Noncoding RNA Mediated Traffic of Foreign mRNA into Chloroplasts Reveals a Novel Signaling Mechanism in Plants

Communication between chloroplasts and the nucleus is one of the milestones of the evolution of plants on earth. Proteins encoded by ancestral chloroplast-endogenous genes were transferred to the nucleus during the endosymbiotic evolution and originated this communication, which is mainly dependent on specific transit-peptides. However, the identification of nuclear-encoded proteins targeted to the chloroplast lacking these canonical signals suggests the existence of an alternative cellular pathway tuning this metabolic crosstalk. Non-coding RNAS (NcRNAs) are increasingly recognized as regulators of gene expression as they play roles previously believed to correspond to proteins. Avsunviroidae family viroids are the only noncoding functional RNAs that have been reported to traffic inside the chloroplasts. Elucidating mechanisms used by these pathogens to enter this organelle will unearth novel transport pathways in plant cells. Here we show that a viroid-derived NcRNA acting as a 5′UTR-end mediates the functional import of Green Fluorescent Protein (GFP) mRNA into chloroplast. This claim is supported by the observation at confocal microscopy of a selective accumulation of GFP in the chloroplast of the leaves expressing the chimeric vd-5′UTR/GFP and by the detection of the GFP mRNA in chloroplasts isolated from cells expressing this construct. These results support the existence of an alternative signaling mechanism in plants between the host cell and chloroplasts, where an ncRNA functions as a key regulatory molecule to control the accumulation of nuclear-encoded proteins in this organelle. In addition, our findings provide a conceptual framework to develop new biotechnological tools in systems using plant chloroplast as bioreactors. Finally, viroids of the family Avsunviroidae have probably evolved to subvert this signaling mechanism to regulate their differential traffic into the chloroplast of infected cells

Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms

Rate variation in genes from all three genomes has been observed frequently in plant lineages with a parasitic and mycoheterotrophic mode of life. While the loss of photosynthetic ability leads to a relaxation of evolutionary constraints in genes involved in the photosynthetic apparatus, it remains to be determined how prevalent increased substitution rates are in nuclear DNA of non-photosynthetic angiosperms. In this study we infer rates of molecular evolution of 18S rDNA of all parasitic and mycoheterotorphic plant families (except Lauraceae and Polygalaceae) using relative rate tests. In several holoparasitic and mycoheterotrophic plant lineages extremely high substitution rates are observed compared to other photosynthetic angiosperms. The position and frequency of these substitutions have been identified to understand the mutation dynamics of 18S rRNA in achlorophyllous plants. Despite the presence of significantly elevated substitution rates, very few mutations occur in major functional and structural regions of the small ribosomal molecule, providing evidence that the efficiency of the translational apparatus in non-photosynthetic plants has not been affected

Operons

Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from yeasts to filamentous fungi, plants, and animals. Gene clusters can consist of paralogous genes that have most likely arisen by gene duplication. However, there are now many examples of eukaryotic gene clusters that contain functionally related but non-homologous genes and that represent functional gene organizations with operon-like features (physical clustering and co-regulation). These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). The aim of this article is to review features of functional gene clusters in prokaryotes and eukaryotes and the significance of clustering for effective function

Positive effects of ectomycorrhizal colonization on growth of seedlings of a tropical tree across a range of forest floor light conditions

In a shadehouse experiment we tested the effects of light, nutrients and ectomycorrhizal fungi (EMF) on the growth of Vatica albiramis van Slooten (Dipterocarpaceae) seedlings. We hypothesised that it is more advantageous for plants to form connections with EMF and to trade carbon for nutrients with EMF under high light than low light. The relationship between seedling growth and the proportion of ectomycorrhizal root tips was expected as positive in high light and as negative in low light. Light conditions simulated the forest understory (low; 3% full sunlight), a small gap (medium; 11%) and a large gap (high; 33%) and a fully factorial combination of nutrients (F−/+) and ectomycorrhizal colonization (EMF−/+) treatments were applied within light conditions. The application of EMF and nutrients did significantly alter seedling growth across the range of forest floor light conditions, however the key hypothesis was rejected as seedling growth under low light was not affected by increased EMF colonization of root tips (light:EMF colonization χ2 = 2.97, p  = 0.23). In addition, the lack of difference in morphotype abundance across light conditions indicated that light changes may not favour the association to specific EMF in seedlings of this particular dipterocarp species. Our results suggest that antagonistic (non-beneficial to the plant) effects due to ectomycorrhizal colonization under a light constrained environment may not affect seedling growth of Vatica albiramis. Electronic supplementary material: The online version of this article (doi:10.1007/s11104-010-0555-3) contains supplementary material, which is available to authorized users