Posttranscriptional gene silencing (PTGS) is a nucleotide sequence-specific defense mechanism that can target both cellular and viral mRNAs. Here, three types of transgene-induced PTGS and one example of virus-induced PTGS were analyzed in plants. In each case, antisense RNA complementary to the targeted mRNA was detected. These RNA molecules were of a uniform length, estimated at 25 nucleotides, and their accumulation required either transgene sense transcription or RNA virus replication. Thus, the 25-nucleotide antisense RNA is likely synthesized from an RNA template and may represent the specificity determinant of PTGS.

/pdf/a-species-of-small-antisense-rna-in-posttranscriptional-gene-4x7aphjpq5.pdf

A species of small antisense RNA in posttranscriptional gene silencing in plants.

https://rnajc.ucsf.edu/sites/rnajc.ucsf.edu/files/mRNA_methylation.pdf

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

/pdf/the-tomato-genome-sequence-provides-insights-into-fleshy-7a55qpnrdm.pdf

The tomato genome sequence provides insights into fleshy fruit evolution

Agricultural productivity worldwide is subject to increasing environmental constraints, particularly to drought and salinity due to their high magnitude of impact and wide distribution. Traditional breeding programs trying to improve abiotic stress tolerance have had some success, but are limited by the multigenic nature of the trait. Tolerant plants such as Craterostigma plantagenium, Mesembryanthemum crystallinum, Thellungiella halophila and other hardy plants could be valuable tools to dissect the extreme tolerance nature. In the last decade, Arabidopsis thaliana, a genetic model plant, has been extensively used for unravelling the molecular basis of stress tolerance. Arabidopsis also proved to be extremely important for assessing functions for individual stress-associated genes due to the availability of knock-out mutants and its amenability for genetic transformation. In this review, the responses of plants to salt and water stress are described, the regulatory circuits which allow plants to cope wit...

Drought and Salt Tolerance in Plants

In the immature brain, GABA (gamma-aminobutyric acid) is excitatory, and GABA-releasing synapses are formed before glutamatergic contacts in a wide range of species and structures. GABA becomes inhibitory by the delayed expression of a chloride exporter, leading to a negative shift in the reversal potential for choride ions. I propose that this mechanism provides a solution to the problem of how to excite developing neurons to promote growth and synapse formation while avoiding the potentially toxic effects of a mismatch between GABA-mediated inhibition and glutamatergic excitation. As key elements of this cascade are activity dependent, the formation of inhibition adds an element of nurture to the construction of cortical networks.

/pdf/excitatory-actions-of-gaba-during-development-the-nature-of-3djowg9wku.pdf

Excitatory actions of gaba during development: the nature of the nurture.

Elucidating the mechanisms involved in ripening of climacteric fruit and the role that ethylene plays in the process are key to understanding fruit production and quality. In this review, which is based largely on research in tomato, particular attention is paid to the role of specific isoforms of ACC synthase and ACC oxidase in controlling ethylene synthesis during the initiation and subsequent autocatalytic phase of ethylene production during ripening. Recent information on the structure and role of six different putative ethylene receptors in tomato is discussed, including evidence supporting the receptor inhibition model for ripening, possible differences in histidine kinase activity between receptors, and the importance of receptor LeETR4 in ripening. A number of ethylene-regulated ripening-related genes are discussed, including those involved in ethylene synthesis, fruit texture, and aroma volatile production, as well as experiments designed to elucidate the ethylene signalling pathway from receptor through intermediate components similar to those found in Arabidopsis, leading to transcription factors predicted to control the expression of ethylene-regulated genes.

Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening

Regulation of expression of specific genes by antisense RNA is a naturally occurring mechanism in bacteria1,2, although gene regulation by this mechanism has not yet been observed in higher eukaryotes. However, antisense RNA has been shown to reduce expression of specific genes when injected into frog oocytes3 and Drosophila embryos4. Inhibition of expression of artificially introduced genes has been demonstrated by transient expression of antisense RNA constructs in mammalian cells5,6, and plant protoplasts7, and by stable expression in transgenic plants8. Here, we report a striking inhibition of expression of the endogenous, developmentally regulated gene for polygalacturonase in stably transformed tomato expressing antisense RNA.

Antisense RNA inhibition of polygalacturonase gene expression in transgenic tomatoes

ETHYLENE controls many physiological and developmental processes in higher plants, including ripening of fruit, abscission, senescence and responses to wounding1. Although the accumulation of messenger RNAs in ripening fruit and senescing leaves has been correlated with ethylene production and perception2–4, the regulatory mechanisms governing ethylene synthesis and the stimulation of gene expression by ethylene are not understood. We have previously shown that the complementary DNA, pTOM13, corresponds to an mRNA whose synthesis is correlated with that of ethylene in ripening fruit and wounded leaves5,6,8. The pTOM13 mRNA encodes a protein of relative molecular mass 35,0006. The cDNA and three related genomic clones have been sequenced, but the function of the protein is unknown7–9. We show here that antisense RNA, which has previously been used only to reduce the expression of genes of known function10–12, when applied to pTOM13, reduces ethylene synthesis in a gene dosage-dependent manner. Analysis of these novel mutants suggests that pTOM13 encodes a polypeptide involved in the conversion of 1-amino-cyclopropane-1-carboxylic acid to ethylene by the ethylene-forming enzyme (ACC-oxidase).

Antisense gene that inhibits synthesis of the hormone ethylene in transgenic plants

Ethylene regulates many aspects of the plant life cycle, including seed germination, root initiation, flower development, fruit ripening, senescence, and responses to biotic and abiotic stresses. It thus plays a key role in responses to the environment that have a direct bearing on a plant's fitness for adaptation and reproduction. In recent years, there have been major advances in our understanding of the molecular mechanisms regulating ethylene synthesis and action. Screening for mutants of the triple response phenotype of etiolated Arabidopsis seedlings, together with map-based cloning and candidate gene characterization of natural mutants from other plant species, has led to the identification of many new genes for ethylene biosynthesis, signal transduction, and response pathways. The simple chemical nature of ethylene contrasts with its regulatory complexity. This is illustrated by the multiplicity of genes encoding the key ethylene biosynthesis enzymes 1-aminocyclopropane-1-carboxylic acid (ACC) synthase and ACC oxidase, multiple ethylene receptors and signal transduction components, and the complexity of regulatory steps involving signalling relays and control of mRNA and protein synthesis and turnover. In addition, there are extensive interactions with other hormones. This review integrates knowledge from the model plant Arabidopsis and other plant species and focuses on key aspects of recent research on regulatory networks controlling ethylene synthesis and its role in flower development and fruit ripening.

Recent advances in ethylene research

1-Aminocyclopropane-1-carboxylic acid synthase (ACS) is one of the key regulatory enzymes involved in the synthesis of the hormone ethylene and is encoded by a multigene family containing at least eight members in tomato (Lycopersicon esculentum). Increased ethylene production accompanies ripening in tomato, and this coincides with a change in the regulation of ethylene synthesis from auto-inhibitory to autostimulatory. The signaling pathways that operate to bring about this transition from so-called system-1 to system-2 ethylene production are unknown, and we have begun to address these by investigating the regulation of ACS expression during ripening. Transcripts corresponding to four ACS genes, LEACS1A, LEACS2, LEACS4, and LEACS6, were detected in tomato fruit, and expression analysis using the ripening inhibitor (rin) mutant in combination with ethylene treatments and the Never-ripe (Nr) mutant has demonstrated that each is regulated in a unique way. A proposed model suggests that system-1 ethylene is regulated by the expression of LEACS1A and LEACS6. In fruit a transition period occurs in which the RIN gene plays a pivotal role leading to increased expression of LEACS1A and induction of LEACS4. System-2 ethylene synthesis is subsequently initiated and maintained by ethylene-dependent induction of LEACS2.

The Regulation of 1-Aminocyclopropane-1-Carboxylic Acid Synthase Gene Expression during the Transition from System-1 to System-2 Ethylene Synthesis in Tomato

Donald Grierson

Papers

Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening

Antisense RNA inhibition of polygalacturonase gene expression in transgenic tomatoes

Antisense gene that inhibits synthesis of the hormone ethylene in transgenic plants

Recent advances in ethylene research

The Regulation of 1-Aminocyclopropane-1-Carboxylic Acid Synthase Gene Expression during the Transition from System-1 to System-2 Ethylene Synthesis in Tomato