis, suggesting spatial regulation of carotenoid synthesis. These results indicate that developmental prepatterning of LRs requires an uncharacterized carotenoid-derived molecule. We propose that this molecule functions non-cell-autonomously in establishment of the LR prepattern.

To branch or not to branch: the role of pre-patterning in lateral root formation

The establishment of a pre-pattern or competence to form new organs is a key feature of the postembryonic plasticity of plant development, and the elaboration of such pre-patterns leads to remarkable heterogeneity in plant form. In root systems, many of the differences in architecture can be directly attributed to the outgrowth of lateral roots. In recent years, efforts have focused on understanding how the pattern of lateral roots is established. Here, we review recent findings that point to a periodic mechanism for establishing this pattern, as well as roles for plant hormones, particularly auxin, in the earliest steps leading up to lateral root primordium development. In addition, we compare the development of lateral root primordia with in vitro plant regeneration and discuss possible common molecular mechanisms.

In the absence of BYPASS1-related gene function, the bps signal disrupts embryogenesis by an auxin-independent mechanism

Development is often coordinated by biologically active mobile compounds that move between cells or organs. Arabidopsis mutants with defects in the BYPASS1 (BPS1) gene overproduce an active mobile compound that moves from the root to the shoot and inhibits growth. Here, we describe two related Arabidopsis genes, BPS2 and BPS3. Analyses of single, double and triple mutants revealed that all three genes regulate production of the same mobile compound, the bps signal, with BPS1 having the largest role. The triple mutant had a severe embryo defect, including the failure to properly establish provascular tissue, the shoot meristem and the root meristem. Aberrant expression of PINFORMED1, DR5, PLETHORA1, PLETHORA2 and WUSCHEL-LIKE HOMEOBOX5 were found in heart-stage bps triple-mutant embryos. However, auxin-induced gene expression, and localization of the PIN1 auxin efflux transporter, were intact in bps1 mutants, suggesting that the primary target of the bps signal is independent of auxin response. Thus, the bps signal identifies a novel signaling pathway that regulates patterning and growth in parallel with auxin signaling, in multiple tissues and at multiple developmental stages.

Intercellular communication during plant development

Multicellular organisms depend on cell-to-cell communication to coordinate both development and environmental responses across diverse cell types. Intercellular signaling is particularly critical in plants because development is primarily postembryonic and continuous over a plant's life span. Additionally, development is impacted by restrictions imposed by a sessile lifestyle and limitations on relative cell positions. Many non-cell-autonomous signaling mechanisms are known to function in plant development, including those involving receptor kinases, small peptides, and mobile transcription factors. In this review, we focus on recent findings that highlight novel mechanisms in intercellular signaling during development. New details of small RNA movement, including microRNA movement, are discussed, as well as protein movement and distribution of reactive oxygen species (ROS) in ROS signaling. Finally, a novel temporal mechanism for lateral root positioning and the implications for intercellular signaling are considered.

BYPASS1: synthesis of the mobile root-derived signal requires active root growth and arrests early leaf development

BACKGROUND

The Arabidopsis bypass1 (bps1) mutant root produces a biologically active mobile compound that induces shoot growth arrest. However it is unknown whether the root retains the capacity to synthesize the mobile compound, or if only shoots of young seedlings are sensitive. It is also unknown how this compound induces arrest of shoot growth. This study investigated both of these questions using genetic, inhibitor, reporter gene, and morphological approaches.

RESULTS

Production of the bps1 root-synthesized mobile compound was found to require active root growth. Inhibition of postembryonic root growth, by depleting glutathione either genetically or chemically, allowed seedlings to escape shoot arrest. However, the treatments were not completely effective, as the first leaf pair remained radialized, but elongated. This result indicated that the embryonic root transiently synthesized a small amount of the mobile substance. In addition, providing glutathione later in vegetative development caused shoot growth arrest to be reinstated, revealing that these late-arising roots were still capable of producing the mobile substance, and that the older vegetative leaves were still responsive. To gain insight into how leaf development responds to the mobile signal, leaf development was followed morphologically and using the CYCB1,1::GUS marker for G2/M phase cells. We found that arrest of leaf growth is a fully penetrant phenotype, and a dramatic decrease in G2/M phase cells was coincident with arrest. Analyses of stress phenotypes found that late in development, bps1 cotyledons produced necrotic lesions, however neither hydrogen peroxide nor superoxide were abundant as leaves underwent arrest.

CONCLUSIONS

bps1 roots appear to require active growth in order to produce the mobile bps1 signal, but the potential for this compound's synthesis is present both early and late during vegetative development. This prolonged capacity to synthesize and respond to the mobile compound is consistent with a possible role for the mobile compound in linking shoot growth to subterranean conditions. The specific growth-related responses in the shoot indicated that the mobile substance prevents full activation of cell division in leaves, although whether cell division is a direct response remains to be determined.

Arabidopsis thaliana as a model organism in systems biology

Significant progress has been made in identification of genes and gene networks involved in key biological processes. Yet, how these genes and networks are coordinated over increasing levels of biological complexity, from cells to tissues to organs, remains unclear. To address complex biological questions, biologists are increasingly using high-throughput tools and systems biology approaches to examine complex biological systems at a global scale. A system is a network of interacting and interdependent components that shape the system's unique properties. Systems biology studies the organization of system components and their interactions, with the idea that unique properties of that system can be observed only through study of the system as a whole. The application of systems biology approaches to questions in plant biology has been informative. In this review, we give examples of how systems biology is currently being used in Arabidopsis to investigate the transcriptional networks regulating root development, the metabolic response to stress, and the genetic regulation of metabolic variability. From these studies, we are beginning obtain sufficient data to generate more accurate models for system function. Further investigation of plant systems will require data gathering from specific cells and tissues, continued improvement in metabolic technologies, and novel computational methods for data visualization and modeling.

Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis

Asymmetric cell division generates cell types with different specialized functions or fates. This type of division is critical to the overall cellular organization and development of many multicellular organisms. In plants, regulated asymmetric cell divisions are of particular importance because cell migration does not occur. The influence of extrinsic cues on asymmetric cell division in plants is well documented. Recently, candidate intrinsic factors have been identified and links between intrinsic and extrinsic components are beginning to be elucidated. A novel mechanism in breaking symmetry was revealed that involves the movement of typically intrinsic factors between plant cells. As we learn more about the regulation of asymmetric cell divisions in plants, we can begin to reflect on the similarities and differences between the strategies used by plants and animals. Focusing on the underlying molecular mechanisms, this article describes three selected cases of symmetry-breaking events in the model plant Arabidopsis thaliana. These examples occur in early embryogenesis, stomatal development, and ground tissue formation in the root.

Oscillating gene expression determines competence for periodic Arabidopsis root branching

Plants and animals produce modular developmental units in a periodic fashion. In plants, lateral roots form as repeating units along the root primary axis; however, the developmental mechanism regulating this process is unknown. We found that cyclic expression pulses of a reporter gene mark the position of future lateral roots by establishing prebranch sites and that prebranch site production and root bending are periodic. Microarray and promoter-luciferase studies revealed two sets of genes oscillating in opposite phases at the root tip. Genetic studies show that some oscillating transcriptional regulators are required for periodicity in one or both developmental processes. This molecular mechanism has characteristics that resemble molecular clock-driven activities in animal species.

Components of the Arabidopsis mRNA decapping complex are required for early seedling development

To understand the mechanisms controlling vein patterning in Arabidopsis thaliana, we analyzed two phenotypically similar mutants, varicose (vcs) and trident (tdt). We had previously identified VCS, and recently, human VCS was shown to function in mRNA decapping. Here, we report that TDT encodes the mRNA-decapping enzyme. VCS and TDT function together in small cytoplasmic foci that appear to be processing bodies. To understand the developmental requirements for mRNA decapping, we characterized the vcs and tdt phenotypes. These mutants were small and chlorotic, with severe defects in shoot apical meristem formation and cotyledon vein patterning. Many capped mRNAs accumulated in tdt and vcs mutants, but surprisingly, some mRNAs were specifically depleted. In addition, loss of decapping arrested the decay of some mRNAs, while others showed either modest or no decay defects, suggesting that mRNAs may show specificity for particular decay pathways (3' to 5' and 5' to 3'). Furthermore, the severe block to postembryonic development in vcs and tdt and the accompanying accumulation of embryonic mRNAs indicate that decapping is important for the embryo-to-seedling developmental transition.

Dissecting the biosynthetic pathway for the bypass1 root-derived signal

The Arabidopsis BYPASS1 (BPS1) gene is required for normal root and shoot development. In bps1 mutants, grafting and root excision experiments have shown that mutant roots produce a transmissible signal that is capable of arresting shoot development. In addition, we previously showed that growth of bps1 mutants on the carotenoid biosynthesis inhibitor fluridone resulted in partial rescue of both leaf and root defects. These observations suggest that a single mobile carotenoid-derived signal affects both root and shoot development. Here, we describe further characterization of the bps1 root-derived signal using genetic and biosynthetic inhibitor approaches. We characterized leaf and root development in double mutants that combined the bps1 mutant with mutants that have known defects in genes encoding carotenoid processing enzymes or defects in responses to carotenoid-derived abscisic acid. Our studies indicate that the mobile signal is neither abscisic acid nor the MAX-dependent hormone that regulates shoot branching, and that production of the signal does not require the activity of any single carotenoid cleavage dioxygenase. In addition, our studies with CPTA, a lycopene cyclase inhibitor, show that signal production requires synthesis of beta-carotene and its derivatives. Furthermore, we show a direct requirement for carotenoids as signal precursors, as the GUN plastid-to-nucleus signaling pathway is not required for phenotypic rescue. Together, our results suggest that bps1 roots produce a novel mobile carotenoid-derived signaling compound.

SCARFACE encodes an ARF-GAP that is required for normal auxin efflux and vein patterning in Arabidopsis

To identify molecular mechanisms controlling vein patterns, we analyzed scarface (sfc) mutants. sfc cotyledon and leaf veins are largely fragmented, unlike the interconnected networks in wild-type plants. SFC encodes an ADP ribosylation factor GTPase activating protein (ARF-GAP), a class with well-established roles in vesicle trafficking regulation. Quadruple mutants of SCF and three homologs (ARF-GAP DOMAIN1, 2, and 4) showed a modestly enhanced vascular phenotype. Genetic interactions between sfc and pinoid and between sfc and gnom suggest a possible function for SFC in trafficking of auxin efflux regulators. Genetic analyses also revealed interaction with cotyledon vascular pattern2, suggesting that lipid-based signals may underlie some SFC ARF-GAP functions. To assess possible roles for SFC in auxin transport, we analyzed sfc roots, which showed exaggerated responses to exogenous auxin and higher auxin transport capacity. To determine whether PIN1 intracellular trafficking was affected, we analyzed PIN1:green fluorescent protein (GFP) dynamics using confocal microscopy in sfc roots. We found normal PIN1:GFP localization at the apical membrane of root cells, but treatment with brefeldin A resulted in PIN1 accumulating in smaller and more numerous compartments than in the wild type. These data suggest that SFC is required for normal intracellular transport of PIN1 from the plasma membrane to the endosome.

BYPASS1 negatively regulates a root-derived signal that controls plant architecture

Plant architecture is regulated by endogenous developmental programs, but it can also be strongly influenced by cues derived from the environment. For example, rhizosphere conditions such as water and nutrient availability affect shoot and root architecture; this implicates the root as a source of signals that can override endogenous developmental programs. Cytokinin, abscisic acid, and carotenoid derivatives have all been implicated as long-distance signals that can be derived from the root. However, little is known about how root-derived signaling pathways are regulated. Here, we show that BYPASS1 (BPS1), an Arabidopsis gene of unknown function, is required to prevent constitutive production of a root-derived graft-transmissible signal that is sufficient to inhibit leaf initiation, leaf expansion, and shoot apical meristem activity. We show that this root-derived signal is likely to be a novel carotenoid-derived molecule that can modulate both root and shoot architecture.