The role of a long-wavelength pigment form in the chlorophyll biosynthesis

Photoconversion of protochlorophyllide₆₅₀ form was observed in etiolated leaves illuminated with long-wavelength—690 nm—light. This process showed Shibata shift and was found to have a strong temperature dependence between 20 and –40°C. The low rate of reaction, the strong temperature dependence and calculations on the spectral overlap integral of absorption and fluorescence bands in this spectral region indicate that the phototransformation of the 650 nm form of protochlorophyllide may be caused by a back energy migration from a long-wavelength pigment form absorbing around 690 nm; this pigment form is probably a long-wavelength form of protochlorophyll/ide.     

How catalase recognizes H2O2 in a sea of water

Monofunctional heme‐catalases have been studied for many decades but there is still an incomplete understanding of why such a large tetrameric protein with deeply buried active sites is required to accomplish such a simple reaction as H₂O₂ dismutation. Catalase accomplishes this reaction at a high rate although water at 55 M is expected to compete with H₂O₂ for the enzyme's active site. Using molecular dynamics simulations we addressed the question as to how catalase selects H₂O₂ in water. Selection is accomplished through different mechanisms: higher residence time of H₂O₂ in the vicinity of certain prevalent amino acid residues at the protein surface and substrate channel, coordinated motion of the main passage amino acids that is increased in the presence of H₂O₂, a gate valve mechanism consisting of the motion of two contiguous phenylalanine residues that drive water molecules out of the final section of the substrate channel, a hydrophobic barrier before the active site that was crossed more easily by H₂O₂ which kept most of its hydrogen bonds while passing, and finally an increased residence time for H₂O₂ at the active site. These mechanisms, based on the physicochemical differences between H₂O₂ and water, provide an explanation as to why such a large tetrameric protein with deeply buried active sites is required to accomplish efficient H₂O₂ dismutation. Proteins 2014; 82:45–56. © 2013 Wiley Periodicals, Inc.     

Drought can be more critical in the shade than in the sun: a field study of carbon gain and photo-inhibition in a Californian shrub during a dry El Niño year

Diurnal courses of leaf water potential (Ψ_l), gas exchange and chlorophyll fluorescence were measured in natural sun and shade populations of Heteromeles arbutifolia throughout the seasons of an unusually dry El Niño year in Central California. The onset of drought resulted in decreased stomatal conductance and net photosynthesis in both sun and shade plants. However, the decline in Ψ_l was much greater and carbon gain was much more strongly limited by the development of drought stress in the shade than in the sun. Photorespiratory energy dissipation was significantly higher in the sun than in the shade in spring and autumn, but not during the summer. Pre‐dawn photochemical efficiency (F_v/F_m) was significantly higher in the shade than in the sun during the spring but the differences disappeared during the summer and autumn. The strong irradiance in the open field site studied led to a chronic but only mild reduction in F_v/F_m, with values around 0·79. Summer sunflecks led to a sustained photo‐inhibition in shade plants, which exhibited a significant reduction in pre‐dawn F_v/F_m of 10% with the onset of drought. Photo‐inhibition became relatively more important for carbon gain in the shade than in the sun due to the low photochemical efficiency under the low light that follows sunflecks. Sun plants of H. arbutifolia exhibited a rather efficient photoprotection against strong irradiance conferred by both the architecture of the crown and the physiology of the leaves. There is evidence that El Niño events and the associated droughts have become more frequent and severe. Counter‐intuitively, the effects on plant performance of such extreme droughts could be more critical in the shade than in the sun.     

Observation of a unique pattern of bifurcated hydrogen bonds in the crystal structures of the N-glycoprotein linkage region models

Elucidation of the intra- and intermolecular carbohydrate-protein interactions would greatly contribute toward obtaining a better understanding of the structure-function correlations of the protein-linked glycans. The weak interactions involving C-H...O have recently been attracting immense attention in the domain of biomolecular recognition. However, there has been no report so far on the occurrence of C-H...O hydrogen bonds in the crystal structures of models and analogs of N-glycoproteins. We present herein an analysis of C-H...O interactions in the crystal structures of all N-glycoprotein linkage region models and analogs. The study reveals a cooperative network of bifurcated hydrogen bonds consisting of N-H...O and C-H...O interactions seen uniquely for the models. The cooperative network consists of two antiparallel chains of bifurcated hydrogen bonds, one involving N1-H, C2'-H and O1' of the aglycon moiety and the other involving N2-H, C1-H and O1' of the sugar. Such bifurcated hydrogen bonds between the core glycan and protein are likely to play an important role in the folding and stabilization of proteins.     

Probing the role of interfacial waters in protein–DNA recognition using a hybrid implicit/explicit solvation model

When proteins bind to their DNA target sites, ordered water molecules are often present at the protein–DNA interface bridging protein and DNA through hydrogen bonds. What is the role of these ordered interfacial waters? Are they important determinants of the specificity of DNA sequence recognition, or do they act in binding in a primarily nonspecific manner, by improving packing of the interface, shielding unfavorable electrostatic interactions, and solvating unsatisfied polar groups that are inaccessible to bulk solvent? When modeling details of structure and binding preferences, can fully implicit solvent models be fruitfully applied to protein–DNA interfaces, or must the individualistic properties of these interfacial waters be accounted for? To address these questions, we have developed a hybrid implicit/explicit solvation model that specifically accounts for the locations and orientations of small numbers of DNA‐bound water molecules, while treating the majority of the solvent implicitly. Comparing the performance of this model with that of its fully implicit counterpart, we find that explicit treatment of interfacial waters results in a modest but significant improvement in protein side‐chain placement and DNA sequence recovery. Base‐by‐base comparison of the performance of the two models highlights DNA sequence positions whose recognition may be dependent on interfacial water. Our study offers large‐scale statistical evidence for the role of ordered water for protein–DNA recognition, together with detailed examination of several well‐characterized systems. In addition, our approach provides a template for modeling explicit water molecules at interfaces that should be extensible to other systems. Proteins 2013; 81:1318–1329. © 2013 Wiley Periodicals, Inc.     

Evapotranspiration at the land/water interface in a semi-arid drainage basin

1. Evapotranspiration (ET) is a major source of water depletion from riverine systems in arid and semiarid climates. Water budgets have produced estimates of total depletions from riparian vegetation ET for a 320‐km reach of the Middle Rio Grande, New Mexico, U.S.A., that have ranged from 20 to 50% of total depletions from the river. 2. Tower‐based micrometeorological measurements of riparian zone ET throughout the growing season using three‐dimensional eddy covariance provided high quality estimates of ET at the stand scale. 3. A dense stand of salt cedar (111–122 cm year^–1) and a mature cottonwood (Populus deltoides ssp. wislizenia Eckenwelder) stand with an extensive understory of salt cedar (Tamaria ramosissima Ledeb) and Russian olive (Eleagnus angustifolia L.) (123 cm year^–1) had the highest rates of annual ET. A mature cottonwood stand with a closed canopy had intermediate rates of ET (98 cm year^–1). A less dense salt cedar stand had the lowest rates of ET (74–76 cm year^–1). 4. Summer leaf area index (LAI) measurements within the four stands were positively correlated with daily ET rates. LAI measurements throughout the growing season coupled to riparian vegetation classification is a promising method for improving riverine corridor estimates of total annual riparian zone ET along a reach of river. 5. Combining recent estimates of the extent of riparian vegetation along the 320 km length of the Middle Rio Grande, from Landsat 7 imagery with annual growing season measurements of ET at the four riparian stands yields a first‐order riverine corridor estimate of total riparian zone ET of 150–250 × 10⁶ m³ year^–1. This is approximately 20–33% of total estimated depletions along this reach of river.     

Identification and characterization of photosystem II chlorophyll a/b binding proteins in Marchantia polymorpha L.

The minor chlorophyll a/b-binding (CAB) proteins of the liverwort Marchantia polymorpha L. were investigated in order to compare the antenna organization and the light-acclimation potential in lower and higher plants. Homologues to the minor CAB proteins CP24, CP26 and CP29 were identified by the following criteria: enrichment in photosystem II preparations, immunological cross-reactivities, spectroscopic properties and protein-fragment amino acid sequences. The high violaxanthin content of the minor CAB proteins in M. polymorpha indicates that their role in protection from high light is comparable in lower and higher plants. Considerably more-alkaline isoelectric points are found for the minor CAB proteins of M. polymorpha than for their higher-plant counterparts. This might be due to a higher content of basic amino acids. While the N-terminal sequence of angiosperm CP29 contains a threonine that becomes phosphorylated during cold stress, this amino acid is substituted by valine in M. polymorpha. Therefore, the regulatory properties of this protein could differ in lower and higher plants. Received: 25 March 1997 / Accepted: 21 July 1997     

Photosynthetic activity of far-red light in green plants

We have found that long-wavelength quanta up to 780 nm support oxygen evolution from the leaves of sunflower and bean. The far-red light excitations are supporting the photochemical activity of photosystem II, as is indicated by the increased chlorophyll fluorescence in response to the reduction of the photosystem II primary electron acceptor, Q_A. The results also demonstrate that the far-red photosystem II excitations are susceptible to non-photochemical quenching, although less than the red excitations. Uphill activation energies of 9.8 ± 0.5 kJ mol⁻¹ and 12.5 ± 0.7 kJ mol⁻¹ have been revealed in sunflower leaves for the 716 and 740 nm illumination, respectively, from the temperature dependencies of quantum yields, comparable to the corresponding energy gaps of 8.8 and 14.3 kJ mol⁻¹ between the 716 and 680 nm, and the 740 and 680 nm light quanta. Similarly, the non-photochemical quenching of far-red excitations is facilitated by temperature confirming thermal activation of the far-red quanta to the photosystem II core. The observations are discussed in terms of as yet undisclosed far-red forms of chlorophyll in the photosystem II antenna, reversed (uphill) spill-over of excitation from photosystem I antenna to the photosystem II antenna, as well as absorption from thermally populated vibrational sub-levels of photosystem II chlorophylls in the ground electronic state. From these three interpretations, our analysis favours the first one, i.e., the presence in intact plant leaves of a small number of far-red chlorophylls of photosystem II. Based on analogy with the well-known far-red spectral forms in photosystem I, it is likely that some kind of strongly coupled chlorophyll dimers/aggregates are involved. The similarity of the result for sunflower and bean proves that both the extreme long-wavelength oxygen evolution and the local quantum yield maximum are general properties of the plants.     

Cloning and expression of a gene coding for the major light-harvesting chlorophyll a/b protein of photosystem II in the green alga <Emphasis Type="Italic">Dunaliella salina</Emphasis>

Genes encoding proteins of the major light-harvesting complex of photosystem II (LHCII) in higher plants are well studied. However, little is known about the corresponding genes in the green alga Dunaliella salina, although this knowledge might provide valuable information about the respective roles of each LHCII protein at the molecular level under extreme environmental conditions. Here, we describe an additional LhcII gene from D. salina. An LhcII cDNA cloned by screening a D. salina cDNA library contains an open reading frame encoding a protein of 261 amino acids with a calculated molecular mass of 27.8 kDa. The deduced amino acid sequence shows high homology with other LHCII proteins. Genomic DNA—obtained by PCR using a specific primer set corresponding to the 5′ and 3′ untranslated regions—was used to determine the intron-exon structure. Short-term changes in mRNA levels after a shift from low-light to high-light or dark conditions were analyzed by real-time quantitative PCR, and indicated that this gene expresses different mRNA levels under different light conditions.     

Effects of root herbivory by an insect on a foliar-feeding species,mediated through changes in the host plant

Summary The effects of root herbivory by larvae of the scarabaeid, Phyllopertha horticola, on the growth of Capsella bursa-pastoris were examined. Individuals of Aphis fabae were reared on the leaves to determine what effect, if any, root feeding has on the performance of this insect. The experiment was conducted under two watering regimes (low and high). Low watering and root feeding caused water stress in the plants and this was reflected in a reduction in vegetative biomass and an increase in the proportion of material allocated to reproduction. Supplying plants with ample water in the high treatment enabled the water stress caused by root herbivory to be offset, but not completely overcome. Low watering and root feeding caused an increase in aphid weight and growth rate, while root feeding also increased fecundity and adult longevity. These effects are attributed to an improvement in food quality, measured by total soluble nitrogen, and caused by amino acid mobilization due to the water stress. The implications of these results in agricultural and ecological situations are discussed.     

Permanent phenotypic and genotypic changes of prostate cancer cells cultured in a three-dimensional rotating-wall vessel

A three-dimensional (3D) integrated rotating-wall vessel cell-culture system was used to evaluate the interaction between a human prostate cancer cell line, LNCaP, and microcarrier beads alone, or microcarrier beads previously seeded with either prostate or bone stromal cells. Upon coculture of LNCaP cells with microcarrier beads either in the presence or in the absence of prostate or bone stromal cells, 3D prostate organoids were formed with the expected hormonal responsiveness to androgen, increased cell growth, and prostate-specific antigen production. In this communication, we define permanent phenotypic and genotypic changes of LNCaP cells upon coculture with microcarrier beads alone, or with microcarrier beads previously seeded with either prostate or bone stromal cells. Most notably, we observed selective genetic changes, i.e., chromosomal losses or gains, as evaluated by both conventional cytogenetic and comparative genomic hybridization, in LNCaP sublines derived from the prostate organoids. Moreover, the derivative LNCaP cells appear to have altered growth profiles, and exhibit permanent and stable changes in response to androgen, estrogen, and growth factors. The derivative LNCaP sublines showed increased anchorage-independent growth rate, and enhanced tumorigenicity and metastatic potential when inoculated orthotopically in castrated athymic mice. Our results support the hypothesis that further nonrandom genetic and phenotypic changes in prostate cancer epithelial cells can occur through an event that resembles "adaptive mutation" such as has been described in bacteria subjected to nutritional starvation. The occurrence of such permanent changes may be highly contact dependent, and appears to be driven by specific microenvironmental factors surrounding the tumor cell epithelium grown as 3D prostate organoids.     

Tuning electron transfer by ester-group of chlorophylls in bacterial photosynthetic reaction center

Accessory chlorophylls (B(A/B)) in bacterial photosynthetic reaction center play a key role in charge-separation. Although light-exposed and dark-adapted bRC crystal structures are virtually identical, the calculated B(A) redox potentials for one-electron reduction differ. This can be traced back to different orientations of the B(A) ester-group. This tuning ability of chlorophyll redox potentials modulates the electron transfer from SP* to B(A).     

Impact of the green tea ingredient epigallocatechin gallate and a short pentapeptide (Ile-Ile-Ala-Glu-Lys) on the structural organization of mixed micelles and the related uptake of cholesterol

Background

High levels of blood cholesterol are conventionally linked to an increased risk of developing cardiovascular disease (Grundy, 1986). Here we examine the molecular mode of action of natural products with known cholesterol-lowering activity, such as for example the green tea ingredient epigallocatechin gallate and a short pentapeptide, Ile-Ile-Ala-Glu-Lys.

Analysis of the transformation effect in cytochrome b559 of photosystem II in terms of the model of the heme-quinone redox interaction

Transformation of three-component redox pattern of cytochrome (Cyt) b559 in PS II membrane fragments upon various treatments is manifested in decrease of the relative content (R) of the high potential (HP) redox form of Cyt b559 and concomitant increase in the fractions of the two lower potential forms. Redox titration of Cyt b559 in different types of PS II membrane preparations was performed and revealed that (1) alteration of redox titration curve of Cyt b559 upon treatment of a sample is not specific to the type of treatment; (2) each value of R_HP defines the individual shape of the redox titration curve; (3) population of Cyt b559 may exist in several stable forms with multicomponent redox pattern: three types of three-component redox pattern and one type of two-component redox pattern as well as in the form with a single E_m; (4) transformation of Cyt b559 proceeds as successive conversion between the stable forms with multicomponent redox pattern; (5) upon harsh treatments, Cyt b559 abruptly converts into the state with a single E_m which value is intermediate between the E_m values of the two lower potential forms. Analysis of the data using the model of Cyt b559-quinone redox interaction revealed that diminution of R_HP in a range from 80 to 10% reflects a shift in redox equilibrium between the heme group of Cyt b559 and the interacting quinone, due to a gradual decrease of 90?mV in E_m of the heme group at the virtually unchanged E_m of the quinone component.     

UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion

A non-protein-coding RNA, UCA1, has been cloned from human bladder TCC cell line BLZ-211 by using 5' and 3' RACE. The UCA1 full-length cDNA was 1442 bp. RT-PCR analysis indicated that UCA1 is an embryonic development and bladder cancer-associated RNA. The proliferative, migrative, invasive, and drug resistance behaviors of human bladder TCC cell line BLS-211 were enhanced by exogenous UCA1 expression in vitro. Several potential target genes of UCA1 were identified through microarray analysis. Moreover, the expression of UCA1 also increased tumorigenic potential of BLS-211 cells in nude mice. Results from the present study suggested that UCA1 might play a pivotal role in bladder cancer progression and embryonic development.     

Excess iron-induced changes in the photosynthetic characteristics of sweet potato

Iron (Fe) is an essential nutrient for plant growth and development. In plant tissues, approximately 80% of Fe is found in photosynthetic cells. This study was carried out to determine the effect of different iron concentrations on the photosynthetic characteristics of sweet potato plants. The fluorescence transient of chlorophyll a (OJIP), chlorophyll index and gas exchange were measured in plants grown for seven days in Hoagland solution containing an iron concentration of 0.45, 0.90, 4.50 or 9.00 mM Fe (as Fe-EDTA). The initial and maximum fluorescence increased in the plants receiving 9.00 mM Fe. In the analysis of the fluorescence kinetic difference, L- and K-bands appeared in all of the treatments, but the amplitude was higher in plants receiving 4.50 or 9.00 mM Fe. In plants grown in 9.00 mM Fe, the parameters of the JIP-Test indicated a better efficiency in the capture, absorption and use of light energy, and although the chlorophyll index was higher, the net photosynthesis was lower. The overall data showed that sweet potato plants subjected to high iron concentrations may not exhibit the toxicity symptoms, but the light reactions of photosynthesis can be affect, which may result in a declining net assimilation rate.