Evolutionary and molecular analysis of Dof transcription factors identified a conserved motif for intercellular protein trafficking

The Role of Liriodendron Dof Gene Family in Abiotic Stress Response

The DOF (DNA-binding with one finger) transcription factors are exclusive to plants and play crucial roles in plant growth, development, and environmental adaptation. Although extensive research has been conducted on the Dof gene family in Arabidopsis, maize, and Solanum, investigations concerning the role of this gene family in Liriodendron remain unreported, leaving its biological function largely unknown. In this study, we performed a comprehensive genome-wide identification of the Dof gene family based on the Liriodendron genome, resulting in the discovery of a total of 17 LcDof gene members. Based on the results of phylogenetic analysis, the 17 LcDof proteins were classified into eight subfamilies. The motif analysis revealed the diverse nature of motifs within the D1 subfamily, which includes a distinct type of Dof transcription factor known as CDF (Cycling Dof Factor). We further characterized the chromosomal distribution, gene structure, conserved protein motifs, and cis-elements in the promoter regions. Additionally, utilizing transcriptome data from Liriodendron hybrids and conducting RT-qPCR experiments, we investigated the expression patterns of LhDofs under various abiotic stresses such as drought, cold, and heat stress. Notably, we found that several LhDofs, particularly LhDof4 and LhDof6, were significantly upregulated in response to abiotic stress. Furthermore, we cloned LhDof4 and LhDof6 genes and found that its encoding protein was mainly located in the nucleus by transient transformation in Liriodendron hybrids protoplast. Subsequently, we used LhDof6-overexpressing Liriodendron hybrid seedlings. We found that overexpression of LhDof6 enhanced the cold tolerance of the plants, increasing their survival rate at -20 °C. This result was further validated by changes in physiological indicators.

GHCU, a Molecular Chaperone, Regulates Leaf Curling by Modulating the Distribution of KNGH1 in Cotton

Leaf shape is considered to be one of the most significant agronomic traits in crop breeding. However, the molecular basis underlying leaf morphogenesis in cotton is still largely unknown. In this study, through genetic mapping and molecular investigation using a natural cotton mutant cu with leaves curling upward, the causal gene GHCU is successfully identified as the key regulator of leaf flattening. Knockout of GHCU or its homolog in cotton and tobacco using CRISPR results in abnormal leaf shape. It is further discovered that GHCU facilitates the transport of the HD protein KNOTTED1-like (KNGH1) from the adaxial to the abaxial domain. Loss of GHCU function restricts KNGH1 to the adaxial epidermal region, leading to lower auxin response levels in the adaxial boundary compared to the abaxial. This spatial asymmetry in auxin distribution produces the upward-curled leaf phenotype of the cu mutant. By analysis of single-cell RNA sequencing and spatiotemporal transcriptomic data, auxin biosynthesis genes are confirmed to be expressed asymmetrically in the adaxial-abaxial epidermal cells. Overall, these findings suggest that GHCU plays a crucial role in the regulation of leaf flattening through facilitating cell-to-cell trafficking of KNGH1 and hence influencing the auxin response level.

DOF gene family expansion and diversification

DOF (DNA binding with one finger) proteins are part of a plant-specific transcription factor (TF) gene family widely involved in plant development and stress responses. Many studies have uncovered their structural and functional characteristics in recent years, leading to a rising number of genome-wide identification study approaches, unveiling the DOF family expansion in angiosperm species. Nonetheless, these studies primarily concentrate on particular taxonomic groups. Identifying DOF TFs within less-represented groups is equally crucial, as it enhances our comprehension of their evolutionary history, contributions to plant phenotypic diversity, and role in adaptation. This review summarizes the main findings and progress of genome-wide identification and characterization studies of DOF TFs in Viridiplantae, exposing their roles as players in plant adaptation and a glimpse of their evolutionary history. We also present updated data on the identification and number of DOF genes in native and wild species. Altogether, these data, comprising a phylogenetic analysis of 2124 DOF homologs spanning 83 different species, will contribute to identifying new functional DOF groups, adding to our understanding of the mechanisms driving plant evolution and offering valuable insights into their potential applications.

Assaying Effector Cell-to-Cell Mobility in Plant Tissues Identifies Hypermobility and Indirect Manipulation of Plasmodesmata

In plants, plasmodesmata establish cytoplasmic continuity between cells to allow for communication and resource exchange across the cell wall. While plant pathogens use plasmodesmata as a pathway for both molecular and physical invasion, the benefits of molecular invasion (cell-to-cell movement of pathogen effectors) are poorly understood. To establish a methodology for identification and characterization of the cell-to-cell mobility of effectors, we performed a quantitative live imaging-based screen of candidate effectors of the fungal pathogen Colletotrichum higginsianum. We predicted C. higginsianum effectors by their expression profiles, the presence of a secretion signal, and their predicted and in planta localization when fused to green fluorescent protein. We assayed for cell-to-cell mobility of nucleocytosolic effectors and identified 14 that are cell-to-cell mobile. We identified that three of these effectors are "hypermobile," showing cell-to-cell mobility greater than expected for a protein of that size. To explore the mechanism of hypermobility, we chose two hypermobile effectors and measured their impact on plasmodesmata function and found that even though they show no direct association with plasmodesmata, each increases the transport capacity of plasmodesmata. Thus, our methods for quantitative analysis of cell-to-cell mobility of candidate microbe-derived effectors, or any suite of host proteins, can identify cell-to-cell hypermobility and offer greater understanding of how proteins affect plasmodesmal function and intercellular connectivity. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

GmDof41 regulated by the DREB1-type protein improves drought and salt tolerance by regulating the DREB2-type protein in soybean

Despite their essential and multiple roles in biological processes, the molecular mechanism of Dof transcription factors (TFs) for responding to abiotic stresses is rarely reported in plants. We identified a soybean Dof gene GmDof41 which was involved in the responses to drought, salt, and exogenous ABA stresses. Overexpression of GmDof41 in soybean transgenic hairy roots attenuated H₂O₂ accumulation and regulated proline homeostasis, resulting in the drought and salt tolerance. Yeast one-hybrid and electrophoretic mobility shift assay (EMSA) illustrated that GmDof41 was regulated by the DREB1-type protein GmDREB1B;1 that could improve drought and salt tolerance in plants. Further studies illustrated GmDof41 can directly bind to the promoter of GmDREB2A which encodes a DREB2-type protein and affects abiotic stress tolerance in plants. Collectively, our results suggested that GmDof41 positively regulated drought and salt tolerance by correlating with GmDREB1B;1 and GmDREB2A. This study provides an important basis for further exploring the abiotic stress-tolerance mechanism of Dof TFs in soybean.

Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips

BACKGROUND

Root development and function have central roles in plant adaptation to the environment. The modification of root traits has additionally been a major driver of crop performance since the green revolution; however, the molecular underpinnings and the regulatory programmes defining root development and response to environmental stress remain largely unknown. Single-cell reconstruction of gene regulatory programmes provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes associated with cell type-specific gene expression remain largely unexplored.

RESULTS

To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq (scATAC-seq) to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell type-specific accessibility variance across most of the major cell types and allowed us to identify sets of transcription factors which associate with accessible chromatin regions (ACRs). Using root hair differentiation as a model, we demonstrate that chromatin and gene expression dynamics during cell type differentiation correlate in pseudotime analyses. In addition to developmental trajectories, we describe chromatin responses to heat and identify cell type-specific accessibility changes to this key environmental stimulus.

CONCLUSIONS

We report chromatin landscapes during rice root development at single-cell resolution. Our work provides a framework for the integrative analysis of regulatory dynamics in this important crop organ at single-cell resolution.

Genome-Wide Identification and Analysis of DOF Gene Family in Eugenia uniflora L. (Myrtaceae)

Eugenia uniflora is a Brazilian native plant species with great ecological and economic importance. It is distributed throughout the Atlantic forest, where two distinct populations show local adaptation to the contrasting conditions of restinga and riparian forest. Among various TFs described in plants, the DOF TF family has been reported to affect flowering and vascular development, making them promising candidates for characterization in E. uniflora. In this study, 28 DOF genes were identified by a genome-wide analysis, of which 20 were grouped into 11 MCOGs by Bayesian phylogeny, suggesting a shared functionallity between members. Based on RNA-seq experiments, we have detected eight drought responsive genes, and SNPs identification revealed population unique polymorphisms, implying a role in local adapatation mechanisms. Finally, analysis of conserved motifs through MEME revealed 15 different protein motifs, and a promoter region analysis returned 40 enriched TF binding motifs, both reporting novel biological functions circa the DOF gene family. In general, the DOF family is found to be conserved both in sequence and expression. Furthermore, this study contributes to both DOF literature and the genetic exploration of native species, elucidating their genetic potential and bringing to light new research topics, paving the way to future studies.

Transcription Factor DOF4.1 Regulates Seed Longevity in Arabidopsis via Seed Permeability and Modulation of Seed Storage Protein Accumulation

Seed longevity is modulated by multiple genetic factors in Arabidopsis thaliana. A previous genome-wide association study using the Elevated Partial Pressure of Oxygen (EPPO) aging assay pinpointed a genetic locus associated with this trait. Reverse genetics identified the transcription factor DOF4.1 as a novel seed longevity factor. dof4.1 loss-of-function plants generate seeds exhibiting higher germination after accelerated aging assays. DOF4.1 is expressed during seed development and RNAseq data show several putative factors that could contribute to the dof4.1 seed longevity phenotype. dof4.1 has reduced seed permeability and a higher levels of seed storage proteins mRNAs (cruciferins and napins) in developing seeds, as compared to wild-type seeds. It has been reported that mutant lines defective in cruciferins or napins present reduced seed longevity. The improved longevity of dof4.1 is totally lost in the quadruple mutant dof4.1 cra crb crc, but not in a dof4.1 line depleted of napins, suggesting a prominent role for cruciferins in this process. Moreover, a negative regulation of DOF4.1 expression by the transcription factor DOF1.8 is suggested by co-inoculation assays in Nicotiana benthamiana. Indeed, DOF1.8 expression anticorrelates with that of DOF4.1 during seed development. In summary, modulation of DOF4.1 levels during seed development contributes to regulate seed longevity.

Plasmodesmata and their role in assimilate translocation

During multicellularization, plants evolved unique cell-cell connections, the plasmodesmata (PD). PD of angiosperms are complex cellular domains, embedded in the cell wall and consisting of multiple membranes and a large number of proteins. From the beginning, it had been assumed that PD provide passage for a wide range of molecules, from ions to metabolites and hormones, to RNAs and even proteins. In the context of assimilate allocation, it has been hypothesized that sucrose produced in mesophyll cells is transported via PD from cell to cell down a concentration gradient towards the phloem. Entry into the sieve element companion cell complex (SECCC) is then mediated on three potential routes, depending on the species and conditions, - either via diffusion across PD, after conversion to raffinose via PD using a polymer trap mechanism, or via a set of transporters which secrete sucrose from one cell and secondary active uptake into the SECCC. Multiple loading mechanisms can likely coexist. We here review the current knowledge regarding photoassimilate transport across PD between cells as a prerequisite for translocation from leaves to recipient organs, in particular roots and developing seeds. We summarize the state-of-the-art in protein composition, structure, transport mechanism and regulation of PD to apprehend their functions in carbohydrate allocation. Since many aspects of PD biology remain elusive, we highlight areas that require new approaches and technologies to advance our understanding of these enigmatic and important cell-cell connections.

CDF transcription factors: plant regulators to deal with extreme environmental conditions

In terrestrial environments, water and nutrient availabilities and temperature conditions are highly variable, and especially in extreme environments limit survival, growth, and reproduction of plants. To sustain growth and maintain cell integrity under unfavourable environmental conditions, plants have developed a variety of biochemical and physiological mechanisms, orchestrated by a large set of stress-responsive genes and a complex network of transcription factors. Recently, cycling DOF factors (CDFs), a group of plant-specific transcription factors (TFs), were identified as components of the transcriptional regulatory networks involved in the control of abiotic stress responses. The majority of the members of this TF family are activated in response to a wide range of adverse environmental conditions in different plant species. CDFs regulate different aspects of plant growth and development such as photoperiodic flowering-time control and root and shoot growth. While most of the functional characterization of CDFs has been reported in Arabidopsis, recent data suggest that their diverse roles extend to other plant species. In this review, we integrate information related to structure and functions of CDFs in plants, with special emphasis on their role in plant responses to adverse environmental conditions.

The Tobamoviral Movement Protein: A "Conditioner" to Create a Favorable Environment for Intercellular Spread of Infection

During their evolution, viruses acquired genes encoding movement protein(s) (MPs) that mediate the intracellular transport of viral genetic material to plasmodesmata (Pd) and initiate the mechanisms leading to the increase in plasmodesmal permeability. Although the current view on the role of the viral MPs was primarily formed through studies on tobacco mosaic virus (TMV), the function of its MP has not been fully elucidated. Given the intercellular movement of MPs independent of genomic viral RNA (vRNA), this characteristic may induce favorable conditions ahead of the infection front for the accelerated movement of the vRNA (i.e. the MP plays a role as a "conditioner" of viral intercellular spread). This idea is supported by (a) the synthesis of MP from genomic vRNA early in infection, (b) the Pd opening and the MP transfer to neighboring cells without formation of the viral replication complex (VRC), and (c) the MP-mediated movement of VRCs beyond the primary infected cell. Here, we will consider findings that favor the TMV MP as a "conditioner" of enhanced intercellular virus movement. In addition, we will discuss the mechanism by which TMV MP opens Pd for extraordinary transport of macromolecules. Although there is no evidence showing direct effects of TMV MP on Pd leading to their dilatation, recent findings indicate that MPs exert their influence indirectly by modulating Pd external and structural macromolecules such as callose and Pd-associated proteins. In explaining this phenomenon, we will propose a mechanism for TMV MP functioning as a conditioner for virus movement.

The DOF Transcription Factors in Seed and Seedling Development

The DOF (DNA binding with one finger) family of plant-specific transcription factors (TF) was first identified in maize in 1995. Since then, DOF proteins have been shown to be present in the whole plant kingdom, including the unicellular alga Chlamydomonas reinhardtii. The DOF TF family is characterised by a highly conserved DNA binding domain (DOF domain), consisting of a CX₂C-X₂₁-CX₂C motif, which is able to form a zinc finger structure. Early in the study of DOF proteins, their relevance for seed biology became clear. Indeed, the PROLAMIN BINDING FACTOR (PBF), one of the first DOF proteins characterised, controls the endosperm-specific expression of the zein genes in maize. Subsequently, several DOF proteins from both monocots and dicots have been shown to be primarily involved in seed development, dormancy and germination, as well as in seedling development and other light-mediated processes. In the last two decades, the molecular network underlying these processes have been outlined, and the main molecular players and their interactions have been identified. In this review, we will focus on the DOF TFs involved in these molecular networks, and on their interaction with other proteins.

Genome-wide identification and comparative evolutionary analysis of the Dof transcription factor family in physic nut and castor bean

DNA-binding with one finger (Dof) proteins comprise a plant-specific transcription factor family involved in plant growth, development and stress responses. This study presents a genome-wide comparison of Dof family genes in physic nut (Jatropha curcas) and castor bean (Ricinus communis), two Euphorbiaceae plants that have not experienced any recent whole-genome duplication. A total of 25 or 24 Dof genes were identified from physic nut and castor genomes, respectively, where JcDof genes are distributed across nine out of 11 chromosomes. Phylogenetic analysis assigned these genes into nine groups representing four subfamilies, and 24 orthologous groups were also proposed based on comparison of physic nut, castor, Arabidopsis and rice Dofs. Conserved microsynteny was observed between physic nut and castor Dof-coding scaffolds, which allowed anchoring of 23 RcDof genes to nine physic nut chromosomes. In contrast to how no recent duplicate was present in castor, two tandem duplications and one gene loss were found in the Dof gene family of physic nut. Global transcriptome profiling revealed diverse patterns of Jc/RcDof genes over various tissues, and key Dof genes involved in flower development and stress response were also identified in physic nut. These findings provide valuable information for further studies of Dof genes in physic nut and castor.

Lateral Transport of Organic and Inorganic Solutes

Organic (e.g., sugars and amino acids) and inorganic (e.g., K⁺, Na⁺, PO₄2-, and SO₄2-) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.

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.

The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves

Lycopodiophyta—consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)—form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls—that is, leaves with a single, unbranched vein, emerging from the protostele without a leaf gap—not megaphylls. All leaves represent determinate organs originating on the flanks of indeterminate SAMs. Thus, leaf formation requires the suppression of indeterminacy, that is, of KNOX transcription factors. In seed plants, this is mediated by different groups of transcription factors including ARP and YABBY.

We generated a shoot tip transcriptome of Huperzia selago (Lycopodiales) to examine the genes involved in leaf formation. Our H. selago transcriptome does not contain any ARP homolog, although transcriptomes of Selaginella spp. do. Surprisingly, we discovered a YABBY homolog, although these transcription factors were assumed to have evolved only in seed plants.

The existence of a YABBY homolog in H. selago suggests that YABBY evolved already in the common ancestor of the vascular plants, and subsequently was lost in some lineages like Selaginellales, whereas ARP may have been lost in Lycopodiales. The presence of YABBY in the common ancestor of vascular plants would also support the hypothesis that this common ancestor had a simplex SAM. Furthermore, a comparison of the expression patterns of ARP in shoot tips of Selaginella kraussiana (Harrison CJ, etal. 2005. Independent recruitment of a conserved developmental mechanism during leaf evolution. Nature 434(7032):509–514.) and YABBY in shoot tips of H. selago implies that the development of microphylls, unlike megaphylls, does not seem to depend on the combined activities of ARP and YABBY. Altogether, our data show that Lycopodiophyta are a diverse group; so, in order to understand the role of Lycopodiophyta in evolution, representatives of Lycopodiales, Selaginellales, as well as of Isoetales, have to be examined.

Symplasmic Intercellular Communication through Plasmodesmata

Communication between cells is an essential process for developing and maintaining multicellular collaboration during plant development and physiological adaptation in response to environmental stimuli. The intercellular movement of proteins and RNAs in addition to the movement of small nutrients or signaling molecules such as sugars and phytohormones has emerged as a novel mechanism of cell-to-cell signaling in plants. As a strategy for efficient intercellular communication and long-distance molecule movement, plants have evolved plant-specific symplasmic communication networks via plasmodesmata (PDs) and the phloem.

Identification of Plasmodesmal Localization Sequences in Proteins In Planta

Plasmodesmata (Pd) are cell-to-cell connections that function as gateways through which small and large molecules are transported between plant cells. Whereas Pd transport of small molecules, such as ions and water, is presumed to occur passively, cell-to-cell transport of biological macromolecules, such proteins, most likely occurs via an active mechanism that involves specific targeting signals on the transported molecule. The scarcity of identified plasmodesmata (Pd) localization signals (PLSs) has severely restricted the understanding of protein-sorting pathways involved in plant cell-to-cell macromolecular transport and communication. From a wealth of plant endogenous and viral proteins known to traffic through Pd, only three PLSs have been reported to date, all of them from endogenous plant proteins. Thus, it is important to develop a reliable and systematic experimental strategy to identify a functional PLS sequence, that is both necessary and sufficient for Pd targeting, directly in the living plant cells. Here, we describe one such strategy using as a paradigm the cell-to-cell movement protein (MP) of the Tobacco mosaic virus (TMV). These experiments, that identified and characterized the first plant viral PLS, can be adapted for discovery of PLS sequences in most Pd-targeted proteins.

Arabidopsis flower development--of protein complexes, targets, and transport

Tremendous progress has been achieved over the past 25 years or more of research on the molecular mechanisms of floral organ identity, patterning, and development. While collections of floral homeotic mutants of Antirrhinum majus laid the foundation already at the beginning of the previous century, it was the genetic analysis of these mutants in A. majus and Arabidopsis thaliana that led to the development of the ABC model of floral organ identity more than 20 years ago. This intuitive model kick-started research focused on the genetic mechanisms regulating flower development, using mainly A. thaliana as a model plant. In recent years, interactions among floral homeotic proteins have been elucidated, and their direct and indirect target genes are known to a large extent. Here, we provide an overview over the advances in understanding the molecular mechanism orchestrating A. thaliana flower development. We focus on floral homeotic protein complexes, their target genes, evidence for their transport in floral primordia, and how these new results advance our view on the processes downstream of floral organ identity, such as organ boundary formation or floral organ patterning.

Symplastic communication in organ formation and tissue patterning

Communication between cells is a crucial step to coordinate organ formation and tissue patterning. In plants, the intercellular transport of metabolites and signalling molecules occur symplastically through membranous structures (named plasmodesmata) that traverse the cell wall to connect the cytoplasm and endoplasmic reticulum of neighbouring cells. This review aims to highlight the importance of symplastic communication in plant development. We revisit current literature reporting the effects of changing plasmodesmata in cell morphogenesis, organ initiation and meristem maintenance and comment on recent work involving the identification of novel plasmodesmata regulators and of mobile developmental proteins and RNA molecules. New opportunities for unravelling the dynamic regulation and function of plasmodesmata are also discussed.

Identification of a Functional Plasmodesmal Localization Signal in a Plant Viral Cell-To-Cell-Movement Protein

Our fundamental knowledge of the protein-sorting pathways required for plant cell-to-cell trafficking and communication via the intercellular connections termed plasmodesmata has been severely limited by the paucity of plasmodesmal targeting sequences that have been identified to date. To address this limitation, we have identified the plasmodesmal localization signal (PLS) in the Tobacco mosaic virus (TMV) cell-to-cell-movement protein (MP), which has emerged as the paradigm for dissecting the molecular details of cell-to-cell transport through plasmodesmata. We report here the identification of a bona fide functional TMV MP PLS, which encompasses amino acid residues between positions 1 and 50, with residues Val-4 and Phe-14 potentially representing critical sites for PLS function that most likely affect protein conformation or protein interactions. We then demonstrated that this PLS is both necessary and sufficient for protein targeting to plasmodesmata. Importantly, as TMV MP traffics to plasmodesmata by a mechanism that is distinct from those of the three plant cell proteins in which PLSs have been reported, our findings provide important new insights to expand our understanding of protein-sorting pathways to plasmodesmata.

IMPORTANCE

The science of virology began with the discovery of Tobacco mosaic virus (TMV). Since then, TMV has served as an experimental and conceptual model for studies of viruses and dissection of virus-host interactions. Indeed, the TMV cell-to-cell-movement protein (MP) has emerged as the paradigm for dissecting the molecular details of cell-to-cell transport through the plant intercellular connections termed plasmodesmata. However, one of the most fundamental and key functional features of TMV MP, its putative plasmodesmal localization signal (PLS), has not been identified. Here, we fill this gap in our knowledge and identify the TMV MP PLS.

Intercellular protein movement: deciphering the language of development

Development in multicellular organisms requires the coordinated production of a large number of specialized cell types through sophisticated signaling mechanisms. Non-cell-autonomous signals are one of the key mechanisms by which organisms coordinate development. In plants, intercellular movement of transcription factors and other mobile signals, such as hormones and peptides, is essential for normal development. Through a combination of different approaches, a large number of non-cell-autonomous signals that control plant development have been identified. We review some of the transcriptional regulators that traffic between cells, as well as how changes in symplasmic continuity affect and are affected by development. We also review current models for how mobile signals move via plasmodesmata and how movement is inhibited. Finally, we consider challenges in and new tools for studying protein movement.

Insights into structural and functional diversity of Dof (DNA binding with one finger) transcription factor

The structural, functional and in-silico studies of Dof transcription factor attempted so far reveals immense opportunity to analyze the plant genomes in terms of number of Dof genes and discuss in light of the evolution. The multiple functions of Dof genes needs to explored for crop improvement. Transcription factors play a very vital role in gene regulation at transcriptional level and are being extensively studied across phylas. In recent years, sequencing of plant genomes has led to genome-wide identification and characterizations of diverse types of plant-specific transcription factor gene family providing key insights into their structural and functional diversity. The DNA binding with one finger (Dof), a class belonging to C2H2-type zinc finger family proteins, is a plant-specific transcription factor having multiple roles such as seed maturation and germination, phytohormone and light-mediated regulation and plant responses to biotic and abiotic stresses. Dof proteins are present across plant lineage, from green algae to higher angiosperm, and represent a unique class of transcription factor having bifunctional binding activities, with both DNA and proteins, to regulate the complex transcriptional machinery in plant cells. The structural and functional diversity of the Dof transcription factor family along with the bioinformatics analysis highlighting the phylogeny of Dof families is reviewed in light of its importance in plant biotechnology for crop improvement.

A model system for analyzing intercellular communication through plasmodesmata using moss protonemata and leaves

Plant growth, development, and environmental responses require the proper regulation of intercellular movement of signals and nutrients. For this, plants have specialized cytoplasmic channels, the plasmodesmata (PD), which allow the symplasmic movement of micro- and macromolecules between neighboring cells. Internal and external signals spatio-temporally regulate the movement of molecules through the PD to control plant development and environmental responses. Although some aspects of targeted movement of molecules have been revealed, the mechanisms of non-targeted, diffusible flow of molecules through PD, and its regulation and function, remain poorly understood, particularly at the cellular level. Previously, we developed a system to quantitatively analyze non-targeted movement of a photoconvertible fluorescent protein, Dendra2, at the single-cell level in the filamentous protonemata tissue of the moss Physcomitrella patens. In protonemata, one-dimensional intercellular communication can be easily observed and quantitatively analyzed at the cellular level. In this review, we describe how protonemata and leaves of P. patens can be used to study symplasmic movement through PD, and discuss how this system can help improve our understanding of PD regulation and function in development and environmental responses in plants.

GAL4 transactivation-based assay for the detection of selective intercellular protein movement

Several plant proteins function as intercellular messenger to specify cell fate and coordinate plant development. Such intercellular communication can be achieved by direct, selective, or nonselective (diffusion-based) trafficking through plasmodesmata (PD), the symplasmic membrane-lined nanochannels adjoining two cells. A trichome rescue trafficking assay was reported to allow the detection of protein movement in Arabidopsis leaf tissue using transgenic gene expression. Here, we provide a protocol to dissect the mode of intercellular protein movement in Arabidopsis root. This assay system involves a root ground tissue-specific GAL4/UAS transactivation expression system in combination with fluorescent reporter proteins. In this system, mCherry, a red fluorescent protein, can move cell to cell via diffusion, while mCherry-H2B is tightly cell autonomous. Thus, a protein fused to mCherry-H2B that can move out from the site of synthesis likely contains a selective trafficking signal to impart a cell-to-cell gain-of-trafficking function to the cell-autonomous mCherry-H2B. This approach can be adapted to investigate the cell-to-cell trafficking properties of any protein of interest.

Transcription factor-mediated cell-to-cell signalling in plants

Plant cells utilize mobile transcription factors to transmit intercellular signals when they perceive environmental stimuli or initiate developmental programmes. Studies on these novel cell-to-cell signals have accumulated multiple pieces of evidence showing that non-cell-autonomous transcription factors play pivotal roles in most processes related to the formation and development of plant organs. Recent studies have explored the evolution of mobile transcription factors and proposed mechanisms for their trafficking through plasmodesmata, where a selective system exists to facilitate this process. Mobile transcription factors contribute to the diversity of the intercellular signalling network, which is also established by peptides, hormones, and RNAs. Crosstalk between mobile transcription factors and other intercellular molecules leads to the development of complex biological signalling networks in plants. The regulation of plasmodesmata appears to have been another major step in controlling the intercellular trafficking of transcription factors based on studies of many plasmodesmal components. Furthermore, diverse omics approaches are being successfully applied to explore a large number of candidate transcription factors as mobile signals in plants. Here, we review these fascinating discoveries to integrate current knowledge of non-cell-autonomous transcription factors.

Comparison of the Oilseed rape mosaic virus and Tobacco mosaic virus movement proteins (MP) reveals common and dissimilar MP functions for tobamovirus spread

Tobacco mosaic virus (TMV) is a longstanding model for studying virus movement and macromolecular transport through plasmodesmata (PD). Its movement protein (MP) interacts with cortical microtubule (MT)-associated ER sites (C-MERs) to facilitate the formation and transport of ER-associated viral replication complexes (VRCs) along the ER-actin network towards PD. To investigate whether this movement mechanism might be conserved between tobamoviruses, we compared the functions of Oilseed rape mosaic virus (ORMV) MP with those of MP(TMV). We show that MP(ORMV) supports TMV movement more efficiently than MP(TMV). Moreover, MP(ORMV) localizes to C-MERs like MP(TMV) but accumulates to lower levels and does not localize to larger inclusions/VRCs or along MTs, patterns regularly seen for MP(TMV). Our findings extend the role of C-MERs in viral cell-to-cell transport to a virus commonly used for functional genomics in Arabidopsis. Moreover, accumulation of tobamoviral MP in inclusions or along MTs is not required for virus movement.

Identification of evolutionarily conserved amino acid residues in homeodomain of KNOX proteins for intercellular trafficking

Maize knotted (KN1) homeodomain (HD) protein is a well-known mobile transcription factor crucial for stem cell maintenance. Recent studies have revealed that the trihelical HD of knotted1-like homeobox (KNOX) proteins is necessary and sufficient for selective cell-to-cell trafficking. Also, the efficient trafficking ability for HD is likely to be acquired during the evolution of early nonvascular land plants. Here, using the point-mutated HD of KN1 and shoot meristemless (STM) in the trichome rescue system, together with molecular structure modeling, we have found the evolutionarily conserved amino acid residues, such as arginine in helix α1 and leucine in helix α3, which are essential for intercellular trafficking. Our studies provided important clues for the 3-dimensional protein structure required for cell-to-cell movement of non-cell-autonomous transcription factors.

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.

Plasmodesmata dynamics are coordinated by intracellular signaling pathways

Membrane-lined channels called plasmodesmata (PD) connect the cytoplasts of adjacent plant cells across the cell wall, permitting intercellular movement of small molecules, proteins, and RNA. Recent genetic screens for mutants with altered PD transport identified genes suggesting that chloroplasts play crucial roles in coordinating PD transport. Complementing this discovery, studies manipulating expression of PD-localized proteins imply that changes in PD transport strongly impact chloroplast biology. Ongoing efforts to find genes that control root and stomatal development reveal the critical role of PD in enforcing tissue patterning, and newly discovered PD-localized proteins show that PD influence development, intracellular signaling, and defense against pathogens. Together, these studies demonstrate that PD function and formation are tightly integrated with plant physiology.

Characterization of the pumpkin Translationally-Controlled Tumor Protein CmTCTP

In higher plants, the phloem plays a central role in the delivery of nutrients and signals from source to sink tissues. These signals likely coordinate different aspects of plant development, as well as its response to environmental cues. Although some phloem-transported proteins and RNAs may function as signaling molecules in plants, their mode of action remains poorly understood. Previous analysis of transcripts from CMV-infected pumpkin (Cucurbita maxima cv Big Max) identified a Translationally-Controlled Tumor Protein (TCTP) mRNA homolog, designated CmTCTP. In the present work this transcript was analyzed in terms of its expression pattern. This RNA accumulates, both in healthy and CMV-infected plants, in developing and mature phloem in petiole and roots, as well as in apices at high levels. The protein was present at lower levels in most cell types, and almost no signal was detected in apices, suggesting translational regulation of this RNA. Additionally, CmTCTP harbored by Agrobacterium rhizogenes is capable of inducing whole plant regeneration. These data suggest a role for CmTCTP in growth regulation, possibly through long-distance signaling.

The plant-specific dof transcription factors family: new players involved in vascular system development and functioning in Arabidopsis

In higher plants phloem and xylem are responsible for long-distance transport of water, nutrients, and signals that act systemically at short or long-distance to coordinate developmental processes. The formation of the plant vascular system is a complex process that integrates signaling events and gene regulation at transcriptional and posttranscriptional levels. Thanks to transcriptomic and proteomic analysis we start to better understand the mechanisms underlying the formation and the functioning of the vascular system. The role of the DNA-binding with one finger (Dof TFs), a group of plant-specific transcription factors, recently emerged as part of the transcriptional regulatory networks acting on the formation and functioning of the vascular tissues. More than half of the members of this TF family are expressed in the vascular system. In addition some of them have been proposed to be mobile proteins, suggesting a possible role in the control of short- or long-distance signaling as well. This review summarizes the current knowledge on Dof TFs family in Arabidopsis with a special focus on their role in vascular development and functioning.