SUMMARY Cyanobacteria are ecologically important photosynthetic prokaryotes that also serve as popular model organisms for studies of photosynthesis and gene regulation. Both molecular and ecological studies of cyanobacteria benefit from real-time information on photosynthesis and acclimation. Monitoring in vivo chlorophyll fluorescence can provide noninvasive measures of photosynthetic physiology in a wide range of cyanobacteria and cyanolichens and requires only small samples. Cyanobacterial fluorescence patterns are distinct from those of plants, because of key structural and functional properties of cyanobacteria. These include significant fluorescence emission from the light-harvesting phycobiliproteins; large and rapid changes in fluorescence yield (state transitions) which depend on metabolic and environmental conditions; and flexible, overlapping respiratory and photosynthetic electron transport chains. The fluorescence parameters FV/FM, FV′/FM′,qp,qN, NPQ, and φPS II were originally developed to extract information from the fluorescence signals of higher plants. In this review, we consider how the special properties of cyanobacteria can be accommodated and used to extract biologically useful information from cyanobacterial in vivo chlorophyll fluorescence signals. We describe how the pattern of fluorescence yield versus light intensity can be used to predict the acclimated light level for a cyanobacterial population, giving information valuable for both laboratory and field studies of acclimation processes. The size of the change in fluorescence yield during dark-to-light transitions can provide information on respiration and the iron status of the cyanobacteria. Finally, fluorescence parameters can be used to estimate the electron transport rate at the acclimated growth light intensity.

Photosynthetic and metabolic acclimation to low growth temperatures were studied in Arabidopsis (Heynh.). Plants were grown at 23 degrees C and then shifted to 5 degrees C. We compared the leaves shifted to 5 degrees C for 10 d and the new leaves developed at 5 degrees C with the control leaves on plants that had been left at 23 degrees C. Leaf development at 5 degrees C resulted in the recovery of photosynthesis to rates comparable with those achieved by control leaves at 23 degrees C. There was a shift in the partitioning of carbon from starch and toward sucrose (Suc) in leaves that developed at 5 degrees C. The recovery of photosynthetic capacity and the redirection of carbon to Suc in these leaves were associated with coordinated increases in the activity of several Calvin-cycle enzymes, even larger increases in the activity of key enzymes for Suc biosynthesis, and an increase in the phosphate available for metabolism. Development of leaves at 5 degrees C also led to an increase in cytoplasmic volume and a decrease in vacuolar volume, which may provide an important mechanism for increasing the enzymes and metabolites in cold-acclimated leaves. Understanding the mechanisms underlying such structural changes during leaf development in the cold could result in novel approaches to increasing plant yield.

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Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula ϫ tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.Leaf senescence is the final stage in leaf development, and understanding senescence is important not only for purely scientific reasons, but also for practical purposes. Premature senescence leads, for example, to decreased photosynthetic capacity, and consequently lower yield. Senescence is not simply the passive death of a leaf because of aging, but is a tightly controlled process during which cell components are degraded in a coordinated fashion and, when nutrients have been relocated to other parts of the plant body, the cell finally dies (Gan and Amasino, 1997;Nooden et al., 1997). Despite the resemblance with apoptosis of animal cells (Yen and Yang, 1998), a form of programmed cell death, only a few orthologs of genes regulating apoptosis have been found in plants, indicating that there are significant differences between the processes (Koonin and Aravind, 2002). Plant cells respond to some animal apoptosis regulators (e.g. Danon et al., 2000), so there must be common elements between the processes. However, it seems as if plants have developed a unique mode of cell death (Beers, 1997) that, if understood, may give insight into processes that are important for cell integrity and viability. However, very little is known about the details of plant leaf senescence.During the last decade, studies of leaf senescence, focusing especially on Arabidopsis, and other annual species to a lesser extent, have identified a number of senescence-associated genes (SAGs) and cellular mechanisms of senescence have begun to be elucidated, as reviewed by various authors (BuchananWollaston, 1997;Nam, 1997;Quirino et al., 2000). The most obvious visual phenotype of senescen...

Trees present a life form of paramount importance for terrestrial ecosystems and human societies because of their ecological structure and physiological function and provision of energy and industrial materials. The genus Populus is the internationally accepted model for molecular tree biology. We have analyzed 102,019 Populus ESTs that clustered into 11,885 clusters and 12,759 singletons. We also provide >4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the Populus genome sequence. A public web-based EST database (POPULUSDB) provides digital expression profiles for 18 tissues that comprise the majority of differentiated organs. The coding content of Populus and Arabidopsis genomes shows very high similarity, indicating that differences between these annual and perennial angiosperm life forms result primarily from differences in gene regulation. The high similarity between Populus and Arabidopsis will allow studies of Populus to directly benefit from the detailed functional genomic information generated for Arabidopsis, enabling detailed insights into tree development and adaptation. These data will also valuable for functional genomic efforts in Arabidopsis.A fter the completion of the Arabidopsis genome sequence (1) and the publication of near-complete sequences of indica and japonica rice (2, 3), plant researchers have been able to scan these genomes to identify and compare genes of interest. Arabidopsis and rice represent the two major angiosperm phylogenetic groups, dicotyledons and monocotyledons, respectively. They diverged Ϸ170 million years ago (4) and differ in numerous physiological traits. Within these groups, however, great diversity also exists in life history and plant structure. Some of the most striking differences observed are those between woody (trees and shrubs) and herbaceous species. Trees and shrubs form hard, long-lasting structures that are distinct from the soft stems and branches of herbs, especially annuals. The lignocellulosic cell walls of trees and shrubs are critical for their survival, stature, competitive ability, and provision of habitat, and they have a dramatic influence on ecosystem cycles. Trees and shrubs are found intermixed with herbaceous plants in many phylogenetic groups within the angiosperms, showing that the tree growth habit has been lost or acquired many times during evolution (5). The herbaceous life form is often considered to be the derived state, evolving numerous times from tree-like ancestors (6).The tree life form imposes several different physiological and morphological constraints compared with those of herbaceous plants. Many of the processes that distinguish trees from herbs take years to fully develop and express themselves (e.g., wood formation, vegetative phenology, maturation, and the juvenility͞maturity transition) and are therefore not easily studied in herbs. The need for a tree model system for functional genomics has therefore become evident (7). The genus Populus, consisting of Ϸ40 species distributed i...

Summary• Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources.• As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data.• Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided.• PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at www.popgenie.org or via www.populusgenome.info.

To test the hypothesis that the up-regulation of sucrose biosynthesis during cold acclimation is essential for the development of freezing tolerance, the acclimation responses of wild-type (WT) Arabidopsis thaliana ∞ C was associated with an increase in freezing tolerance relative to WT ( ----9.1 and ----7.2 ∞ ∞ ∞ ∞ C, respectively). In contrast, both antisense lines showed impaired development of freezing tolerance ( ----5.2 and ----5.8 ∞ ∞ ∞ ∞ C for antifbp and antisps, respectively) when shifted to 5 ∞ ∞ ∞ ∞ C. In the new leaves developed at 5 ∞ ∞ ∞ ∞ C the recovery of photosynthesis as typically seen in WT was strongly inhibited in both antisense lines and this inhibition was associated with a further failure of both antisense lines to cold acclimate. Thus, functional sucrose biosynthesis at low temperature in the over-sps plants reduced the inhibition of photosynthesis, maintained the mobilization of carbohydrates from source leaves to sinks and increased the rate at which freezing tolerance developed. Modification of sucrose metabolism therefore represents an additional approach that will have benefits both for the development of freezing tolerance and over-wintering, and for the supply of exportable carbohydrate to support growth at low temperatures.

Summary Arabidopsis thaliana plants were grown at 23°C and changes in carbohydrate metabolism, photosynthesis and photosynthetic gene expression were studied after the plants were shifted to 5°C. The responses of leaves shifted to 5°C after development at 23°C are compared to leaves that developed at 5°C. Shifting warm developed leaves to 5°C lead to a severe suppression of photosynthesis that correlated with a rapid and sustained accumulation of hexose phosphates and soluble sugars. Associated with the suppression of photosynthesis and the accumulation of soluble sugars was a reduction in the amount of transcript for genes encoding photosynthetic proteins (cab and rbcS). In contrast, leaves that developed at 5°C showed an increase in photosynthesis and control levels of photosynthetic gene expression. This recovery occurred even though leaves that developed at 5°C maintained large pools of soluble sugars. Leaves that developed at 5°C also showed a strong upregulation of the cytosolic pathway for soluble sugar synthesis but not of the chloroplastic pathway for starch synthesis. This was shown at the level of both enzyme activity and the amount of transcript. Thus, development of Arabidopsis leaves at 5°C resulted in metabolic changes that enabled them to produce and accumulate large soluble sugar pools without any associated suppression of photosynthesis or photosynthetic gene expression. These changes were also associated with enhanced freezing tolerance. We suggest that this reprogramming of carbohydrate metabolism associated with development at low temperature is essential to the development of full freezing tolerance and for winter survival of over‐wintering herbaceous annuals.