@phdthesis{Borghi2021, author = {Borghi, Gian Luca}, title = {Evolution and diversity of photosynthetic metabolism in C3, C3-C4 intermediate and C4 plants}, doi = {10.25932/publishup-52220}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-522200}, school = {Universit{\"a}t Potsdam}, pages = {163}, year = {2021}, abstract = {In C3 plants, CO2 diffuses into the leaf and is assimilated by the Calvin-Benson cycle in the mesophyll cells. It leaves Rubisco open to its side reaction with O2, resulting in a wasteful cycle known as photorespiration. A sharp fall in atmospheric CO2 levels about 30 million years ago have further increased the side reaction with O2. The pressure to reduce photorespiration led, in over 60 plant genera, to the evolution of a CO2-concentrating mechanism called C4 photosynthesis; in this mode, CO2 is initially incorporated into 4-carbon organic acids, which diffuse to the bundle sheath and are decarboxylated to provide CO2 to Rubisco. Some genera, like Flaveria, contain several species that represent different steps in this complex evolutionary process. However, the majority of terrestrial plant species did not evolve a CO2-concentrating mechanism and perform C3 photosynthesis. This thesis compares photosynthetic metabolism in several species with C3, C4 and intermediate modes of photosynthesis. Metabolite profiling and stable isotope labelling were performed to detect inter-specific differences changes in metabolite profile and, hence, how a pathway operates. The results obtained were subjected to integrative data analyses like hierarchical clustering and principal component analysis, and were deepened by correlation analyses to uncover specific metabolic features and reaction steps that were conserved or differed between species. The main findings are that Calvin-Benson cycle metabolite profiles differ between C3 and C4 species and between different C3 species, including a very different response to rising irradiance in Arabidopsis and rice. These findings confirm Calvin-Benson cycle operation diverged between C3 and C4 species and, most unexpectedly, even between different C3 species. Moreover, primary metabolic profiles supported the current C4 evolutionary model in the genus Flaveria and also provided new insights and opened up new questions. Metabolite profiles also point toward a progressive adjustment of the Calvin-Benson cycle during the evolution of C4 photosynthesis. Overall, this thesis point out the importance of a metabolite-centric approach to uncover underlying differences in species apparently sharing the same photosynthetic routes and as a valid method to investigate evolutionary transition between C3 and C4 photosynthesis.}, language = {en} } @article{CleggGaedkeBoehreretal.2012, author = {Clegg, Mark R. and Gaedke, Ursula and B{\"o}hrer, Bertram and Spijkerman, Elly}, title = {Complementary ecophysiological strategies combine to facilitate survival in the hostile conditions of a deep chlorophyll maximum}, series = {Oecologia}, volume = {169}, journal = {Oecologia}, number = {3}, publisher = {Springer}, address = {New York}, issn = {0029-8549}, doi = {10.1007/s00442-011-2225-4}, pages = {609 -- 622}, year = {2012}, abstract = {In the deep, cooler layers of clear, nutrient-poor, stratified water bodies, phytoplankton often accumulate to form a thin band or "deep chlorophyll maximum" (DCM) of ecological importance. Under such conditions, these photosynthetic microorganisms may be close to their physiological compensation points and to the boundaries of their ecological tolerance. To grow and survive any resulting energy limitation, DCM species are thought to exhibit highly specialised or flexible acclimation strategies. In this study, we investigated several of the adaptable ecophysiological strategies potentially employed by one such species, Chlamydomonas acidophila: a motile, unicellular, phytoplanktonic flagellate that often dominates the DCM in stratified, acidic lakes. Physiological and behavioural responses were measured in laboratory experiments and were subsequently related to field observations. Results showed moderate light compensation points for photosynthesis and growth at 22A degrees C, relatively low maintenance costs, a behavioural preference for low to moderate light, and a decreased compensation point for photosynthesis at 8A degrees C. Even though this flagellated alga exhibited a physiologically mediated diel vertical migration in the field, migrating upwards slightly during the day, the ambient light reaching the DCM was below compensation points, and so calculations of daily net photosynthetic gain showed that survival by purely autotrophic means was not possible. Results suggested that strategies such as low-light acclimation, small-scale directed movements towards light, a capacity for mixotrophic growth, acclimation to low temperature, in situ exposure to low O-2, high CO2 and high P concentrations, and an avoidance of predation, could combine to help overcome this energetic dilemma and explain the occurrence of the DCM. Therefore, corroborating the deceptive ecophysiological complexity of this and similar organisms, only a suite of complementary strategies can facilitate the survival of C. acidophila in this DCM.}, language = {en} } @article{DamarajuSchledeEckhardtetal.2011, author = {Damaraju, Sridevi and Schlede, Stephanie and Eckhardt, Ulrich and Lokstein, Heiko and Grimm, Bernhard}, title = {Functions of the water soluble chlorophyll-binding protein in plants}, series = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, volume = {168}, journal = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, number = {12}, publisher = {Elsevier}, address = {Jena}, issn = {0176-1617}, doi = {10.1016/j.jplph.2011.02.007}, pages = {1444 -- 1451}, year = {2011}, abstract = {Functional aspects of water soluble chlorophyll-binding protein (WSCP) in plants were investigated during the courses of leaf senescence, chlorophyll biogenesis, stress response and photoprotection. The cDNA sequence encoding WSCP from cauliflower was cloned into a binary vector to facilitate Agrobacterium tumefaciens mediated transformation of Nicotiana tabacum. The resultant transgenic tobacco plants overexpressed the CauWSCP gene under the control of a 35S-promoter. Analyses of protein and pigment contents indicate that WSCP overexpression does not enhance chlorophyll catabolism in vivo, thus rendering a role of WSCP in Chl degradation unlikely. Accumulation of higher levels of protochlorophyllide in WSCP overexpressor plants corroborates a proposed temporary storage and carrier function of WSCP for chlorophyll and late precursors. Although WSCP overexpressor plants did not show significant differences in non-photochemical quenching of chlorophyll fluorescence, they are characterized by significantly lower zeaxanthin accumulation and peroxidase activity at different light intensities, even at high light intensities of 700-900 mu mol photons m(-2) s(-1). These results suggest a photoprotective function of the functional chlorophyll binding-WSCP tetramer by shielding of chlorophylls from molecular oxygen.}, language = {en} } @article{EbenhoehHouwaartLoksteinetal.2011, author = {Ebenhoeh, Oliver and Houwaart, Torsten and Lokstein, Heiko and Schlede, Stephanie and Tirok, Katrin}, title = {A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence}, series = {Biosystems : journal of biological and information processing sciences}, volume = {103}, journal = {Biosystems : journal of biological and information processing sciences}, number = {2}, publisher = {Elsevier}, address = {Oxford}, issn = {0303-2647}, doi = {10.1016/j.biosystems.2010.10.011}, pages = {196 -- 204}, year = {2011}, abstract = {Under natural conditions, plants are exposed to rapidly changing light intensities. To acclimate to such fluctuations, plants have evolved adaptive mechanisms that optimally exploit available light energy and simultaneously minimise damage of the photosynthetic apparatus through excess light. An important mechanism is the dissipation of excess excitation energy as heat which can be measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). In this paper, we present a highly simplified mathematical model that captures essential experimentally observed features of the short term adaptive quenching dynamics. We investigate the stationary and dynamic behaviour of the model and systematically analyse the dependence of characteristic system properties on key parameters such as rate constants and pool sizes. Comparing simulations with experimental data allows to derive conclusions about the validity of the simplifying assumptions and we further propose hypotheses regarding the role of the xanthophyll cycle in NPQ. We envisage that the presented theoretical description of the light reactions in conjunction with short term adaptive processes serves as a basis for the development of more detailed mechanistic models by which the molecular mechanisms of NPQ can be theoretically studied.}, language = {en} } @article{FranckvonBlohMuelleretal.2011, author = {Franck, Siegfried and von Bloh, Werner and M{\"u}ller, Christoph and Bondeau, Alberte and Sakschewski, B.}, title = {Harvesting the sun new estimations of the maximum population of planet Earth}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {222}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, number = {12}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2011.03.030}, pages = {2019 -- 2026}, year = {2011}, abstract = {The maximum population, also called Earth's carrying capacity, is the maximum number of people that can live on the food and other resources available on planet Earth. Previous investigations estimated the maximum carrying capacity as large as about 1 trillion people under the assumption that photosynthesis is the limiting process. Here we use a present state-of-the-art dynamic global vegetation model with managed planetary land surface, Lund-Potsdam-Jena managed Land (LPJmL), to calculate the yields of the most productive crops on a global 0.5 degrees x 0.5 degrees grid. Using the 2005 crop distribution the model predicts total harvested calories that are sufficient for the nutrition of 11.4 billion people. We define scenarios where humankind uses the whole land area for agriculture, saves the rain forests and the boreal evergreen forests or cultivates only pasture to feed animals. Every scenario is run in an extreme version with no allowance for urban and recreational needs and in two soft versions with a certain area per person for non-agricultural use. We find that there are natural limits of the maximum carrying capacity which are independent of any increase in agricultural productivity, if non-agricultural land use is accounted for. Using all land planet Earth can sustain 282 billion people. The save-forests-scenario yields 150 billion people. The scenario that cultivates only pasture to feed animals yields 96 billion people. Nevertheless, we should always have in mind that all our calculated numbers for the carrying capacity refer to extreme scenarios where humankind may only vegetate on this planet. Our numbers are considerably higher than the general median estimate of upper bounds of human population found in the literature in the order of 10 billion.}, language = {en} } @phdthesis{Goetze2010, author = {G{\"o}tze, Jan Philipp}, title = {Influence of protein and solvent environments on quantum chemical properties of photosynthesis enzymes and photoreceptors}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-51135}, school = {Universit{\"a}t Potsdam}, year = {2010}, abstract = {This thesis contains quantum chemical models and force field calculations for the RuBisCO isotope effect, the spectral characteristics of the blue-light sensor BLUF and the light harvesting complex II. The work focuses on the influence of the environment on the corresponding systems. For RuBisCO, it was found that the isotopic effect is almost unaffected by the environment. In case of the BLUF domain, an amino acid was found to be important for the UV/vis spectrum, but unaccounted for in experiments so far (Ser41). The residue was shown to be highly mobile and with a systematic influence on the spectral shift of the BLUF domain chromophore (flavin). Finally, for LHCII it was found that small changes in the geometry of a Chlorophyll b/Violaxanthin chromophore pair can have strong influences regarding the light harvesting mechanism. Especially here it was seen that the proper description of the environment can be critical. In conclusion, the environment was observed to be of often unexpected importance for the molecular properties, and it seems not possible to give a reliable estimate on the changes created by the presence of the environment.}, language = {en} } @article{GoetzeSaalfrank2012, author = {G{\"o}tze, Jan Philipp and Saalfrank, Peter}, title = {Quantum chemical modeling of the kinetic isotope effect of the carboxylation step in RuBisCO}, series = {Journal of molecular modeling}, volume = {18}, journal = {Journal of molecular modeling}, number = {5}, publisher = {Springer}, address = {New York}, issn = {1610-2940}, doi = {10.1007/s00894-011-1207-0}, pages = {1877 -- 1883}, year = {2012}, abstract = {Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most important enzyme for the assimilation of carbon into biomass, features a well-known isotope effect with regards to the CO2 carbon atom. This kinetic isotope effect alpha = k (12)/k (13) for the carboxylation step of the RuBisCO reaction sequence, and its microscopic origin, was investigated with the help of cluster models and quantum chemical methods [B3LYP/6-31G(d,p)]. We use a recently proposed model for the RuBisCO active site, in which a water molecule remains close to the reaction center during carboxylation of ribulose-1,5-bisphosphate [B. Kannappan, J.E. Gready, J. Am. Chem. Soc. 130 (2008), 15063]. Alternative active-site models and/or computational approaches were also tested. An isotope effect alpha for carboxylation is found, which is reasonably close to the one measured for the overall reaction, and which originates from a simple frequency shift of the bending vibration of (CO2)-C-12 compared to (CO2)-C-13. The latter is the dominant mode for the product formation at the transition state.}, language = {en} } @article{KroenerGoetze2012, author = {Kr{\"o}ner, Dominik and G{\"o}tze, Jan Philipp}, title = {Modeling of a violaxanthin-chlorophyll b chromophore pair in its LHCII environment using CAM-B3LYP}, series = {Journal of photochemistry and photobiology : B, Biology}, volume = {109}, journal = {Journal of photochemistry and photobiology : B, Biology}, number = {2}, publisher = {Elsevier}, address = {Lausanne}, issn = {1011-1344}, doi = {10.1016/j.jphotobiol.2011.12.007}, pages = {12 -- 19}, year = {2012}, abstract = {Collecting energy for photosystem II is facilitated by several pigments, xanthophylls and chlorophylls, embedded in the light harvesting complex II (LHCII). One xanthophyll, violaxanthin (Vio), is loosely bound at a site close to a chlorophyll b (Chl). No final answer has yet been found for the role of this specific xanthophyll. We study the electronic structure of Vio in the presence of Chl and under the influence of the LHCII environment, represented by a point charge field (PCF). We compare the capability of the long range corrected density functional theory (DFT) functional CAM-B3LYP to B3LYP for the modeling of the UV/vis spectrum of the Vio + Chl pair. CAM-B3LYP was reported to allow for a very realistic reproduction of bond length alternation of linear polyenes, which has considerable impact on the carotenoid structure and spectrum. To account for the influence of the LHCII environment, the chromophore geometries are optimized using an ONIOM(DFT/6-31G(d):PM6) scheme. Our calculations show that the energies of the locally excited states are almost unaffected by the presence of the partner chromophore or the PCF. There are, however, indications for excitonic coupling of the Chl Soret band and Vio. We propose that Vio may accept energy from blue-light excited Chl.}, language = {en} } @article{SakurabaBalazadehTanakaetal.2012, author = {Sakuraba, Yasuhito and Balazadeh, Salma and Tanaka, Ryouichi and M{\"u}ller-R{\"o}ber, Bernd and Tanaka, Ayumi}, title = {Overproduction of Chl b retards senescence through transcriptional reprogramming in arabidopsis}, series = {Plant \& cell physiology}, volume = {53}, journal = {Plant \& cell physiology}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0032-0781}, doi = {10.1093/pcp/pcs006}, pages = {505 -- 517}, year = {2012}, abstract = {Leaf senescence is a developmentally and environmentally regulated process which includes global changes in gene expression. Using Arabidopsis as a model, we modified Chl arrangement in photosystems by overexpressing the catalytic domain (the C domain) of chlorophyllide a oxygenase (CAO) fused with the linker domain (the B domain) of CAO and green fluorescent protein (GFP). In these plants (referred to as the BCG plants for the B and C domains of CAO and GFP), the Chl a/b ratio was drastically decreased and Chl b was incorporated into core antenna complexes. The BCG plants exhibited a significant delay of both developmental and dark-induced leaf senescence. The photosynthetic apparatus, CO2 fixation enzymes and the chloroplast structure were lost in wild-type plants during senescence, while BCG plants retained them longer than the wild type. Large-scale quantitative real-time PCR analyses of 1,880 transcription factor (TF) genes showed that 241 TFs are differentially expressed between BCG plants and wild-type plants at senescence, similar to 40\% of which are known senescence-associated genes (SAGs). Expression profiling also revealed the down-regulation of a large number of additional non-TF SAGs. In contrast, genes involved in photosynthesis were up-regulated, while those encoding Chl degradation enzymes were down-regulated in BCG plants. These results demonstrate that alteration of pigment composition in the photosynthetic apparatus retards senescence through transcriptional reprogramming.}, language = {en} } @article{SpijkermanLukasWacker2017, author = {Spijkerman, Elly and Lukas, Marcus and Wacker, Alexander}, title = {Ecophysiological strategies for growth under varying light and organic carbon supply in two species of green microalgae differing in their motility}, series = {Phytochemistry : an international journal of plant biochemistry}, volume = {144}, journal = {Phytochemistry : an international journal of plant biochemistry}, publisher = {Elsevier}, address = {Oxford}, issn = {0031-9422}, doi = {10.1016/j.phytochem.2017.08.018}, pages = {43 -- 51}, year = {2017}, abstract = {Mixing events in stratified lakes result in microalgae being exposed to varying conditions in light and organic carbon concentrations. Stratified lakes consist of an upper illuminated strata and a lower, darker strata where organic carbon accumulates. Therefore, in this contribution we explore the importance of dissolved organic carbon for growth under various light intensities by measuring some ecophysiological adaptations in two green microalgae. We compared the non-motile Chlorella vulgaris with the flagellated Chlamydomonas acidophila under auto-, mixo-, and heterotrophic growth conditions. In both algae the maximum photosynthetic and growth rates were highest under mixotrophy, and both algae appeared inhibited in their phosphorus acquisition under heterotrophy. Heterotrophic conditions provoked the largest differences as C. vulgaris produced chlorophyll a in darkness and grew as well as in autotrophic conditions, whereas Chl. acidophila bleached and could not grow heterotrophically. Although the fatty acid composition of both phytoplankton species differed, both species reacted in a similar way to changes in their growth conditions, mainly by a decrease of C18:3n-3 and an increase of C18:1n-9 from auto- to heterotrophic conditions. The two contrasting responses within the group of green microalgae suggest that dissolved organic carbon has a high deterministic potential to explain the survival and behaviour of green algae in the deeper strata of lakes.}, language = {en} }