Double labeling of KNOTTED1 mRNA and protein reveals multiple potential sites of protein trafficking in the shoot apex

Quantification of plasmodesmata frequency under three-dimensional view using focused ion beam-scanning electron microscopy and image analysis

The quantitative study of plasmodesmata (PD) frequency is routine in plant science for providing information on the potential of intercellular transportation. Here, we report quantification of plasmodesmatal frequency in virus-infected tobacco vascular tissues using serial sectioning and image analysis. The image datasets were collected by focused ion beam-scanning electron microscopy (FIB-SEM), and the measurements of plasmodesmatal frequency were performed after image analysis with commercial computational programs. With a 5-nm step size (less than half the diameter of PD) during FIB sectioning, exhaustive PD sampling was performed in regions of interest. Segmentation of cell wall (CW) and PD from the background densities was performed manually, and PD were assigned automatically to individual CW interfaces by image analysis and then quantified. The PD quantification results were used to compare the plamodesmatal frequencies among different CW interfaces of individual cells and the average frequencies among different cell types were calculated. CWs lacking PD distribution were found in several cellular types, and the PD frequency were used to determine the possible pathways of PD-based symplasmic transportation. The method enables imaging of samples of several cells containing multiple CW interfaces and minimizes PD omission during sectioning and imaging.

RNA In Situ Hybridization of Detecting Cucumber Mosaic Virus in Shoots of Nicotiana benthamiana Plants

RNA in situ hybridization, a histological technique derived from Southern blotting and northern blotting, has been an important approach in biology studies for many years. In the studies of virus-plant interactions, RNA in situ hybridization provides a direct visualization of viral RNA in host plants. Here, we provide a detailed protocol for viral RNA in situ hybridization that has been successfully used to detect Cucumber mosaic virus genome (CMV) RNAs in shoots of N. benthamiana plants.

The dynamics of maize leaf development: Patterned to grow while growing a pattern

Leaves are a significant component of the shoot system in grasses, functioning in light capture and photosynthesis. Leaf width, length, and angle are expressions of development that collectively define canopy architecture. Thus, the distinctive morphology of grass leaves is an interdependent readout of developmental patterning and growth along the proximal-distal, medial-lateral, and adaxial-abaxial axes. Here, we review the chronology of patterning and growth, namely along the proximal-distal axis, during maize leaf development. We underscore that patterning and growth occur simultaneously, making use of shared developmental gradients and molecular pathways.

Network analyses identify a transcriptomic proximodistal prepattern in the maize leaf primordium

The formation of developmental boundaries is a common feature of multicellular plants and animals, and impacts the initiation, structure and function of all organs. Maize leaves comprise a proximal sheath that encloses the stem, and a distal photosynthetic blade that projects away from the plant axis. An epidermally derived ligule and a joint-like auricle develop at the blade/sheath boundary of maize leaves. Mutations disturbing the ligule/auricle region disrupt leaf patterning and impact plant architecture, yet it is unclear how this developmental boundary is established. Targeted microdissection followed by transcriptomic analyses of young leaf primordia were utilized to construct a co-expression network associated with development of the blade/sheath boundary. Evidence is presented for proximodistal gradients of gene expression that establish a prepatterned transcriptomic boundary in young leaf primordia, before the morphological initiation of the blade/sheath boundary in older leaves. This work presents a conceptual model for spatiotemporal patterning of proximodistal leaf domains, and provides a rich resource of candidate gene interactions for future investigations of the mechanisms of blade/sheath boundary formation in maize.

Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

BACKGROUND

Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions.

RESULTS

In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves.

CONCLUSIONS

Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.

Developmental genetics of maize vegetative shoot architecture

More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01208-1.

Moving with purpose and direction: transcription factor movement and cell fate determination revisited

Cell diversity in a multicellular organism relies on cell-cell communication where cells must receive positional information as input signals to adopt their proper cell fate in the right place and at the right time. This process is achieved through triggering signaling cascades that drive cellular changes during development. In plants, signaling through mobile transcription factors (TF) plays a central role in development. Rather than acting cell-autonomously and exclusive to their expression domains, many TFs move between cells and deploy regulatory networks and cell type-specific effectors to achieve their biological functions. Here, we highlight a few examples of mobile TFs central to cell fate specification in Arabidopsis.

Coordination of Leaf Development Across Developmental Axes

Leaves are initiated as lateral outgrowths from shoot apical meristems throughout the vegetative life of the plant. To achieve proper developmental patterning, cell-type specification and growth must occur in an organized fashion along the proximodistal (base-to-tip), mediolateral (central-to-edge), and adaxial–abaxial (top-bottom) axes of the developing leaf. Early studies of mutants with defects in patterning along multiple leaf axes suggested that patterning must be coordinated across developmental axes. Decades later, we now recognize that a highly complex and interconnected transcriptional network of patterning genes and hormones underlies leaf development. Here, we review the molecular genetic mechanisms by which leaf development is coordinated across leaf axes. Such coordination likely plays an important role in ensuring the reproducible phenotypic outcomes of leaf morphogenesis.

Conceptual and Methodological Considerations on mRNA and Proteins as Intercellular and Long-Distance Signals

High-throughput studies identified approximately one-fifth of Arabidopsis protein-encoding transcripts to be graft transmissible and to move over long distances in the phloem. In roots, one-fifth of transcription factors were annotated as non-cell autonomous, moving between cells. Is this massive transport a way of interorgan and cell-cell communication or does it serve different purposes? On the tissue level, many microRNAs (miRNAs) and all small interfering RNAs (siRNAs) act non-cell autonomously. Why are these RNAs and proteins not just expressed in cells where they exert their function? Short- and long-distance transport of these macromolecules raises the question of whether all mobile mRNAs and transcription factors could be defined as signaling molecules. Since the answer is not clear yet, we will discuss in this review conceptual approaches to this phenomenon using a single mobile signaling macromolecule, FLOWERING LOCUS T, which has been characterized extensively. We conclude that careful individual studies of mobile macromolecules are necessary to uncover their biological function and the observed massive mobility. To stimulate such studies, we provide a review summarizing the resourceful wealth of experimental approaches to this intriguing question and discuss methodological scopes and limits.

Regulation of Division and Differentiation of Plant Stem Cells

A major challenge in developmental biology is unraveling the precise regulation of plant stem cell maintenance and the transition to a fully differentiated cell. In this review, we highlight major themes coordinating the acquisition of cell identity and subsequent differentiation in plants. Plant cells are immobile and establish position-dependent cell lineages that rely heavily on external cues. Central players are the hormones auxin and cytokinin, which balance cell division and differentiation during organogenesis. Transcription factors and miRNAs, many of which are mobile in plants, establish gene regulatory networks that communicate cell position and fate. Small peptide signaling also provides positional cues as new cell types emerge from stem cell division and progress through differentiation. These pathways recruit similar players for patterning different organs, emphasizing the modular nature of gene regulatory networks. Finally, we speculate on the outstanding questions in the field and discuss how they may be addressed by emerging technologies.

Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network

The Arabidopsis homeodomain transcription factor SHOOT MERISTEMLESS (STM) is crucial for shoot apical meristem (SAM) function, yet the components and structure of the STM gene regulatory network (GRN) are largely unknown. Here, we show that transcriptional regulators are overrepresented among STM-regulated genes and, using these as GRN components in Bayesian network analysis, we infer STM GRN associations and reveal regulatory relationships between STM and factors involved in multiple aspects of SAM function. These include hormone regulation, TCP-mediated control of cell differentiation, AIL/PLT-mediated regulation of pluripotency and phyllotaxis, and specification of meristem-organ boundary zones via CUC1. We demonstrate a direct positive transcriptional feedback loop between STM and CUC1, despite their distinct expression patterns in the meristem and organ boundary, respectively. Our further finding that STM activates expression of the CUC1-targeting microRNA miR164c combined with mathematical modelling provides a potential solution for this apparent contradiction, demonstrating that these proposed regulatory interactions coupled with STM mobility could be sufficient to provide a mechanism for CUC1 localisation at the meristem-organ boundary. Our findings highlight the central role for the STM GRN in coordinating SAM functions.

SHOOT MERISTEMLESS trafficking controls axillary meristem formation, meristem size and organ boundaries in Arabidopsis

The shoot stem cell niche, contained within the shoot apical meristem (SAM) is maintained in Arabidopsis by the homeodomain protein SHOOT MERISTEMLESS (STM). STM is a mobile protein that traffics cell-to-cell, presumably through plasmodesmata. In maize, the STM homolog KNOTTED1 shows clear differences between mRNA and protein localization domains in the SAM. However, the STM mRNA and protein localization domains are not obviously different in Arabidopsis, and the functional relevance of STM mobility is unknown. Using a non-mobile version of STM (2xNLS-YFP-STM), we show that STM mobility is required to suppress axillary meristem formation during embryogenesis, to maintain meristem size, and to precisely specify organ boundaries throughout development. STM and organ boundary genes CUP SHAPED COTYLEDON1 (CUC1), CUC2 and CUC3 regulate each other during embryogenesis to establish the embryonic SAM and to specify cotyledon boundaries, and STM controls CUC expression post-embryonically at organ boundary domains. We show that organ boundary specification by correct spatial expression of CUC genes requires STM mobility in the meristem. Our data suggest that STM mobility is critical for its normal function in shoot stem cell control.

Ectopic KNOX Expression Affects Plant Development by Altering Tissue Cell Polarity and Identity

Plant development involves two polarity types: tissue cell (asymmetries within cells are coordinated across tissues) and regional (identities vary spatially across tissues) polarity. Both appear altered in the barley (Hordeum vulgare) Hooded mutant, in which ectopic expression of the KNOTTED1-like Homeobox (KNOX) gene, BKn3, causes inverted polarity of differentiated hairs and ectopic flowers, in addition to wing-shaped outgrowths. These lemma-specific effects allow the spatiotemporal analysis of events following ectopic BKn3 expression, determining the relationship between KNOXs, polarity, and shape. We show that tissue cell polarity, based on localization of the auxin transporter SISTER OF PINFORMED1 (SoPIN1), dynamically reorients as ectopic BKn3 expression increases. Concurrently, ectopic expression of the auxin importer LIKE AUX1 and boundary gene NO APICAL MERISTEM is activated. The polarity of hairs reflects SoPIN1 patterns, suggesting that tissue cell polarity underpins oriented cell differentiation. Wing cell files reveal an anisotropic growth pattern, and computational modeling shows how polarity guiding growth can account for this pattern and wing emergence. The inverted ectopic flower orientation does not correlate with SoPIN1, suggesting that this form of regional polarity is not controlled by tissue cell polarity. Overall, the results suggest that KNOXs trigger different morphogenetic effects through interplay between tissue cell polarity, identity, and growth.

Detection of Mycobacterium tuberculosis and Mycobacterium bovis in Sahiwal cattle from an organized farm using ante-mortem techniques

Aim:

The aim of this study was to investigate the prevalence of bovine tuberculosis (TB) and detection of Mycobacterium bovis in cattle from an organized dairy farm.

Materials and Methods:

A total of 121 animals (93 females and 28 males) of 1 year and above were studied for the prevalence of bovine TB using single intradermal comparative cervical tuberculin (SICCT) test, bovine gamma-interferon (γ-IFN) enzyme immunoassay, and polymerase chain reactions (PCRs).

Results:

Out of total 121 animals, 17 (14.04%) animals were positive reactors to SICCT test while only one (0.82%) animal for γ-IFN assay. By PCR, Mycobacterium TB complex was detected in 19 (15.70%) animals out of which 4 (3.30%) animal were also positive for M. bovis.

Conclusions:

Diagnosis of bovine TB can be done in early stage in live animals with multiple approaches like skin test followed by a molecular technique like PCR which showed promising results.

Flagellar membrane fusion and protein exchange in trypanosomes; a new form of cell-cell communication?

Diverse structures facilitate direct exchange of proteins between cells, including plasmadesmata in plants and tunnelling nanotubes in bacteria and higher eukaryotes.  Here we describe a new mechanism of protein transfer, flagellar membrane fusion, in the unicellular parasite Trypanosoma brucei. When fluorescently tagged trypanosomes were co-cultured, a small proportion of double-positive cells were observed. The formation of double-positive cells was dependent on the presence of extracellular calcium and was enhanced by placing cells in medium supplemented with fresh bovine serum. Time-lapse microscopy revealed that double-positive cells arose by bidirectional protein exchange in the absence of nuclear transfer.  Furthermore, super-resolution microscopy showed that this process occurred in ≤1 minute, the limit of temporal resolution in these experiments. Both cytoplasmic and membrane proteins could be transferred provided they gained access to the flagellum. Intriguingly, a component of the RNAi machinery (Argonaute) was able to move between cells, raising the possibility that small interfering RNAs are transported as cargo. Transmission electron microscopy showed that shared flagella contained two axonemes and two paraflagellar rods bounded by a single membrane. In some cases flagellar fusion was partial and interactions between cells were transient. In other cases fusion occurred along the entire length of the flagellum, was stable for several hours and might be irreversible. Fusion did not appear to be deleterious for cell function: paired cells were motile and could give rise to progeny while fused. The motile flagella of unicellular organisms are related to the sensory cilia of higher eukaryotes, raising the possibility that protein transfer between cells via cilia or flagella occurs more widely in nature.

Keep on growing: building and patterning leaves in the grasses

Monocot leaves have unique features that arise early in their development. Maturing leaves protectively enclose younger leaves and the meristem, the pool of founder cells from which a leaf emerges. Through the maturation process, proximal sheath and distal blade tissues differentiate and are separated by the ligule and auricle structures. Here we review current research focusing on the contribution of gene regulatory factors and phytohormones on the patterning and differentiation of monocot leaves primarily focusing on research in the grasses (Poaceae). The 10000 members of the grasses include the true grain cereals (wheat, rice, maize, etc.), biofuel crops such as sugarcane, pasture grasses, and bamboo. They are the most studied of the monocots due to their tremendous agricultural and agronomic importance.

Transcriptomic analyses indicate that maize ligule development recapitulates gene expression patterns that occur during lateral organ initiation

Development of multicellular organisms proceeds via the correct interpretation of positional information to establish boundaries that separate developmental fields with distinct identities. The maize (Zea mays) leaf is an ideal system to study plant morphogenesis as it is subdivided into a proximal sheath and a distal blade, each with distinct developmental patterning. Specialized ligule and auricle structures form at the blade-sheath boundary. The auricles act as a hinge, allowing the leaf blade to project at an angle from the stem, while the ligule comprises an epidermally derived fringe. Recessive liguleless1 mutants lack ligules and auricles and have upright leaves. We used laser microdissection and RNA sequencing to identify genes that are differentially expressed in discrete cell/tissue-specific domains along the proximal-distal axis of wild-type leaf primordia undergoing ligule initiation and compared transcript accumulation in wild-type and liguleless1-R mutant leaf primordia. We identified transcripts that are specifically upregulated at the blade-sheath boundary. A surprising number of these "ligule genes" have also been shown to function during leaf initiation or lateral branching and intersect multiple hormonal signaling pathways. We propose that genetic modules utilized in leaf and/or branch initiation are redeployed to regulate ligule outgrowth from leaf primordia.

Genome-wide study of KNOX regulatory network reveals brassinosteroid catabolic genes important for shoot meristem function in rice

In flowering plants, knotted1-like homeobox (KNOX) transcription factors play crucial roles in establishment and maintenance of the shoot apical meristem (SAM), from which aerial organs such as leaves, stems, and flowers initiate. We report that a rice (Oryza sativa) KNOX gene Oryza sativa homeobox1 (OSH1) represses the brassinosteroid (BR) phytohormone pathway through activation of BR catabolism genes. Inducible overexpression of OSH1 caused BR insensitivity, whereas loss of function showed a BR-overproduction phenotype. Genome-wide identification of loci bound and regulated by OSH1 revealed hormonal and transcriptional regulation as the major function of OSH1. Among these targets, BR catabolism genes CYP734A2, CYP734A4, and CYP734A6 were rapidly upregulated by OSH1 induction. Furthermore, RNA interference knockdown plants of CYP734A genes arrested growth of the SAM and mimicked some osh1 phenotypes. Thus, we suggest that local control of BR levels by KNOX genes is a key regulatory step in SAM function.

Evolutionary aspects of non-cell-autonomous regulation in vascular plants: structural background and models to study

Plasmodesmata (PD) serve for the exchange of information in form of miRNA, proteins, and mRNA between adjacent cells in the course of plant development. This fundamental role of PD is well established in angiosperms but has not yet been traced back to the evolutionary ancient plant taxa where functional studies lag behind studies of PD structure and ontogenetic origin. There is convincing evidence that the ability to form secondary (post-cytokinesis) PD, which can connect any adjacent cells, contrary to primary PD which form during cytokinesis and link only cells of the same lineage, appeared in the evolution of higher plants at least twice: in seed plants and in some representatives of the Lycopodiophyta. The (in)ability to form secondary PD is manifested in the symplasmic organization of the shoot apical meristem (SAM) which in most taxa of seedless vascular plants differs dramatically from that in seed plants. Lycopodiophyta appear to be suitable models to analyze the transport of developmental regulators via PD in SAMs with symplasmic organization both different from, as well as analogous to, that in angiosperms, and to understand the evolutionary aspects of the role of this transport in the morphogenesis of vascular plant taxa.

Cell-to-cell communication in plants, animals, and fungi: a comparative review

Cell-to-cell communication is a prerequisite for differentiation and development in multicellular organisms. This communication has to be tightly regulated to ensure that cellular components such as organelles, macromolecules, hormones, or viruses leave the cell in a precisely organized way. During evolution, plants, animals, and fungi have developed similar ways of responding to this biological challenge. For example, in higher plants, plasmodesmata connect adjacent cells and allow communication to regulate differentiation and development. In animals, two main general structures that enable short- and long-range intercellular communication are known, namely gap junctions and tunneling nanotubes, respectively. Finally, filamentous fungi have also developed specialized structures called septal pores that allow intercellular communication via cytoplasmic flow. This review summarizes the underlying mechanisms for intercellular communication in these three eukaryotic groups and discusses its consequences for the regulation of differentiation and developmental processes.

Cell-to-cell communication in plants, animals, and fungi: a comparative review

Cell-to-cell communication is a prerequisite for differentiation and development in multicellular organisms. This communication has to be tightly regulated to ensure that cellular components such as organelles, macromolecules, hormones, or viruses leave the cell in a precisely organized way. During evolution, plants, animals, and fungi have developed similar ways of responding to this biological challenge. For example, in higher plants, plasmodesmata connect adjacent cells and allow communication to regulate differentiation and development. In animals, two main general structures that enable short- and long-range intercellular communication are known, namely gap junctions and tunneling nanotubes, respectively. Finally, filamentous fungi have also developed specialized structures called septal pores that allow intercellular communication via cytoplasmic flow. This review summarizes the underlying mechanisms for intercellular communication in these three eukaryotic groups and discusses its consequences for the regulation of differentiation and developmental processes.

Unraveling the KNOTTED1 regulatory network in maize meristems

KNOTTED1 (KN1)-like homeobox (KNOX) transcription factors function in plant meristems, self-renewing structures consisting of stem cells and their immediate daughters. We defined the KN1 cistrome in maize inflorescences and found that KN1 binds to several thousand loci, including 643 genes that are modulated in one or multiple tissues. These KN1 direct targets are strongly enriched for transcription factors (including other homeobox genes) and genes participating in hormonal pathways, most significantly auxin, demonstrating that KN1 plays a key role in orchestrating the upper levels of a hierarchical gene regulatory network that impacts plant meristem identity and function.

In situ hybridization for the precise localization of transcripts in plants

With the advances in genomics research of the past decade, plant biology has seen numerous studies presenting large-scale quantitative analyses of gene expression. Microarray and next generation sequencing approaches are being used to investigate developmental, physiological and stress response processes, dissect epigenetic and small RNA pathways, and build large gene regulatory networks^1-3. While these techniques facilitate the simultaneous analysis of large gene sets, they typically provide a very limited spatiotemporal resolution of gene expression changes. This limitation can be partially overcome by using either profiling method in conjunction with lasermicrodissection or fluorescence-activated cell sorting^4-7. However, to fully understand the biological role of a gene, knowledge of its spatiotemporal pattern of expression at a cellular resolution is essential. Particularly, when studying development or the effects of environmental stimuli and mutants can the detailed analysis of a gene's expression pattern become essential. For instance, subtle quantitative differences in the expression levels of key regulatory genes can lead to dramatic phenotypes when associated with the loss or gain of expression in specific cell types.

Several methods are routinely used for the detailed examination of gene expression patterns. One is through analysis of transgenic reporter lines. Such analysis can, however, become time-consuming when analyzing multiple genes or working in plants recalcitrant to transformation. Moreover, an independent validation to ensure that the transgene expression pattern mimics that of the endogenous gene is typically required. Immunohistochemical protein localization or mRNA in situ hybridization present relatively fast alternatives for the direct visualization of gene expression within cells and tissues. The latter has the distinct advantage that it can be readily used on any gene of interest. In situ hybridization allows detection of target mRNAs in cells by hybridization with a labeled anti-sense RNA probe obtained by in vitro transcription of the gene of interest.

Here we outline a protocol for the in situ localization of gene expression in plants that is highly sensitivity and specific. It is optimized for use with paraformaldehyde fixed, paraffin-embedded sections, which give excellent preservation of histology, and DIG-labeled probes that are visualized by immuno-detection and alkaline-phosphatase colorimetric reaction. This protocol has been successfully applied to a number of tissues from a wide range of plant species, and can be used to analyze expression of mRNAs as well as small RNAs^8-14.

Compound leaf development in the palm Chamaedorea elegans is KNOX-independent

PREMISE OF THE STUDY

How a leaf acquires its shape is a major and largely unresolved question in plant biology. This problem is particularly complex in the case of compound leaves, where the leaf blade is subdivided into leaflets. In many eudicots with compound leaves, class I KNOTTED1-LIKE HOMEOBOX (KNOX) genes are upregulated in the leaf primordium and promote leaflet initiation, while KNOX genes are restricted to the shoot apical meristem in simple-leaved plants. In monocots, however, little is known about the extent of KNOX contribution to compound leaf development, and we aimed to address this issue in the palm Chamaedorea elegans.

METHODS

We investigated the accumulation pattern of KNOX proteins in shoot apical meristems and leaf primordia of the palm C. elegans using immunolocalization experiments.

KEY RESULTS

KNOX proteins accumulated in vegetative and inflorescence apical meristems and in the subtending stem tissue, but not in the plicated regions of the leaf primordia. These plicated areas form during primary morphogenesis and are the only meristematic tissue in the developing primordium. In addition, KNOX proteins did not accumulate in any region of the developing leaf during secondary morphogenesis, when leaflets separate to create the final pinnately compound leaf.

CONCLUSIONS

The compound leaf character in palms, C. elegans in particular and likely other pinnately compound palms, does not depend on the activities of KNOX proteins.

To gate, or not to gate: regulatory mechanisms for intercellular protein transport and virus movement in plants

Cell-to-cell signal transduction is vital for orchestrating the whole-body physiology of multi-cellular organisms, and many endogenous macromolecules, proteins, and nucleic acids function as such transported signals. In plants, many of these molecules are transported through plasmodesmata (Pd), the cell wall-spanning channel structures that interconnect plant cells. Furthermore, Pd also act as conduits for cell-to-cell movement of most plant viruses that have evolved to pirate these channels to spread the infection. Pd transport is presumed to be highly selective, and only a limited repertoire of molecules is transported through these channels. Recent studies have begun to unravel mechanisms that actively regulate the opening of the Pd channel to allow traffic. This macromolecular transport between cells comprises two consecutive steps: intracellular targeting to Pd and translocation through the channel to the adjacent cell. Here, we review the current knowledge of molecular species that are transported though Pd and the mechanisms that control this traffic. Generally, Pd traffic can occur by passive diffusion through the trans-Pd cytoplasm or through the membrane/lumen of the trans-Pd ER, or by active transport that includes protein-protein interactions. It is this latter mode of Pd transport that is involved in intercellular traffic of most signal molecules and is regulated by distinct and sometimes interdependent mechanisms, which represent the focus of this article.

Distal expression of knotted1 in maize leaves leads to reestablishment of proximal/distal patterning and leaf dissection

Maize (Zea mays) leaves provide a useful system to study how proximal/distal patterning is established because of the distinct tissues found in the distal blade and the proximal sheath. Several mutants disrupt this pattern, including the dominant knotted1-like homeobox (knox) mutants. knox genes encode homeodomain proteins of the TALE superclass of transcription factors. Class I knox genes are expressed in the meristem and down-regulated as leaves initiate. Gain-of-function phenotypes result from misexpression in leaves. We identified a new dominant allele of maize knotted1, Kn1-DL, which contains a transposon insertion in the promoter in addition to a tandem duplication of the kn1 locus. In situ hybridization shows that kn1 is misexpressed in two different parts of the blade that correlate with the different phenotypes observed. When kn1 is misexpressed along the margins, flaps of sheath-like tissue form along the margins. Expression in the distal tip leads to premature termination of the midrib into a knot and leaf bifurcation. The gain-of-function phenotypes suggest that kn1 establishes proximal/distal patterning when expressed in distal locations and lead to the hypothesis that kn1 normally participates in the establishment of proximal/distal polarity in the incipient leaf.

Transfer of genetic material between the chloroplast and nucleus: how is it related to stress in plants?

BACKGROUND

The presence of chloroplast-related DNA sequences in the nuclear genome is generally regarded as a relic of the process by which genes have been transferred from the chloroplast to the nucleus. The remaining chloroplast encoded genes are not identical across the plant kingdom indicating an ongoing transfer of genes from the organelle to the nucleus.

SCOPE

This review focuses on the active processes by which the nuclear genome might be acquiring or removing DNA sequences from the chloroplast genome. Present knowledge of the contribution to the nuclear genome of DNA originating from the chloroplast will be reviewed. In particular, the possible effects of stressful environments on the transfer of genetic material between the chloroplast and nucleus will be considered. The significance of this research and suggestions for the future research directions to identify drivers, such as stress, of the nuclear incorporation of plastid sequences are discussed.

CONCLUSIONS

The transfer to the nuclear genome of most of the protein-encoding functions for chloroplast-located proteins facilitates the control of gene expression. The continual transfer of fragments, including complete functional genes, from the chloroplast to the nucleus has been observed. However, the mechanisms by which the loss of functions and physical DNA elimination from the chloroplast genome following the transfer of those functions to the nucleus remains obscure. The frequency of polymorphism across chloroplast-related DNA fragments within a species will indicate the rate at which these DNA fragments are incorporated and removed from the chromosomes.

DETORQUEO, QUIRKY, and ZERZAUST represent novel components involved in organ development mediated by the receptor-like kinase STRUBBELIG in Arabidopsis thaliana

Intercellular signaling plays an important role in controlling cellular behavior in apical meristems and developing organs in plants. One prominent example in Arabidopsis is the regulation of floral organ shape, ovule integument morphogenesis, the cell division plane, and root hair patterning by the leucine-rich repeat receptor-like kinase STRUBBELIG (SUB). Interestingly, kinase activity of SUB is not essential for its in vivo function, indicating that SUB may be an atypical or inactive receptor-like kinase. Since little is known about signaling by atypical receptor-like kinases, we used forward genetics to identify genes that potentially function in SUB-dependent processes and found recessive mutations in three genes that result in a sub-like phenotype. Plants with a defect in DETORQEO (DOQ), QUIRKY (QKY), and ZERZAUST (ZET) show corresponding defects in outer integument development, floral organ shape, and stem twisting. The mutants also show sub-like cellular defects in the floral meristem and in root hair patterning. Thus, SUB, DOQ, QKY, and ZET define the STRUBBELIG-LIKE MUTANT (SLM) class of genes. Molecular cloning of QKY identified a putative transmembrane protein carrying four C(2) domains, suggesting that QKY may function in membrane trafficking in a Ca(2+)-dependent fashion. Morphological analysis of single and all pair-wise double-mutant combinations indicated that SLM genes have overlapping, but also distinct, functions in plant organogenesis. This notion was supported by a systematic comparison of whole-genome transcript profiles during floral development, which molecularly defined common and distinct sets of affected processes in slm mutants. Further analysis indicated that many SLM-responsive genes have functions in cell wall biology, hormone signaling, and various stress responses. Taken together, our data suggest that DOQ, QKY, and ZET contribute to SUB-dependent organogenesis and shed light on the mechanisms, which are dependent on signaling through the atypical receptor-like kinase SUB.

In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana

BACKGROUND

MADS domain transcription factors play important roles in various developmental processes in flowering plants. Members of this family play a prominent role in the transition to flowering and the specification of floral organ identity. Several studies reported mRNA expression patterns of the genes encoding these MADS domain proteins, however, these studies do not provide the necessary information on the temporal and spatial localisation of the proteins. We have made GREEN FLUORESCENT PROTEIN (GFP) translational fusions with the four MADS domain proteins SEPALLATA3, AGAMOUS, FRUITFULL and APETALA1 from the model plant Arabidopsis thaliana and analysed the protein localisation patterns in living plant tissues by confocal laser scanning microscopy (CLSM).

RESULTS

We unravelled the protein localisation patterns of the four MADS domain proteins at a cellular and subcellular level in inflorescence and floral meristems, during development of the early flower bud stages, and during further differentiation of the floral organs. The protein localisation patterns revealed a few deviations from known mRNA expression patterns, suggesting a non-cell autonomous action of these factors or alternative control mechanisms. In addition, we observed a change in the subcellular localisation of SEPALLATA3 from a predominantly nuclear localisation to a more cytoplasmic localisation, occurring specifically during petal and stamen development. Furthermore, we show that the down-regulation of the homeodomain transcription factor WUSCHEL in ovular tissues is preceded by the occurrence of both AGAMOUS and SEPALLATA3 proteins, supporting the hypothesis that both proteins together suppress WUSCHEL expression in the ovule.

CONCLUSION

This approach provides a highly detailed in situ map of MADS domain protein presence during early and later stages of floral development. The subcellular localisation of the transcription factors in the cytoplasm, as observed at certain stages during development, points to mechanisms other than transcriptional control. Together this information is essential to understand the role of these proteins in the regulatory processes that drive floral development and leads to new hypotheses.

Morphogenesis and patterning at the organ boundaries in the higher plant shoot apex

Formation of lateral organ primordia from the shoot apical meristem creates boundaries that separate the primordium from surrounding tissue. Morphological and gene expression studies indicate the presence of a distinct set of cells that define the boundaries in the plant shoot apex. Cells at the boundary usually display reduced growth activity that results in separation of adjacent organs or tissues and this morphological boundary coincides with the border of different cell identities. Such morphogenetic and patterning events and their spatial coordination are controlled by a number of boundary-specific regulatory genes. The boundary may also act as a reference point for the generation of new meristems such as axillary meristems. Many of the genes involved in meristem initiation are expressed in the boundary. This review summarizes the cellular characters of the shoot organ boundary and the roles of regulatory genes that control different aspects of this unique region in plant development.

Cell differentiation and organ initiation at the shoot apical meristem

Plants continuously generate organs at the flanks of their shoot apical meristems (SAMs). The patterns in which these organs are initiated, also called patterns of phyllotaxis, are highly stereotypic and characteristic for a particular species or developmental stage. This stable, predictable behaviour of the meristem has led to the idea that organ initiation must be based on simple and robust mechanisms. This conclusion is less evident, however, if we consider the very dynamic behaviour of the individual cells. How dynamic cellular events are coordinated and how they are linked to the regular patterns of organ initiation is a major issue in plant developmental biology.

Plant viral movement proteins: Agents for cell-to-cell trafficking of viral genomes

Plants viruses spread throughout their hosts using a number of pathways, the most common being movement cell to cell through plasmodesmata (PD), unique intercellular organelles of the plant kingdom, and between organs by means of the vascular system. Pioneering studies on plant viruses revealed that PD allow the cell-to-cell trafficking of virally encoded proteins, termed the movement proteins (MPs). This non-cell-autonomous protein (NCAP) pathway is similarly employed by the host to traffic macromolecules. Viral MPs bind RNA/DNA in a sequence nonspecific manner to form nucleoprotein complexes (NPC). Host proteins are then involved in the delivery of MPs and NPC to the PD orifice, and a role for the cytoskeleton has been implicated. Trafficking of NCAPs through the PD structure involves three steps in which the MP: (a) interacts with a putative PD docking complex, (b) induces dilation in the PD microchannels, and (c) binds to an internal translocation system for delivery into the neighboring cytoplasm. Viral genera that use this NCAP pathway have evolved a combination of a MP and ancillary proteins that work in concert to enable the formation of a stable NPC that can compete with endogenous NCAPs for the PD trafficking machinery. Incompatible MP-host protein interactions may underlie observed tissue tropisms and restricted infection domains. These pivotal discoveries are discussed in terms of the need to develop a more comprehensive understanding of the (a) three-dimensional structure of MPs, (b) PD supramolecular complex, and (c) host proteins involved in this cell-to-cell trafficking process.

The role of knox genes in plant development

knox genes encode homeodomain-containing transcription factors that are required for meristem maintenance and proper patterning of organ initiation. In plants with simple leaves, knox genes are expressed exclusively in the meristem and stem, but in dissected leaves, they are also expressed in leaf primordia, suggesting that they may play a role in the diversity of leaf form. This hypothesis is supported by the intriguing phenotypes found in gain-of-function mutations where knox gene misexpression affects leaf and petal shape. Similar phenotypes are also found in recessive mutations of genes that function to negatively regulate knox genes. KNOX proteins function as heterodimers with other homeodomains in the TALE superclass. The gibberellin and lignin biosynthetic pathways are known to be negatively regulated by KNOX proteins, which results in indeterminate cell fates.

Regulation of short-distance transport of RNA and protein

The intercellular trafficking of proteins and RNAs has emerged as a novel mechanism of cell-cell communication in plant development. Plasmodesmata (PD), intercellular cytoplasmic channels, have a central role in cell-cell trafficking of regulatory proteins and RNAs. Recent studies have demonstrated that plants use either a selective or a non-selective PD trafficking pathway for regulatory proteins. Moreover, plants have developed strategies to regulate both selective and non-selective movement. Recent work has focused especially on integrating the recent understanding of the function and mechanisms of intercellular macromolecule movement through PD.

Plasmodesmata form and function

Intercellular transport via plasmodesmata controls cell fate decisions in plants, and is of fundamental importance in viral movement, disease resistance, and the spread of RNAi signals. Although plasmodesmata appear to be unique to plant cells, they may have structural and functional similarities to the newly discovered tunneling nanotubes that connect animal cells. Recently, proteins that localize to plasmodesmata have been identified, and a microtubule-associated protein was found to negatively regulate the trafficking of viral movement proteins. Other advances have delivered new insights into the function and molecular nature of plasmodesmata and have shown that protein trafficking through plasmodesmata is developmentally regulated, opening up the possibility that the genetic control of plasmodesmal function will soon be understood.

Between the sheets: inter-cell-layer communication in plant development

The cells of plant meristems and embryos are arranged in an organized, and sometimes extremely beautiful, layered pattern. This pattern is maintained by the controlled orientation of cell divisions within layers. However, despite this layered structure, cell behaviour during plant development is not lineage dependent, and does not occur in a mosaic fashion. Many studies, both classical and recent, have shown that plant cell identity can be re-specified according to position, allowing plants to show remarkable developmental plasticity. However, the layered structure of meristems and the implications of this during plant development, remain subjects of some speculation. Of particular interest is the question of how cell layers communicate, and how communication between cell layers could allow coordinated developmental processes to take place. Recent research has uncovered several examples both of the molecular mechanisms by which cell layers can communicate, and of how this communication can infringe on developmental processes. A range of examples is used to illustrate the diversity of mechanisms potentially implicated in cell-layer communication during plant development.

Plasmodesmata as a supracellular control network in plants

The evolution of intercellular communication had an important role in the increasing complexity of both multicellular and supracellular organisms. Plasmodesmata, the intercellular organelles of the plant kingdom, establish an effective pathway for local and long-distance signalling. In higher plants, this pathway involves the trafficking of proteins and various forms of RNA that function non-cell-autonomously to affect developmental programmes.

Different subcellular localization and trafficking properties of KNOX class 1 homeodomain proteins from rice

Genes of the KN1-like homeobox (KNOX) class 1 encode transcription factors involved in shoot apical meristem development and maintenance. We studied the subcellular localization of Green Fluorescent Protein-tagged rice KNOX proteins (Oskn1-3) after particle bombardment of onion and rice cells and after transformation of Arabidopsis and rice with constitutive and inducible expression constructs. In all test systems, the three rice KNOX proteins showed nuclear and cytoplasmic localization patterns. However, Oskn1 additionally showed in some cells a distribution over punctae moving randomly in the cytosol. Use of an inducible expression system indicated a nuclear presence of Oskn1 in cells of the shoot apical meristem and post-transcriptional down-regulation in early leaf primordia. Arabidopsis and rice test systems were used to study effects of plant hormones and auxin transport inhibition on KNOX protein localization. Application of GA3 or 1-NAA shifted protein localization completely to the cytoplasm and resulted in loss of the punctae formed by Oskn1. Conversely, NPA application induced a complete nuclear localization of the KNOX proteins. To study intercellular movement of the KNOX proteins we set up a novel co-bombardment assay in which trafficking of untagged KNOX proteins was visualized through the co-trafficking of green fluorescent or blue fluorescent marker proteins. In multiple independent experiments Oskn1 trafficked more extensively to neighboring cells than Oskn2 and Oskn3. Differences in the localization and trafficking properties of Oskn1, Oskn2 and Oskn3 correlate with differences in mRNA localization patterns and functional differences between the rice KNOX genes and their putative orthologues from other species.

Macromolecular Transport and Signaling Through Plasmodesmata

Plasmodesmata (Pd) are channels in the plant cell wall that in conjunction with associated phloem form an intercellular communication network that supports the cell-to-cell and long-distance trafficking of a wide spectrum of endogenous proteins and ribonucleoprotein complexes. The trafficking of such macromolecules is of importance in the orchestration of non-cell autonomous developmental and physiological processes. Plant viruses encode movement proteins (MPs) that subvert this communication network to facilitate the spread of infection. These viral proteins thus represent excellent experimental keys for exploring the mechanisms involved in intercellular trafficking and communication via Pd.

Plasmodesmata at the crossroads between development, dormancy, and defense

Plants are frequently exposed to environmental stress and organisms that seek to benefit from their autotrophic nature. To cope with these challenges plants have developed stress-resistance mechanisms, which involve sensing, activation of signal transduction cascades, changes in gene expression, and physiological adjustment. Exposure to one kind of stress often leads to cross-tolerance, that is, resistance to different kinds of stresses. The search for a common underlying mechanism concentrates mostly on changes in cellular physiology and gene expression. We focus on the cross-protective measures that are taken at the level above the single cell. We argue that the controlled alterations in symplasmic permeability that underlie development also play a role in survival and defense strategies. In development, most of the alterations are transient and dynamic, whereas the more persistent alterations function predominantly in dormancy and defense and are under the control of two key enzymes: 1,3-β-D-glucan synthase and 1,3-β-D-glucanase. 1,3-β-D-Glucan synthase functions in the narrowing or closing of plasmodesmata, whereas 1,3-β-D-glucanase counteracts this process. We propose that the closing of symplasmic paths constitutes an unspecific but effective early measure in adaptation and defense, which is accompanied by specific strategies tailored to the various challenges plants face.Key words: cross-adaptation, dormancy sphincter, 1,3-β-D-glucanase, 1,3-β-D-glucan synthase, meristem, overwintering, plasmodesmata, virus movement.

Developmental regulation and significance of KNOX protein trafficking in Arabidopsis

Intercellular communication delivers critical information for position-dependent specification of cell fate. In plants, a novel mechanism for cell-to-cell communication involves the intercellular trafficking of regulatory proteins and mRNAs. The maize KNOTTED1 (KN1) gene acts non cell-autonomously in the maize leaf, and KN1 was the first plant protein shown to traffic cell-to-cell, presumably through plasmodesmata. We have compared the intercellular trafficking of green fluorescent protein (GFP) fusions of KN1 and Arabidopsis KN1-related homeobox proteins to that of the viral movement protein from turnip vein clearing tobamovirus. We show that there is specific developmental regulation of GFP approximately KN1 trafficking. GFP -- KN1 was able to traffic from the inner layers of the leaf to the epidermis, but not in the opposite direction, from epidermis to mesophyll. However, GFP or the GFP -- movement protein fusion moved readily out of the epidermis. GFP -- KN1 was however able to traffic out of the epidermal (L1) layer in the shoot apical meristem, indicating that KN1 movement out of the L1 was developmentally regulated. GFP -- KNAT1/BREVIPEDICELLUS and GFP -- SHOOTMERISTEMLESS fusions could also traffic from the L1 to the L2/L3 layers of the meristem. In a test for the functional significance of trafficking, we showed that L1-specific expression of KN1 or of KNAT1 was able to partially complement the strong shootmeristemless-11 (stm-11) mutant. However, a cell-autonomous GUS fusion to KN1 showed neither trafficking ability nor complementation of stm-11 when expressed in the L1. These results suggest that the activity of KN1 and related homeobox proteins is maintained following intercellular trafficking, and that trafficking may be required for their normal developmental function.

Dispatch. Intercellular signaling: an elusive player steps forth

Plasmodesmata play a central role in cell-to-cell communication in plants, allowing transport of regulatory proteins and mRNAs. A recent study has identified a specific protein that regulates the intercellular transport of macromolecules in plants, known as non-cell autonomous pathway protein 1.