Reef-building corals and other tropical anthozoans harbor endosymbiotic dinoflagellates. It is now recognized that the dinoflagellates are fundamental to the biology of their hosts, and their carbon and nitrogen metabolisms are linked in important ways. Unlike free living species, growth of symbiotic dinoflagellates is unbalanced and a substantial fraction of the carbon fixed daily by symbiont photosynthesis is released and used by the host for respiration and growth. Release of frxed carbon as low molecular weight compounds by freshly isolated symbiotic dinoflagellates is evoked by a factor (i.e., a chemical agent) present in a homogenate of host tissue. We have identified this "host factore in the Hawaiian coral Pocillopora damicornis as a set of free amino acids. Synthetic amino acid mixtures, based on the measured free amino acid pools of P. damicornis tissues, not only elicit the selective release of 14C-labeled photosynthetic products from isolated symbiotic dinoflagellates but also enhance total "4CO2 fixation.Dinoflagellates freshly isolated from the Hawaiian coral Pocillopora damicornis and the Pacific giant clam Tridacna crocea and incubated in sea water with a crude homogenate of their own host tissue fix 14C02 in the light and release a substantial fraction of the fixed carbon to the incubation medium, principally as [14C]glycerol, [14C]alanine, and [14C]glucose. In contrast, release of labeled organic carbon compounds by freshly isolated dinoflagellates incubated in sea water alone is always significantly less. Moreover, as a crude homogenate of animal tissue from the one host species also induces dinoflagellates from another host species to selectively release fixed carbon, the inducing factor would appear to be nonspecific (1).Release of fixed carbon by symbiotic dinoflagellates has been demonstrated in several cnidarian symbioses. Although a host factor (HF) has never been identified, its properties, depending on the host, have been described as heat labile (1-3) or heat stable (1, 4), enhancing carbon fixation (2) or not enhancing carbon fixation (3), absent from aposymbiotic hosts but inducible by reinfection with dinoflagellates, constitutive in aposymbiotic hosts (5), evoking release of fixed carbon from cultured symbiotic dinoflagellates and free-living nonsymbiotic dinoflagellates, not evoking the release of fixed carbon from cultured symbiotic dinoflagellates and free-living nonsymbiotic dinoflagellates (5, 6), and behaving like a substance with a molecular mass of <10 kDa (3) or -1 kDa (5). Here we identify HF in the Hawaiian reef coral P. damicornis as a set of free amino acids (FAAs) that not only evoke the selective release of photosynthate from symbiotic dinoflagellates in vitro but also enhance dinoflagellate carbon fixation. P. damicornis and the tropical sea anemone Aiptasia pulchella were collected from Checker Reef adjacent to the Hawaiian Institute of Marine Biology, Oahu, Hawaii, and the animals were transported by air to the University of California, Los Angeles. The c...

The tropical rainforest mesocosm within the Biosphere 2 Laboratory, a model system of some 110 species developed over 12 years under controlled environmental conditions, has been subjected to a series of comparable drought experiments during 2000-2002. In each study, the mesocosm was subjected to a 4-6 week drought, with welldefined rainfall events before and after the treatment. Ecosystem CO 2 uptake rate ( A eco ) declined 32% in response to the drought, with changes occurring within days and being reversible within weeks, even though the deeper soil layers did not become significantly drier and leaf-level water status of most large trees was not greatly affected. The reduced A eco during the drought reflected both morphological and physiological responses. It is estimated that the drought-induced 32% reduction of A eco has three principal components: (1) leaf fall increased two-fold whereas leaf expansion growth of some canopy dominants declined to 60%, leading to a 10% decrease in foliage coverage of the canopy. This might be the main reason for the persistent reduction of A eco after rewatering. (2) The maximum photosynthetic electron transport rate at high light intensities in remaining leaves was reduced to 71% for three of the four species measured, even though no chronic photoinhibition occurred. (3) Stomata closed, leading to a reduced ecosystem water conductance to water vapour (33% of pre-drought values), which not only reduced ecosystem carbon uptake rate, but may also have implications for water and energy budgets of tropical ecosystems. Additionally, individual rainforest trees responded differently, expressing different levels of stress and stress avoiding mechanisms. This functional diversity renders the individual response heterogeneous and has fundamental implications to scale leaf level responses to ecosystem dynamics.Key-words : chlorophyll fluorescence; drought; leaf area; leaf fall; leaf growth; net ecosystem CO 2 exchange; photosynthesis; photosynthetic electron transport; tropical rainforest; tropical trees.Abbreviations : A eco , ecosystem photosynthetic CO 2 uptake rate ( m mol CO 2 m -2 s -1 ); c i , apparent intercellular CO 2 concentration (p.p.m.); ET, ecosystem evapotranspiration (mmol H 2 O m -2 s -1 ); ETR, photosynthetic electron transport rate ( m mol electrons m -2 s -1 ); F 0 , ground fluorescence of the dark-adapted leaf; F m , maximum fluorescence of the dark-adapted leaf; F , fluorescence of the light-adapted leaf; F m ¢ , maximum fluorescence of the light-adapted leaf; F v / F m , pre-dawn potential quantum yield of photosystem (PS) II (

A set of 58 nuclearly encoded thylakoid-integral membrane proteins from four plant species was identified, and their amino termini were assigned unequivocally based upon mass spectrometry of intact proteins and peptide fragments. The dataset was used to challenge the Web tools ChloroP, TargetP, SignalP, PSORT, Predotar, and MitoProt II for predicting organelle targeting and transit peptide proteolysis sites. ChloroP and TargetP reliably predicted chloroplast targeting but only reliably predicted transit peptide cleavage sites for soluble proteins targeted to the stroma. SignalP (eukaryote settings) accurately predicted the transit peptide cleavage site for soluble proteins targeted to the lumen. SignalP (Gramnegative bacteria settings) reliably predicted peptide cleavage of integral thylakoid proteins inserted into the membrane via the "spontaneous" pathway. The processing sites of more common thylakoid-integral proteins inserted by the signal recognition peptide-dependent pathway were not well predicted by any of the programs. The results suggest the presence of a second thylakoid processing protease that recognizes the transit peptide of integral proteins inserted via the spontaneous mechanism and that this mechanism may be related to the secretory mechanism of Gram-negative bacteria. Molecular & Cellular Proteomics 2:1068 -1085, 2003.Advances in genome sequencing (1-3) have provided a huge resource that is driving the field of bioinformatics. Besides providing a readout that approximates the primary structure of a particular gene product, there are many facets of expression, such as organellar targeting, that can be addressed via computational analysis of genomic data. Posttranslational modification sites, including signal peptide cleavage sites, may be predicted, although the accuracy of such predictive algorithms is often rooted in the knowledge base used for their development.Proteomics, the systematic study of large sets of proteins expressed by a particular cell type or tissue, is largely possible because of recent technological and computational advances. Contemporary proteomics is based on the following three components: analytical separation of proteins from complex starting material, identification of the proteins, and subsequent sorting and classification of the datasets using bioinformatics software tools. The availability of complete genome sequences, improvements in techniques for protein separation and displays (4 -6), and new developments in mass spectrometry (MS) 1 for protein identification (7-10) have arguably outpaced developments in bioinformatics. Using the complete mitochondrial, plastid, and nuclear Arabidopsis thaliana genomes (2, 11, 12) and results from recent proteomics experiments (13-16), it is possible to test the performance of algorithms that are commonly used to predict organellar targeting of nuclear gene products and transit peptide cleavage sites. Thus, it is timely to reevaluate the various tools at our disposal. The chloroplast is a fascinating organelle not only because ...