Photosynthesis Research (v.134, #1)

Molecular motors are multi-subunit complexes that are indispensable for accomplishing various tasks of the living cells. One such molecular motor is the FOF1 ATP synthase that synthesizes ATP at the expense of the membrane proton gradient. Elucidating the molecular origin of the motor function is challenging despite significant advances in various experimental fields. Currently atomic simulations of whole motor complexes cannot reach to functionally relevant time scales that extend beyond the millisecond regime. Moreover, to reveal the underlying molecular origin of the function, one must model the coupled chemical and conformational events using physically and chemically meaningful multiscaling techniques. In this review, we discuss our approach to model the action of the F1 and FO molecular motors, where emphasis is laid on elucidating the molecular origin of the driving force that leads to directional rotation at the expense of ATP hydrolysis or proton gradients. We have used atomic structures of the motors and used hierarchical multiscaling techniques to generate low dimensional functional free energy surfaces of the complete mechano-chemical process. These free energy surfaces were studied further to calculate important characteristics of the motors, such as, rotational torque, temporal dynamics, occurrence of intermittent dwell states, etc. We also studied the result of mutating various parts of the motor domains and our observations correspond very well with the experimental findings. Overall, our studies have generated a cumulative understanding of the motor action, and especially highlight the crucial role of electrostatics in establishing the mechano-chemical coupling.
Keywords: Bioenergetics; Multiscale computer simulation; ATP synthase; Rotational torque; Coarse grained model

Crassulacean acid metabolism (CAM) was demonstrated in four small endemic Australian terrestrial succulents from the genus Calandrinia (Montiaceae) viz. C. creethiae, C. pentavalvis, C. quadrivalvis and C. reticulata. CAM was substantiated by measurements of CO2 gas-exchange and nocturnal acidification. In all species, the expression of CAM was overwhelmingly facultative in that nocturnal H+ accumulation was greatest in droughted plants and zero, or close to zero, in plants that were well-watered, including plants that had been droughted and were subsequently rewatered, i.e. the inducible component was proven to be reversible. Gas-exchange measurements complemented the determinations of acidity. In all species, net CO2 uptake was restricted to the light in well-watered plants, and cessation of watering was followed by a progressive reduction of CO2 uptake in the light and a reduction in nocturnal CO2 efflux. In C. creethiae, C. pentavalvis and C. reticulata net CO2 assimilation was eventually observed in the dark, whereas in C. quadrivalvis nocturnal CO2 exchange approached the compensation point but did not transition to net CO2 gain. Following rewatering, all species returned to their original well-watered CO2 exchange pattern of net CO2 uptake restricted solely to the light. In addition to facultative CAM, C. quadrivalvis and C. reticulata exhibited an extremely small constitutive CAM component as demonstrated by the nocturnal accumulation in well-watered plants of small amounts of acidity and by the curved pattern of the nocturnal course of CO2 efflux. It is suggested that low-level CAM and facultative CAM are more common within the Australian succulent flora, and perhaps the world succulent flora, than has been previously assumed.
Keywords: Arid; Australian flora; Calandrinia ; Crassulacean acid metabolism (CAM); Montiaceae; Succulents

Leaf photosynthetic rate and mesophyll cell anatomy changes during ontogenesis in backcrossed indica × japonica rice inbred lines by Wenxing He; Shunsuke Adachi; Rowan F. Sage; Taiichiro Ookawa; Tadashi Hirasawa (27-38).
The high-yielding indica rice variety, ‘Takanari’, has the high rate of leaf photosynthesis compared with the commercial japonica varieties. Among backcrossed inbred lines from a cross between ‘Takanari’ and a japonica variety, ‘Koshihikari’, two lines, BTK-a and BTK-b, showed approximately 20% higher photosynthetic rate than that of ‘Takanari’ for a flag leaf at full heading. This is a highest recorded rate of rice leaf photosynthesis. Here, the timing and cause of the increased leaf photosynthesis in the BTK lines were investigated by examining the photosynthesis and related parameters, as well as mesophyll cell anatomy during ontogenesis. Their photosynthetic rate was greater than that of ‘Takanari’ in the 13th leaf, as well as the flag leaf, but there were no differences in the 7th and 10th leaves. There were no consistent differences in the stomatal conductance, or the leaf nitrogen and Rubisco contents in the 13th and flag leaves. The total surface area of mesophyll cells per leaf area (TAmes) in the 13th and flag leaves increased significantly in the BTK lines due to the increased number and developed lobes of mesophyll cells compared with in ‘Takanari’. The mesophyll conductance (g m) became greater in the BTK lines compared with ‘Takanari’ in the flag leaves but not in the 10th leaves. A close correlation was observed between TAmes and g m. We concluded that the increased mesophyll conductance through the development of mesophyll cells during the reproductive period is a probable cause of the greater photosynthetic rate in the BTK lines.
Keywords: Leaf nitrogen content; Leaf position; Mesophyll cell anatomy; Mesophyll conductance; Photosynthesis; Stomatal conductance

Concentration-based self-assembly of phycocyanin by Ido Eisenberg; Dvir Harris; Yael Levi-Kalisman; Shira Yochelis; Asaf Shemesh; Gili Ben-Nissan; Michal Sharon; Uri Raviv; Noam Adir; Nir Keren; Yossi Paltiel (39-49).
Cyanobacteria light-harvesting complexes can change their structure to cope with fluctuating environmental conditions. Studying in vivo structural changes is difficult owing to complexities imposed by the cellular environment. Mimicking this system in vitro is challenging, as well. The in vivo system is highly concentrated, and handling similar in vitro concentrated samples optically is difficult because of high absorption. In this research, we mapped the cyanobacteria antennas self-assembly pathways using highly concentrated solutions of phycocyanin (PC) that mimic the in vivo condition. PC was isolated from the thermophilic cyanobacterium Thermosynechococcus vulcanus and measured by several methods. PC has three oligomeric states: hexamer, trimer, and monomer. We showed that the oligomeric state was changed upon increase of PC solution concentration. This oligomerization mechanism may enable photosynthetic organisms to adapt their light-harvesting system to a wide range of environmental conditions.
Keywords: Phycocyanin; Oligomerization; TEM; SAXS; Native mass spectrometry

Pigment structure in the violaxanthin–chlorophyll-a-binding protein VCP by Manuel J. Llansola-Portoles; Radek Litvin; Cristian Ilioaia; Andrew A. Pascal; David Bina; Bruno Robert (51-58).
Resonance Raman spectroscopy was used to evaluate pigment-binding site properties in the violaxanthin–chlorophyll-a-binding protein (VCP) from Nannochloropsis oceanica. The pigments bound to this antenna protein are chlorophyll-a, violaxanthin, and vaucheriaxanthin. The molecular structures of bound Chl-a molecules are discussed with respect to those of the plant antenna proteins LHCII and CP29, the crystal structures of which are known. We show that three populations of carotenoid molecules are bound by VCP, each of which is in an all-trans configuration. We assign the lower-energy absorption transition of each of these as follows. One violaxanthin population absorbs at 485 nm, while the second population is red-shifted and absorbs at 503 nm. The vaucheriaxanthin population absorbs at 525 nm, a position red-shifted by 2138 cm−1 as compared to isolated vaucheriaxanthin in n-hexane. The red-shifted violaxanthin is slightly less planar than the blue-absorbing one, as observed for the two central luteins in LHCII, and we suggest that these violaxanthins occupy the two equivalent binding sites in VCP at the centre of the cross-brace. The presence of a highly red-shifted vaucheriaxanthin in VCP is reminiscent of the situation of FCP, in which (even more) highly red-shifted populations of fucoxanthin are present. Tuning carotenoids to absorb in the green-yellow region of the visible spectrum appears to be a common evolutionary response to competition with other photosynthetic species in the aquatic environment.
Keywords: Light-harvesting complex; VCP; Resonance Raman; Nannochloropsis oceanica ; Carotenoids

Water deficit is one of the key factors that limits the carbon (C) assimilation and productivity of plants. The effect of variable water deficit on recently root-derived bicarbonate assimilation in Camptotheca acuminate seedlings was investigated. Three-month-old seedlings were subjected to three water regimes, well-watered (WW), moderate stress (MS), and severe stress (SS) induced by polyethyleneglycol, in conjunction with relatively high (H) and low (L) natural 13C-abundance of NaHCO3-labeled treatments in hydroponics for 14 days. The δ13C of the newly expanded leaves in H were generally more enriched in heavy isotopes than were those in L, indicative of the involvement of bicarbonate in aboveground tissues. The C isotope fractionation of newly expanded leaves relative to air (∆13Cair-leaves) ranged from 17.78 to 21.78‰ among the treatments. The ∆13Cair-leaves under the MS and SS treatments in H were both more negative than was that in L. A linear regression between Ci/Ca and ∆13Cair-leaves in both L and H were different from the theoretical regression. On the basis of the two end-member mixing model, the proportion of fixed CO2 supplied from bicarbonate contributing to the total photosynthetically inorganic C assimilation were 10.34, 20.05 and 16.60% under the WW, MS, and SS treatments, respectively. These results indicated that the increase in water deficit decreased the atmospheric CO2 gain but triggered a compensatory use of bicarbonate in C. acuminate seedlings.
Keywords: Water deficit; Bicarbonate utilization; Carbon assimilation; Carbon isotope fractionation

Carbon use efficiencies and allocation strategies in Prochlorococcus marinus strain PCC 9511 during nitrogen-limited growth by Kristina Felcmanová; Martin Lukeš; Eva Kotabová; Evelyn Lawrenz; Kimberly H. Halsey; Ondřej Prášil (71-82).
We studied cell properties including carbon allocation dynamics in the globally abundant and important cyanobacterium Prochlorococcus marinus strain PCC 9511 grown at three different growth rates in nitrogen-limited continuous cultures. With increasing nitrogen limitation, cellular divinyl chlorophyll a and the functional absorption cross section of Photosystem II decreased, although maximal photosynthetic efficiency of PSII remained unaltered across all N-limited growth rates. Chl-specific gross and net carbon primary production were also invariant with nutrient-limited growth rate, but only 20% of Chl-specific gross carbon primary production was retained in the biomass across all growth rates. In nitrogen-replete cells, 60% of the assimilated carbon was incorporated into the protein pool while only 30% was incorporated into carbohydrates. As N limitation increased, new carbon became evenly distributed between these two pools. While many of these physiological traits are similar to those measured in other algae, there are also distinct differences, particularly the lower overall efficiency of carbon utilization. The latter provides new information needed for understanding and estimating primary production, particularly in the nutrient-limited tropical oceans where P. marinus dominates phytoplankton community composition.
Keywords: Prochlorococcus marinus ; Cyanobacteria; Primary production; Nitrogen limitation; Carbon allocation

Paul Henry Latimer (1925–2011): discoverer of selective scattering in photosynthetic systems by Margaret Gwyn Latimer; Thomas T. Bannister; Govindjee (83-91).
We provide here a brief tribute to Paul Henry Latimer (November 25, 1925 to October 1, 2011), a dedicated biological physicist, discoverer of selective scattering in biological systems, a wonderful teacher, husband, and father. We provide here a glimpse of his personal and professional life, including reminiscences from F. Dudley Bryant, Dan A. Cross, Bobby E. Pyle, Bryan L. Seiber, and Bruce A. Seiber.
Keywords: Light scattering; Selective scattering; Eugene Rabinowitch; Robert Emerson; Sieve effect; James Franck

The paths of Andrew A. Benson: a radio-autobiography by Arthur M. Nonomura; Barry Holtz; Karl Y. Biel; Robert Cooney; George Lorimer; Govindjee (93-105).
Andrew A. Benson, one of the greatest biochemists of our time, is celebrated on his centennial by the authors with whom he interacted performing experiments or contemplating metabolic pathways in a wide range of biological kingdoms. He charted the chemical flow of energy in cells, tissues, organs, plants, animals, and ecosystems. Benson collaborated with hundreds of colleagues to examine the natural history of autotrophy, mixotrophy, and heterotrophy while elucidating metabolic pathways. We present here a biological perspective of his body of studies. Benson lived from September 24, 1917, to January 16, 2015. Out of over 1000 autoradiograms he produced in his life, he left a legacy of 50 labeled autoradiograms to the authors who tell the story of his life’s work that resulted in Benson’s Protocol (Nonomura et al., Photosynth Res 127:369–378, 2016) that has been applied, over the years, for the elucidation of major metabolic pathways by many scientists.
Keywords: Carbon reactions of photosynthesis; Golden age of metabolic biology; Radioisotope