Phytochrome genes in higher plants: Structure,expression, and evolution

© 2006 Springer. All Rights Reserved. Phytochromes play critical roles in monitoring light quantity, quality, and periodicity in plants and they relay this photosensory information to a large number of signaling pathways that regulate plant growth and development. Given these complex functions, it is not surprising that the phytochrome apoproteins are encoded by small multigene families and that different forms of phytochrome regulate different aspects of photomorphogenesis. Over the course of the last decade, progress has been made in defining the number, molecular properties, and biological activities of the photoreceptors that constitute a plant R/FR sensing system. This chapter summarizes our current understanding of the structure of the genes that encode the phytochrome apoproteins (the PHY genes), the expression patterns of those genes, the nature of the phytochrome apoprotein family, and PHY gene evolution in seed plants. Phytochrome was discovered and its basic photochemical properties were first described through physiological studies of light-sensitive seed germination and photoperiodic effects on flowering (Borthwick, et al., 1948, Borthwick, et al., 1952). The pigment itself was initially isolated from extracts of dark-grown (etiolated) plant tissue in 1959 (Butler, et al., 1959), but it was not until much later that phytochrome was purified to homogeneity in an undegraded form (Vierstra and Quail, 1983). DNA sequences of gene and cDNA clones for oat etiolated-tissue spectroscopically in planta and purified in its native form, this dark-tissue phytochrome (now called phyA) remains the most completely biochemically and spectroscopically characterized form of the receptor. At various times throughout the first 40 years of the study of the abundant etiolated-tissue phytochrome, evidence for the presence and activity of additional forms of phytochrome, often referred to as green-tissue or light-stable phytochromes, was obtained. Initially, in physiological experiments, it was sometimes not possible to correlate specific in vivo phytochrome activities with the phytochrome provided the first complete descriptions of the apoprotein (Hershey et al., 1985). Because it accumulates to levels that permit it to be assayed known spectroscopic properties of the molecule. Later, direct evidence for multiple species of phytochrome in plants and in plant extracts was obtained using both spectroscopic and immunochemical methods (reviewed in Pratt, 1995). The molecular identities of these additional phytochrome forms were ultimately deduced from cDNA clones that were isolated by nucleic acid similarity to etiolated-tissue phytochrome sequences (Sharrock and Quail, 1989). More recently, analysis of a large number of complete and partial PHY gene or cDNA sequences from a broad sampling of plant phylogenetic groups and sequencing of several plant genomes have resulted in a much clearer and more general picture of what constitutes a higher plant R/FR photoreceptor family. It is likely that the major types of long-wavelength photosensing pigments have now been identified and the challenge that lies ahead is to understand how the signalling mechanisms, expression patterns, and interactions of these molecules contribute to plant responses to the R/FR environment. Extending the investigation of phytochrome gene families and their functions to additional angiosperm and gymnosperm genera will be an integral component of this effort and of our ability to utilize this growing understanding of phytochrome function to modify the agricultural properties of plants and to better understand the history of land plants

Plastid tubules in higher plants: an analysis of form and function

Besides photosynthesis, plastids are responsible for starch storage, fatty acid biosynthesis and nitrate metabolism. Our understanding of plastids can be improved with observation by microscopy, but this has been hampered by the invisibility of many plastid types. By targeting green fluorescent protein (GFP) to the plastid in transgenic plants, the visualisation of plastids has become routinely possible. Using GFP, motile, tubular protrusions can be observed to emanate from the plastid envelope into the surrounding cytoplasm. These structures, called stromules, vary considerably in frequency and length between different plastid types, but their function is poorly understood. During tomato fruit ripening, chloroplasts in the pericarp cells differentiate into chromoplasts. As chlorophyll degrades and carotenoids accumulate, plastid and stromule morphology change dramatically. Stromules become significantly more abundant upon chromoplast differentiation, but only in one cell type where plastids are large and sparsely distributed within the cell. Ectopic chloroplast components inhibit stromule formation, whereas preventing chloroplast development leads to increased numbers of stromules. Together, these findings imply that stromule function is closely related to the differentiation status, and thus role, of the plastid in question. In tobacco seedlings, stromules in hypocotyl epidermal cells become longer as plastids become more widely distributed within the cell, implying a plastid density-dependent regulation of stromules. Co-expression of fluorescent proteins targeted to plastids, mitochondria and peroxisomes revealed a close spatio-temporal relationship between stromules and other organelles. Stromule and plastid fusion could not be induced under conditions which promote substantial fusion of mitochondria. Data are presented suggesting that organelles may be able to pass between cells, and an experiment was designed to test this possibility in the C4 photosynthetic cells of maize. Inhibitor studies have shown that stromule and plastid movement is dependent on the actin cytoskeleton and the ATPase activity of myosin. An Arabidopsis gene, CHUP1, is responsible for chloroplast relocation in response to light intensity and encodes a chloroplast-localised actin-binding protein. To assess whether this protein is involved in stromule movement, CHUP1 was down-regulated with RNAi. Whilst plants with reduced CHUP1 expression exhibited a chup1 mutant phenotype, no significant effect on stromules was discovered. It was thus concluded that chloroplast relocation and stromule formation are two independent processes that employ different actin-dependent mechanisms. It is proposed that stromules act primarily to increase the plastid surface area in response to a number of developmental and environmental factors

Plastid tubules in higher plants: an analysis of form and function

Besides photosynthesis, plastids are responsible for starch storage, fatty acid biosynthesis and nitrate metabolism. Our understanding of plastids can be improved with observation by microscopy, but this has been hampered by the invisibility of many plastid types. By targeting green fluorescent protein (GFP) to the plastid in transgenic plants, the visualisation of plastids has become routinely possible. Using GFP, motile, tubular protrusions can be observed to emanate from the plastid envelope into the surrounding cytoplasm. These structures, called stromules, vary considerably in frequency and length between different plastid types, but their function is poorly understood. During tomato fruit ripening, chloroplasts in the pericarp cells differentiate into chromoplasts. As chlorophyll degrades and carotenoids accumulate, plastid and stromule morphology change dramatically. Stromules become significantly more abundant upon chromoplast differentiation, but only in one cell type where plastids are large and sparsely distributed within the cell. Ectopic chloroplast components inhibit stromule formation, whereas preventing chloroplast development leads to increased numbers of stromules. Together, these findings imply that stromule function is closely related to the differentiation status, and thus role, of the plastid in question. In tobacco seedlings, stromules in hypocotyl epidermal cells become longer as plastids become more widely distributed within the cell, implying a plastid density-dependent regulation of stromules. Co-expression of fluorescent proteins targeted to plastids, mitochondria and peroxisomes revealed a close spatio-temporal relationship between stromules and other organelles. Stromule and plastid fusion could not be induced under conditions which promote substantial fusion of mitochondria. Data are presented suggesting that organelles may be able to pass between cells, and an experiment was designed to test this possibility in the C4 photosynthetic cells of maize. Inhibitor studies have shown that stromule and plastid movement is dependent on the actin cytoskeleton and the ATPase activity of myosin. An Arabidopsis gene, CHUP1, is responsible for chloroplast relocation in response to light intensity and encodes a chloroplast-localised actin-binding protein. To assess whether this protein is involved in stromule movement, CHUP1 was down-regulated with RNAi. Whilst plants with reduced CHUP1 expression exhibited a chup1 mutant phenotype, no significant effect on stromules was discovered. It was thus concluded that chloroplast relocation and stromule formation are two independent processes that employ different actin-dependent mechanisms. It is proposed that stromules act primarily to increase the plastid surface area in response to a number of developmental and environmental factors

The identification of potential cis- and trans-acting factors in the regulation of DARK INDUCIBLE 3 (DIN3) expression during darkness and chilling in Arabidopsis thaliana

Plant responses to environmental stimuli are co-ordinated by a variety of sensing and signalling mechanisms, which bring appropriate internal changes so that plants are able to adapt to a changing environment. It was the aim of this project to investigate the regulation of one gene: DARK INDUCIBLE 3 (DIN3), specifically the cis- and transacting factors. To achieve these aims, the investigative approach centred on gene expression analysis of linker-scan mutation analysis of 50 base-pairs (bp) of the minimal functional promoter of DIN3. To investigate the contribution made by transacting factors, the effects of over-expression of candidate transcription factor genes were analysed. This project determined that in addition to dark-induced expression already described in the literature, the dark-induction of DIN3 expression could be repressed by low temperature. Specific motifs within the crucial 50bp of the DIN3 promoter were found to be necessary for dark-induced expression, which together was hypothesised to constitute a sugar-responsive sequence. No cis-acting regulatory motifs were found to contribute definitely to the cold responsiveness of DIN3. None of the transcription factor genes investigated, were revealed to have a major role in the dark and cold responsiveness of DIN3. The results of this project suggest that there is considerable cross-talk between dark/sugar regulation and low temperature at the cisand trans-acting level

Phototrophic Bacteria

Microorganisms is pleased to publish this book, which reprints papers that appeared in a Special Issue on “Phototrophic Bacteria”, with Guest Editors Robert Blankenship and Matthew Sattley. This Special Issue included research on all types of phototrophic bacteria, including both anoxygenic and oxygenic forms. Research on these bacterial organisms has greatly advanced our understanding of the basic principles that underlie the energy storage that takes place in all types of photosynthetic organisms, including both bacterial and eukaryotic forms. Topics of interest include: microbial physiology, microbial ecology, microbial genetics, evolutionary microbiology, systems microbiology, agricultural microbiology, microbial biotechnology, and environmental microbiology, as all are related to phototrophic bacteria