Secondary growth of the Arabidopsis hypocotyl-vascular development in dimensions

Here comes the sun: integration of light, temperature, and auxin during herbaceous plant grafting

MAIN CONCLUSION

Light and temperature can regulate auxin production which has been recently shown to be key during graft healing, suggesting that abiotic factors may be vital variables for future graft studies. Grafting is an important horticultural tool used to combine advantageous plant traits. Despite its broad usage, the mechanisms that underlie graft healing remain poorly understood. Recent work has highlighted the influence of high temperature-mediated auxin flow on graft success. Light and temperature sensing utilize partially overlapping mechanisms to regulate auxin biosynthesis, signaling, and transport. In this review, we explore the sensors and transcriptional regulators that modulate auxin response, specifically emphasizing how these components regulate graft success and vascular reconnection. We also discuss areas of graft biology regulated by auxin and underexplored areas of photobiology that may be key to a better understanding of graft mechanisms. This review underscores the importance of translating genetic findings from model systems into horticultural crops to expand our knowledge of economically valuable techniques like grafting.

Environmental Control of Hypocotyl Elongation

The hypocotyl is the embryonic stem connecting the primary root to the cotyledons. Hypocotyl length varies tremendously depending on the conditions. This developmental plasticity and the simplicity of the organ explain its success as a model for growth regulation. Light and temperature are prominent growth-controlling cues, using shared signaling elements. Mechanisms controlling hypocotyl elongation in etiolated seedlings reaching the light differ from those in photoautotrophic seedlings. However, many common growth regulators intervene in both situations. Multiple photoreceptors including phytochromes, which also respond to temperature, control the activity of several transcription factors, thereby eliciting rapid transcriptional reprogramming. Hypocotyl growth often depends on sensing in green tissues and interorgan communication comprising auxin. Hypocotyl auxin, in conjunction with other hormones, determines epidermal cell elongation. Plants facing cues with opposite effects on growth control hypocotyl elongation through intricate mechanisms. We discuss the status of the field and end by highlighting open questions.

Identification of Functional Brassinosteroid Receptor Genes in Oaks and Functional Analysis of QmBRI1

Brassinosteroids (BRs) play important regulatory roles in plant growth and development, with functional BR receptors being crucial for BR recognition or signaling. Although functional BR receptors have been extensively studied in herbaceous plants, they remain largely under-studied in forest tree species. In this study, nine BR receptors were identified in three representative oak species, of which BRI1s and BRL1s were functional BR receptors. Dispersed duplications were a driving force for oak BR receptor expansion, among which the Brassinosteroid-Insensitive-1 (BRI1)-type genes diverged evolutionarily from most rosids. In oak BRI1s, we identified that methionine in the conserved Asn-Gly-Ser-Met (NGSM) motif was replaced by isoleucine and that the amino acid mutation occurred after the divergence of Quercus and Fagus. Compared with QmBRL1, QmBRI1 was relatively highly expressed during BR-induced xylem differentiation and in young leaves, shoots, and the phloem and xylem of young stems of Quercus mongolica. Based on Arabidopsis complementation experiments, we proved the important role of QmBRI1 in oak growth and development, especially in vascular patterning and xylem differentiation. These findings serve as an important supplement to the findings of the structural, functional and evolutionary studies on functional BR receptors in woody plants and provide the first example of natural mutation occurring in the conserved BR-binding region (NGSM motif) of angiosperm BRI1s.

Natural variation in the prolyl 4-hydroxylase gene PtoP4H9 contributes to perennial stem growth in Populus

Perennial trees must maintain stem growth throughout their entire lifespan to progressively increase in size as they age. The overarching question of the molecular mechanisms that govern stem perennial growth in trees remains largely unanswered. Here we deciphered the genetic architecture that underlies perennial growth trajectories using genome-wide association studies (GWAS) for measures of growth traits across years in a natural population of Populus tomentosa. By analyzing the stem growth trajectory, we identified PtoP4H9, encoding prolyl 4-hydroxylase 9, which is responsible for the natural variation in the growth rate of diameter at breast height (DBH) across years. Quantifying the dynamic genetic contribution of PtoP4H9 loci to stem growth showed that PtoP4H9 played a pivotal role in stem growth regulation. Spatiotemporal expression analysis showed that PtoP4H9 was highly expressed in cambium tissues of poplars of various ages. Overexpression and knockdown of PtoP4H9 revealed that it altered cell expansion to regulate cell wall modification and mechanical characteristics, thereby promoting stem growth in Populus. We showed that natural variation in PtoP4H9 occurred in a BASIC PENTACYSTEINE transcription factor PtoBPC1-binding promoter element controlling PtoP4H9 expression. The geographic distribution of PtoP4H9 allelic variation was consistent with the modes of selection among populations. Altogether, our study provides important genetic insights into dynamic stem growth in Populus, and we confirmed PtoP4H9 as a potential useful marker for breeding or genetic engineering of poplars.

Axes and polarities in leaf vein formation

For multicellular organisms to develop, cells must grow, divide, and differentiate along preferential or exclusive orientations or directions. Moreover, those orientations, or axes, and directions, or polarities, must be coordinated between cells within and between tissues. Therefore, how axes and polarities are coordinated between cells is a key question in biology. In animals, such coordination mainly depends on cell migration and direct interaction between proteins protruding from the plasma membrane. Both cell movements and direct cell-cell interactions are prevented in plants by cell walls that surround plant cells and keep them apart and in place. Therefore, plants have evolved unique mechanisms to coordinate their cell axes and polarities. Here I will discuss evidence suggesting that understanding how leaf veins form may uncover those unique mechanisms. Indeed, unlike previously thought, the cell-to-cell polar transport of the plant hormone auxin along developing veins cannot account for many features of vein patterning. Instead, those features can be accounted for by models of vein patterning that combine polar auxin transport with auxin diffusion through plasmodesmata along the axis of developing veins. Though it remains unclear whether such a combination of polar transport and axial diffusion of auxin can account for the formation of the variety of vein patterns found in plant leaves, evidence suggests that such a combined mechanism may control plant developmental processes beyond vein patterning.

Phloem development

The evolution of the plant vascular system is a key process in Earth history because it enabled plants to conquer land and transform the terrestrial surface. Among the vascular tissues, the phloem is particularly intriguing because of its complex functionality. In angiosperms, its principal components are the sieve elements, which transport phloem sap, and their neighboring companion cells. Together, they form a functional unit that sustains sap loading, transport, and unloading. The developmental trajectory of sieve elements is unique among plant cell types because it entails selective organelle degradation including enucleation. Meticulous analyses of primary, so-called protophloem in the Arabidopsis thaliana root meristem have revealed key steps in protophloem sieve element formation at single-cell resolution. A transcription factor cascade connects specification with differentiation and also orchestrates phloem pole patterning via noncell-autonomous action of sieve element-derived effectors. Reminiscent of vascular tissue patterning in secondary growth, these involve receptor kinase pathways, whose antagonists guide the progression of sieve element differentiation. Receptor kinase pathways may also safeguard phloem formation by maintaining the developmental plasticity of neighboring cell files. Our current understanding of protophloem development in the A. thaliana root has reached sufficient detail to instruct molecular-level investigation of phloem formation in other organs.

Deep machine learning for cell segmentation and quantitative analysis of radial plant growth

Plants produce the major part of terrestrial biomass and are long-term deposits of atmospheric carbon. This capacity is to a large extent due to radial growth of woody species - a process driven by cambium stem cells located in distinct niches of shoot and root axes. In the model species Arabidopsis thaliana, thousands of cells are produced by the cambium in radial orientation generating a complex organ anatomy enabling long-distance transport, mechanical support and protection against biotic and abiotic stressors. These complex organ dynamics make a comprehensive and unbiased analysis of radial growth challenging and asks for tools for automated quantification. Here, we combined the recently developed PlantSeg and MorphographX image analysis tools, to characterize tissue morphogenesis of the Arabidopsis hypocotyl. After sequential training of segmentation models on ovules, shoot apical meristems and adult hypocotyls using deep machine learning, followed by the training of cell type classification models, our pipeline segments complex images of transverse hypocotyl sections with high accuracy and classifies central hypocotyl cell types. By applying our pipeline on both wild type and phloem intercalated with xylem (pxy) mutants, we also show that this strategy faithfully detects major anatomical aberrations. Collectively, we conclude that our established pipeline is a powerful phenotyping tool comprehensively extracting cellular parameters and providing access to tissue topology during radial plant growth.

Genetic mechanisms of aging in plants: What can we learn from them?

Plants hold all records in longevity. Their aging is a complex process. In the presented review, we analyzed published data on various aspects of plant aging with focus on any inferences that could shed a light on aging in animals and help to fight it in human. Plant aging can be caused by many factors, such as telomere depletion, genomic instability, loss of proteostasis, changes in intercellular interaction, desynchronosis, autophagy misregulation, epigenetic changes and others. Plants have developed a number of mechanisms to increase lifespan. Among these mechanisms are gene duplication ("genetic backup"), the active work of telomerases, abundance of meristematic cells, capacity of maintaining the meristems permanently active and continuous activity of phytohormones. Plant aging usually occurs throughout the whole perennial life, but could be also seasonal senescence. Study of causes for seasonal aging can also help to uncover the mechanisms of plant longevity. The influence of different factors such as microbiome communities, glycation, alternative oxidase activity, mitochondrial dysfunction on plant longevity was also reviewed. Adaptive mechanisms of long-lived plants are considered. Further comparative study of the mechanisms underlying longevity of plants is necessary. This will allow us to reach a potentially new level of understanding of the aging process of plants.

Translational profile of developing phellem cells in Arabidopsis thaliana roots

The phellem is a specialized boundary tissue providing the first line of defense against abiotic and biotic stresses in organs undergoing secondary growth. Phellem cells undergo several differentiation steps, which include cell wall suberization, cell expansion, and programmed cell death. Yet, the molecular players acting particularly in phellem cell differentiation remain poorly described, particularly in the widely used model plant Arabidopsis thaliana. Using specific marker lines we followed the onset and progression of phellem differentiation in A. thaliana roots and further targeted the translatome of newly developed phellem cells using translating ribosome affinity purification followed by mRNA sequencing (TRAP-SEQ). We showed that phellem suberization is initiated early after phellogen (cork cambium) division. The specific translational landscape was organized in three main domains related to energy production, synthesis and transport of cell wall components, and response to stimulus. Novel players in phellem differentiation related to suberin monomer transport and assembly as well as novel transcription regulators were identified. This strategy provided an unprecedented resolution of the translatome of developing phellem cells, giving a detailed and specific view on the molecular mechanisms acting on cell differentiation in periderm tissues of the model plant Arabidopsis.

Laying it on thick: a study in secondary growth

The development of secondary vascular tissue enhances the transport capacity and mechanical strength of plant bodies, while contributing a huge proportion of the world's biomass in the form of wood. Cell divisions in the cambium, which constitutes the vascular meristem, provide progenitors from which conductive xylem and phloem are derived. The cambium is a somewhat unusual stem cell population in two respects, making it an interesting subject for developmental research. Firstly, it arises post-germination, and thus represents a model for understanding stem cell initiation beyond embryogenesis. Secondly, xylem and phloem differentiate on opposing sides of cambial stem cells, making them bifacial in nature. Recent discoveries in Arabidopsis thaliana have provided insight into the molecular mechanisms that regulate the initiation, patterning, and maintenance of the cambium. In this review, the roles of intercellular signalling via mobile transcription factors, peptide-receptor modules, and phytohormones are described. Crosstalk between these regulatory pathways is becoming increasingly apparent, yet the underlying mechanisms are not fully understood. Future study of the interaction between multiple independently identified regulators, as well as the functions of their orthologues in trees, will deepen our understanding of radial growth in plants.

Bifacial cambium stem cells generate xylem and phloem during radial plant growth

A reduced rate of stem cell division is considered a widespread feature which ensures the integrity of genetic information during somatic development of plants and animals. Radial growth of plant shoots and roots is a stem cell-driven process that is fundamental for the mechanical and physiological support of enlarging plant bodies. In most dicotyledonous species, the underlying stem cell niche, the cambium, generates xylem inwards and phloem outwards. Despite the importance and intriguing dynamics of the cambium, the functional characterization of its stem cells is hampered by the lack of experimental tools for accessing distinct cambium sub-domains. Here, we use the hypocotyl of Arabidopsis thaliana to map stem cell activity in the proliferating cambium. Through pulse labeling and genetically encoded lineage tracing, we find that a single bifacial stem cell generates both xylem and phloem cell lineages. This cell is characterized by a specific combination of PXY (TDR), SMXL5 and WOX4 gene activity and a high division rate in comparison with tissue-specific progenitors. Our analysis provides a cellular fate map of radial plant growth, and suggests that stem cell quiescence is not a general prerequisite for life-long tissue production.

This article has an associated ‘The people behind the papers’ interview.

Highlighted Article: A single bifacial stem cell that is characterized by the combined activity of PXY (TDR), SMXL5 and WOX4 genes generates both wood and bast during radial plant growth.

Plant Vascular Tissues-Connecting Tissue Comes in All Shapes

For centuries, humans have grown and used structures based on vascular tissues in plants. One could imagine that life would have developed differently without wood as a resource for building material, paper, heating energy, or fuel and without edible tubers as a food source. In this review, we will summarise the status of research on Arabidopsis thaliana vascular development and subsequently focus on how this knowledge has been applied and expanded in research on the wood of trees and storage organs of crop plants. We will conclude with an outlook on interesting open questions and exciting new research opportunities in this growing and important field.

Coordination of cell polarity and the patterning of leaf vein networks

During development, the behavior of cells in tissues is coordinated along specific orientations or directions by coordinating the polar localization of components in those cells. The coordination of such cell polarity is perhaps nowhere more spectacular than in developing leaves, where the polarity of hundreds of cells is coordinated in the leaf epidermis and inner tissue to pattern vein networks. Available evidence suggests that the spectacular coordination of cell polarity that patterns vein networks is controlled by auxin transport and levels, and by genes that have been implicated in the polar localization of auxin transporters.

Overexpression and cosuppression of xylem-related genes in an early xylem differentiation stage-specific manner by the AtTED4 promoter

Tissue-specific overexpression of useful genes, which we can design according to their cause-and-effect relationships, often gives valuable gain-of-function phenotypes. To develop genetic tools in woody biomass engineering, we produced a collection of Arabidopsis lines that possess chimeric genes of a promoter of an early xylem differentiation stage-specific gene, Arabidopsis Tracheary Element Differentiation-related 4 (AtTED4) and late xylem development-associated genes, many of which are uncharacterized. The AtTED4 promoter directed the expected expression of transgenes in developing vascular tissues from young to mature stage. Of T2 lines examined, 42%, 49% and 9% were judged as lines with the nonrepeat type insertion, the simple repeat type insertion and the other repeat type insertion of transgenes. In 174 T3 lines, overexpression lines were confirmed for 37 genes, whereas only cosuppression lines were produced for eight genes. The AtTED4 promoter activity was high enough to overexpress a wide range of genes over wild-type expression levels, even though the wild-type expression is much higher than AtTED4 expression for several genes. As a typical example, we investigated phenotypes of pAtTED4::At5g60490 plants, in which both overexpression and cosuppression lines were included. Overexpression but not cosuppression lines showed accelerated xylem development, suggesting the positive role of At5g60490 in xylem development. Taken together, this study provides valuable results about behaviours of various genes expressed under an early xylem-specific promoter and about usefulness of their lines as genetic tools in woody biomass engineering.

Perception of root-active CLE peptides requires CORYNE function in the phloem vasculature

Arabidopsis root development is orchestrated by signaling pathways that consist of different CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptide ligands and their cognate CLAVATA (CLV) and BARELY ANY MERISTEM (BAM) receptors. How and where different CLE peptides trigger specific morphological or physiological changes in the root is poorly understood. Here, we report that the receptor‐like protein CLAVATA 2 (CLV2) and the pseudokinase CORYNE (CRN) are necessary to fully sense root‐active CLE peptides. We uncover BAM3 as the CLE45 receptor in the root and biochemically map its peptide binding surface. In contrast to other plant peptide receptors, we found no evidence that SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) proteins act as co‐receptor kinases in CLE45 perception. CRN stabilizes BAM3 expression and thus is required for BAM3‐mediated CLE45 signaling. Moreover, protophloem‐specific CRN expression complements resistance of the crn mutant to root‐active CLE peptides, suggesting that protophloem is their principal site of action. Our work defines a genetic framework for dissecting CLE peptide signaling and CLV/BAM receptor activation in the root.

Vascular Morphodynamics During Secondary Growth

Quantification of vascular morphodynamics during secondary growth has been hampered by the scale of the process. Even in the tiny model plant Arabidopsis thaliana, the xylem can include more than 2000 cells in a single cross section, rendering manual counting impractical. Moreover, due to its deep location, xylem is an inaccessible tissue, limiting live imaging. A novel method to visualize and measure secondary growth progression has been proposed: "the Quantitative Histology" approach. This method is based on a detailed anatomical atlas, and image segmentation coupled with machine learning to automatically extract cell shapes and identify cell type. Here we present a new version of this approach, with a user-friendly interface implemented in the open source software LithoGraphX.

Environmental and hormonal control of cambial stem cell dynamics

Perennial trees have the amazing ability to adjust their growth rate to both adverse and favorable seasonally reoccurring environmental conditions over hundreds of years. In trunks and stems, the basis for the tuning of seasonal growth rate is the regulation of cambial stem cell activity. Cambial stem cell quiescence and dormancy protect the tree from potential physiological and genomic damage caused by adverse growing conditions and may permit a long lifespan. Cambial dormancy and longevity are both aspects of a tree's life for which the study of cambial stem cell behavior in the annual model plant Arabidopsis is inadequate. Recent functional analyses of hormone perception and catabolism mutants in Populus indicate that shoot-derived long-range signals, as well as local cues, steer cambial activity. Auxin is central to the regulation of cambial activity and probably also maintenance. Emerging genome editing and phenotyping technologies will enable the identification of down-stream targets of hormonal action and facilitate the genetic dissection of complex traits of cambial biology.

Novel tools for quantifying secondary growth

Secondary growth occurs in dicotyledons and gymnosperms, and results in an increased girth of plant organs. It is driven primarily by the vascular cambium, which produces thousands of cells throughout the life of several plant species. For instance, even in the small herbaceous model plant Arabidopsis, manual quantification of this massive process is impractical. Here, we provide a comprehensive overview of current methods used to measure radial growth. We discuss the issues and problematics related to its quantification. We highlight recent advances and tools developed for automated cellular phenotyping and its future applications.

Cambial stem cells and their niche

Unlike animals, plants often have an indefinite genetic potency to form new organs throughout their entire lifespan. Growth and organogenesis are driven by cell divisions in meristems at distinct sites within the plant. Since the meristems contributing to axial thickening in dicots (cambia) are separated from places where axes elongate (apical meristems); there is a need of communication to coordinate growth. In their behavior, some meristematic cells resemble animal stem cells whose daughter cells either maintain the capacity to divide over a long period of time or undergo differentiation. The behavior of stem cells is regulated by their microenvironment, the so called niche. The stem- and niche-cell concept is now also widely accepted for apical meristems. An integral part of the cambial niche has recently been localized to the phloem. It steers cell division activity in the cambium via the release of a peptide signal and may be a hub to integrate signals from other stem cell populations to coordinate growth. Although these signals have yet to be determined, the discovery of the cambial niche cells will pave the way for a better understanding of inter-meristematic communication and cambial stem cell behavior.