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RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure–function field.

Catechyl lignin (C-lignin) is a linear homopolymer of caffeyl alcohol found in the seed coats of diverse plant species. Its properties make it a natural source of carbon fibers and high-value chemicals, but the mechanism of in planta polymerization of caffeyl alcohol remains unclear. In the ornamental plant Cleome hassleriana, lignin biosynthesis in the seed coat switches from guaiacyl lignin to C-lignin at ∼12 d after pollination. Here we found that the transcript profile of the laccase gene ChLAC8 parallels the accumulation of C-lignin during seed coat development. Recombinant ChLAC8 oxidizes caffeyl and sinapyl alcohols, generating their corresponding dimers or trimers in vitro, but cannot oxidize coniferyl alcohol. We propose a basis for this substrate preference based on molecular modeling/docking experiments. Suppression of ChLAC8 expression led to significantly reduced C-lignin content in the seed coats of transgenic Cleome plants. Feeding of (13)C-caffeyl alcohol to the Arabidopsis (Arabidopsis thaliana) caffeic acid o-methyltransferase mutant resulted in no incorporation of (13)C into C-lignin, but expressing ChLAC8 in this genetic background led to appearance of C-lignin with >40% label incorporation. These results indicate that ChLAC8 is required for C-lignin polymerization and determines lignin composition when caffeyl alcohol is available.

The class IV homeodomain leucine zipper transcription factor GLABRA2 (GL2) acts in a complex regulatory circuit that regulates the differentiation of trichomes in Arabidopsis thaliana. We describe a genetic interaction with HOMEODOMAIN GLABROUS11 (HDG11), previously identified as a negative regulator of trichome branching. gl2 hdg11 double mutants display enhanced trichome cell-type differentiation defects. Transgenic expression of HDG11 using the GL2 promoter partially suppresses gl2 trichome phenotypes. Vice versa, expression of GL2 under the control of its native promoter partially complements hdg11 ectopic branching. Since gl2 hdg11 and gl2 myb23 double mutants and the triple mutant display similar trichome differentiation defects, we investigated a connection to the R2R3-MYB transcription factor MYB23. We show that MYB23 transcript levels are significantly reduced in shoots from gl2 mutants and that GL2 can drive the expression of a MYB23-promoter fusion to green fluorescent protein. Yeast one-hybrid, chromatin immunoprecipitation, and in planta reporter gene experiments indicate that an L1-box in the MYB23 promoter acts as a GL2 binding site. Taken together, our findings reveal a functional redundancy between GL2 and HDG11, two homeodomain leucine zipper transcription factors previously thought to mediate opposing functions in trichome morphogenesis. A model is proposed in which GL2 transcript levels are maintained through a positive feedback loop involving GL2 activation of MYB23.

Through the wonders of fermentation, simple sugars derived from enzymatic degradation of cellulose and hemicellulose in the plant cell wall are converted to the biofuel cellulosic ethanol, an attractive alternative to fossil fuels and grain-derived ethanol ([Solomon et al., 2007][1]). Before this

Plant surface waxes form an outer barrier that protects the plant from many forms of environmental stress. The deposition of cuticular waxes on the plant surface is regulated by external environmental changes, including light and dark cycles. However, the underlying molecular mechanisms controlling light regulation of wax production are still poorly understood, especially at the posttranscriptional level. In this paper, we report the regulation of cuticular wax production by the miR156-SPL9 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9) module in Arabidopsis (Arabidopsis thaliana). When compared with wild-type plants, miR156 and SPL9 mutants showed significantly altered cuticular wax amounts in both stems and leaves. Furthermore, it was found that SPL9 positively regulates gene expression of the alkane-forming enzyme ECERIFERUM1 (CER1), as well as the primary (1-) alcohol-forming enzyme ECERIFERUM4 (CER4), to enhance alkane and 1-alcohol synthesis, respectively. Our results indicate that complex formation of SPL9 with a negative regulator of wax synthesis, DEWAX, will hamper SPL9 DNA binding ability, possibly by interfering with SPL9 homodimerization. Combined with their diurnal gene and protein expressions, this dynamic repression-activation transcriptional module defines a dynamic mechanism that may allow plants to optimize wax synthesis during daily cycles. These findings provide a regulatory framework for environmental signal integration in the regulation of wax synthesis.

The year 2019 marks 30 years since The Plant Cell began publishing. To celebrate this milestone, we invited several current and former editorial board members and others to contribute their perspectives on influential papers published in The Plant Cell . These editorial perspectives will be

In this paper, we report the results of a detailed investigation into abscisic acid (ABA)[mdash]stimulated elevations of guard cell cytosolic-free Ca2+ ([Ca2+]cyt). Fluorescence ratio photometry and ratio imaging techniques were used to investigate this phenomenon. Guard cells of open and closed (opened to 10 to 12 [mu]m before treatment with ABA) stomata were microinjected with the fluorescent Ca2+ indicator Indo-1. Resting [Ca2+]cyt ranged from 50 to 350 nM. ABA (100 nM) stimulated an increase in [Ca2+]cyt in 68 and 81% of guard cells microinjected in the open and closed configuration, respectively. All stomata were observed to close in response to ABA. Increases ranged from 100 to 750 nM above the resting concentration and were arbitrarily grouped into five "classes." ABA-stimulated increases in [Ca2+]cyt were not uniformly distributed across the cytosol of guard cells. Rapid transient increases in [Ca2+]cyt were also observed in the guard cells of stomata microinjected in the closed configuration. We concluded that the ABA-induced turgor loss in guard cells is a Ca2+-dependent process.

Shoot branching is critical in determining plant architecture, and much of the plasticity of plant form arises from axillary buds, which exist at the base of each leaf and can remain dormant indefinitely or grow out to produce a branch. Axillary bud outgrowth is therefore important to plant responses to the environment and to agronomic characteristics including yield. As with so many other aspects of plant development, phytohormones are vital to branching: Axillary bud outgrowth is regulated by strigolactones, auxins, and cytokinins. Axillary meristem (AM) initiation has received less attention than outgrowth, but it appears to involve brassinosteroids(reviewedinJanssen etal., 2014). Now, companion papers report that localized auxin minima are needed for the formation of AMs in the shoot apex (Q. Wang et al., pages

Pollen tube reorientation is a dynamic cellular event that is crucial for successful fertilization. We have shown previously that pollen tube orientation is regulated by cytosolic free calcium ([Ca 2 ] c ). In this paper, we studied the activity of a Ca 2 -dependent protein kinase during reorientation. The kinase activity was assayed in living cells by using confocal ratio imaging of BODIPY FL bisindolylmaleimide. We found that growing pollen tubes exhibited higher protein kinase activity in the apical region, whereas nongrowing cells showed uniform distribution. Modification of growth direction by diffusion of inhibitors/activators from a micropipette showed the spatial redistribution of kinase activity to predict the new growth orientation. Localized increases in [Ca 2 ] c induced by photolysis of caged Ca 2 that led to reorientation also increased kinase activity. Molecular and immunological assays suggest that this kinase may show some functional homology with protein kinase C. We suggest that the tip-localized gradient of kinase activity promotes Ca 2 -mediated exocytosis and may act to regulate Ca 2 channel activity.

The unsolved problem of how the pollen and pistil components of angiosperm self-incompatibility (SI) are inherited has a long history ([Lewis, 1960][1]). A recent paper provides evidence, based on transgenic experiments in Solanum chacoense , that a single amino acid difference between proteins

The extracellular matrix (ECM) has been implicated in the primary developmental processes of many organisms. A family of secretory adhesive glycoproteins called substrate adhesion molecules (SAMs) is believed to confer these dynamic capabilities to the ECM in animals. In this paper, we report the existence of SAM-like genes and gene products in flowering plants. Hybridizations with a human vitronectin cDNA probe and genomic DNA from broad bean, soybean, and tomato revealed vitronectin-like sequences. Human vitronectin antibodies cross-react with a 55-kilodalton protein in leaf and root protein extracts from lily, broad bean, soybean, and tomato. In addition, immunocytochemical staining of frozen sections of lily leaf and broad bean gynoecium demonstrated that vitronectin-like proteins were localized to the ECM on the cell surface, with the most intense labeling residing in the transmitting tract of broad bean gynoecium.

I am fortunate indeed to be assuming the editorship of THE PLANT CELL, a journal that has maintained its preeminence during the past decade by bringing to you some of the most important and significant research papers in modern plant biology. By continuing to realize the goals that were set for it

In my July 1998 editorial, I outlined how THE PLANT CELL would be covering and tracking progress in the field of genomics. I am pleased to be able to say that the journal has been extending the range of research articles that it publishes to include a wide spectrum of papers that encompass genomics

Rhizobium and its allies (Azorhizobium, Bradyrhizobium, and Sinorhizobium) are Gram-negative bacteria that cause the development of root (and sometimes stem) nodules on plant hosts, which the bacteria inhabit as nitrogen-fixing endosymbionts. The early stages of this process, including gene expression in the bacterium and cell growth, division, and differentiation in the host, are mediated by signal exchange between the eukaryotic host and the prokaryotic symbiont (Figure l A , left). The plant produces a signal, usually aflavonoid, that induces gene expression in the bacterium; the bacterium subsequently synthesizes a signal that triggers early nodule development on the plant. The developmental time line for nodulation has been described in several reviews and essays (Sprent, 1989; Truchet et al., 1989; Brewin, 1991; Brewin et al., 1992; Hirsch, 1992; Kijne et al., 1992; Ridge, 1992; Vijn et al., 1993) and is only considered briefly here. Nodules can take on several patterns during development, the form of the nodule being determined by the plant, not the bacterium. One major form is the indeterminate (also called meristematic or cylindrical) type, which develops on alfalfa, clover, and pea roots. A second major type is the spherical or determinate nodule, which is formed by soybean, Phaseolus, and Lofus. A comparison of these symbiotic nodules with those of nonlegumes is presented elsewhere in this issue (see Pawlowski and Bisseling, 1996). The twin hallmarks of early nodulation are its developmental complexity and its specificity. The developmental process in the plant involves architectural changes at the cell and organ levels (for example, root hair morphogenesis, cortical cell enlargement, and vascular patterning) as well as interna1 cellular differentiation that includes cytoplasmic activation, cell division, and new gene expression. Structural and developmental studies of nodule formation remain an important part of the overall Rhizobium research picture. Indeed, new views of infection thread formation, cell wall modifications, and intracellular rearrangements in root hairs and elsewhere have recently appeared (Kijne et al., 1992; van Brussel et al., 1992; van Spronsen et al., 1994; DeBoer and Djordjevic, 1995; Ridge, 1995). The exciting tools of video microscopy and image analysis are making it possible to obtain dynamic views of early plant reactions to Rhizobium signals (Allen et al., 1994; Sanchez et al., 1996). Thus, in addition to its inherent interest as a model for understanding plant-microbe interactions, the specificity and timing of early nodulation events make the Rhizobium-plant symbiosis an attractive model system for general plant cell biology studies. The specificity of nodulation is likewise remarkable: with one known exception, the Rhizobium nodulation habit is restricted to a single plant taxon, the Fabaceae, or legume family. Within this family, individual species, strains, or biovars of bacteria nodulate a restricted set of host plants that are usually but not always related. The signal model (Figure 1) provides an explanation for the species-leve1 pattern of host specificity. But we cannot yet answer the larger mechanistic and evolutionary question: Why only legumes? Because a short review cannot catalog complete lists of referentes, even recent ones, the focus of this article is to put selected papers in context: Why is it important for plant biologists to be concerned with bacterial genes, their regulation, and activities? Where do the questions lie in the study of the plant response? What new genetic and cellular methods are needed for their resolution?

The idea that viruses move through plants in two distinct modes was accurately concluded by G. Samuel in a 1934 paper describing the transport of tobacco mosaic virus (TMV) through solanaceous hosts: “lt is considered that these facts favour the theory of a slow cell to cell movement of the virus via the plasmodesmen, combined with a rapid distribution through the plant via the phloem” (Samuel, 1934). It is now firmly established that plant viruses move from cell to cell and over long distances by exploiting and modifying preexisting pathways for macromolecular movement within cells, between cells, and between organs. In this review, we focus on the roles of vira1 and host components in the movement of viruses through these pathways. Exhaustive coverage of all aspects of movement is not possible, but the reader is referred to several excellent reviews that emphasize various facets of shortand long-range virus transport (Atabekov and Taliansky, 1990; Maule, 1991; Deom et al., 1992; Citovsky, 1993; Leisner and Turgeon, 1993; Lucas and Gilbertson, 1994; Lucas, 1995).

In the solanaceous plant Nicotiana alata, self-incompatibility is controlled by a single, multiallelic locus (S locus) expressed in both pollen and pistil. Previously, we have shown cosegregation between alleles of the S locus and alleles of a gene that encodes a glycoprotein with ribonuclease activity (S-RNase). Furthermore, expression of the S-RNase gene is apparently confined to the pistil and is correlated with the onset of self-incompatibility. In this paper, we report that the S-RNase gene is also expressed at low levels in developing pollen. A transcript in developing pollen hybridized to a cDNA encoding the S2-RNase allele of the parent plant and did not hybridize to cDNAs encoding other S-RNase alleles. Two cDNAs for the S2-RNase were cloned from a library derived from anthers of a plant homozygous for the S2 allele and both corresponded to the coding sequence of the S2-RNase. The product of the S-RNase gene was detected by immunocytochemistry in the intine of mature, hydrated pollen grains. These results are interpreted in the light of current knowledge of the structure of the S locus.

In this paper we demonstrate that RNA sequences present upstream and downstream of a reporter gene coding region play an important role in determining the amount of protein produced from an mRNA. A translational enhancer, omega, derived from tobacco mosaic virus, when present at the 5'-end of beta-glucuronidase mRNA increased the efficiency of translation 16-fold to 18-fold in electroporated tobacco or carrot protoplasts, and threefold to 11-fold in maize or rice protoplasts. The presence of omega did not alter the half-life of the mRNA in vivo. We also demonstrate for the first time that a minimum polyadenylated tail length of 25 adenylate residues is sufficient to substantially increase the expression and half-life of the reporter mRNA in plants. When in vitro-produced mRNAs were synthesized such that extra sequence was added to the 3'-end of the poly(A) tail, however, the final level of expression was decreased up to 80%. Omega, the translational enhancer, and a poly(A) tail function independently of each other; their combined effect on translation, when both are present in an mRNA, is the multiplication of their individual effects. Histochemical analysis for the presence of beta-glucuronidase in tobacco established that virtually all viable cells receive mRNA during electroporation. Video image analysis of tobacco protoplasts electroporated with luciferase mRNA demonstrated that there is a wide range in the level of expression of this marker. Carrier RNA, when present during electroporation, had only a modest effect on increasing mRNA uptake. Reporter mRNA expression in electroporated protoplasts was directly proportional to the input mRNA up to at least 30 micrograms/ml.

From a high-salt extract of the purified thylakoid membrane, an 18-kD protein was detected. This protein was translated by the chloroplast ribosomes and could form a stable DNA-protein complex with a cloned chloroplast DNA replicative origin [Nie, Z.Q., Chang, D.Y., and Wu, M. (1987) Mol. Gen. Genet. 209, 265-269]. In this paper, the 18-kD protein is linked to frxB, a chloroplast-encoded, ferredoxin-type, iron-sulfur protein, by N-terminal microsequencing of the purified protein and computer analysis. The identification is further supported empirically by the fact that the electron paramagnetic resonance spectra of the protein indicate the presence of iron-sulfur clusters. A polyclonal antibody raised against a synthetic pentadecameric peptide with amino acid sequence corresponds to the highly conserved region of the frxB protein and reacts strongly and specifically with the 18-kD protein band in protein gel blot analyses. The 18-kD iron-sulfur protein is found to be related to a subunit of the respiratory chain NADH dehydrogenase by its cross-reaction with a polyclonal antibody raised against highly purified NADH-ubiquinone oxidoreductase, a key enzyme of the respiratory chain. These data are consistent with chlororespiration, and, thus, possible implication of chlororespiration in regulating the initiation of chloroplast DNA replication is discussed.