Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.     

Interaction between nitrogen and photon flux density in birch seedlings at steady-state nutrition

Birch ( Betula pendula Roth.) was investigated under steady-state nutrition and growth at different incident photon flux densities (PFD) and different relative addition rates of nitrogen. PFD had a strong influence on the relative growth rate at optimum nutrition and on the nitrogen productivity (growth rate per unit of nitrogen) but little effect on the formal relationships between nitrogen and growth, i.e. PFD and nitrogen nutrition are orthogonal growth factors. At a given suboptimum nitrogen (the same distance from optimum), increased PFD increased the relative growth rate and, therefore, the relative uptake rate and the required relative addition rate in accordance with the theoretical equality between these three parameters at steady-state nutrition. Correspondingly, at a given suboptimum relative addition rate, increased PFD decreased nitrogen status (larger distance from optimum) at an unchanged relative growth rate. Nutrient uptake rate, dry matter content, and partitioning of biomass and nutrients are strongly influenced by nitrogen status. PFD influences these characteristics, but only to an extent corresponding to its effect on the nitrogen status. The influence of PDF on the relative growth rate at optimum and on nitrogen productivity is well described by hyperbolic relationships, similar to reported PFD/photosynthesis relationships. These expressions for plant growth as well as the productivities of leaf area and quantum appear to be valuable characteristics of plant responses to light and nutrition. Although the calculated PFD/growth relationships indicate saturation at high values of PFD, a more realistic estimate of PFD at which saturation occurs is about 30 mol m⁻² day⁻¹, where the highest relative growth rate and nitrogen productivity were experimentally determined. No significant effect was observed because of day length differences between the present and previous experiments.     

Structure of heavy and light chain subunits of type A botulinum neurotoxin analyzed by circular dichroism and fluorescence measurements

Summary The secondary and tertiary structural features of botulinum neurotoxin (NT) serotype A, a dichain protein (M_r 145 000), and its two subunits, the heavy (H) and light (L) chains (M_r 97 000 and 53 000, respectively) were examined using circular dichroism and fluorescence spectorscopy. Nearly 70% of the amino acid residues in each of the three polypeptide preparations were found in ordered structure (sum of helix, sheet and turns). Also, the helix, sheet, turns and random coil contents of the dichain NT were nearly equal to the weighted mean of each of these secondary structure parameters of the L and H chains; e.g., sum of helix of L chain (22%) and H chain (18.7%), as weighted mean, 19.8% was similar to that of NT (20%). These agreements suggested that the secondary structures of the subunits of the dichain NT do not significantly change when they are separated as isolated L and H chains. Fluorescence emission maximum of L chain, 4 nm less (blue shift) than that of H chain, suggested relatively more hydrophobic environment of fluorescent tryptophan residue(s) of L chain. Tryptophan fluorescence quantum yields of L chain, H chain and the NT, 0.072, 0.174 and 0.197, respectively, suggested that a) an alteration in the micro-environment of the tryptophan residues was possibly caused by interactions of L and H chain subunits of the NT and b) quantum yields for L and H chains were altered when they are together as subunits of the NT. Possible implications of structural features of the L and H chains, their interactions and the molecular mechanism of action of botulinum NT are assessed.     

Photosynthetic properties of leaves of a yellow green mutant of wheat compared to its wild type

We investigated several photosynthetic parameters of a virescent mutant of durum wheat and of its wild-type. Electron transport rate to ferricyanide was the same in the two genotypes when expressed on leaf area basis while O₂ evolution of the leaf tissue in saturating light and CO₂ was slightly higher in the yellow genotype. RuBPCase was also slightly higher. Quantum yield per absorbed light was similar in the two genotypes. P700 and Cyt f were less concentrated in the mutant while PS II was only marginally lower. The light response curve of CO₂ assimilation indicated higher level of photosynthesis of the mutant in high light, which corresponded to a lower non-photochemical quenching compared to the wild-type. It is concluded that the reaction centres, cyt f and chlorophyll are not limiting factors of electron transport in wheat seedlings and that electron transport capacity is in excess with respect to that needed for driving photosynthesis. Since the differences in photosynthesis reflect differences in RuBPCase activity, it is suggested that this enzyme limits photosynthesis in wheat seedlings also at high light intensities.Abbreviations cyt f cytochrome f - chl chlorophyll - PS II photosystem II - Pn_max maximum photosynthesis - RuBCase Ribulose, 1-5,bisphosphate carboxylase     

Photoinhibition of holly (Ilex aquifolium) in the field during the winter

The distribution of holly ( Ilex aquifolium ) and its habitat preferences indicate a sensitivity to low temperature, particularly when exposed to high light. Experiments were conducted to determine whether photoinhibition of photosynthesis occurs in holly leaves in the field in United Kingdom during the winter. Photosynthetic efficiency was assessed in holly leaves that were exposed to or shaded from direct sunlight using measurements of photosynthetic oxygen evolution and chlorophyll fluorescence. Field measurements were conducted over 3 weeks during January and February. Correlation of the measurements of photosynthetic efficiency with weather conditions indicated that holly was suffering photoinhibition, particularly in leaves exposed to direct sunlight. Controlled environment studies demonstrated that exposure of leaves to low temperature and high light resulted in reductions in photosynthetic efficiency; however, leaves recovered rapidly when exposed to a higher temperature and reduced light level.     

Photosynthetic productivity of an immature maize crop: changes in quantum yield of CO2 assimilation, conversion efficiency and thylakoid proteins

Abstract. The effect of growth temperatures on quantum yield (φ) was examined for leaves at different stages of development within the immature canopies of two crops of field grown maize ( Zea mays cv. LG11) sown on 3 May and 20 June 1990. During the period of 23 to 49d after sowing, the crop sown on the 3 May experienced temperatures below 10°C on 19 occasions compared with only two for the crop sown on 20 June. A period of severe chilling at the end of May and the beginning of June was associated with a marked reduction in φ for all leaves in the early-sown crop. This chill-induced depression in φ was greater in recently emerged than more mature leaves in the canopy and was found to be accompanied by modifications in the polypeptide profiles of thylakoids isolated from the leaves. During the chilling period, decreases in some polypeptides, notably in the range of 41–42 and 20kDa apparent molecular size, and increases of polypeptides of c. 15–16kDa were observed compared with leaves developing at warmer temperatures in July. The efficiency of converting intercepted radiation into dry matter (conversion efficiency) was 42% lower in the early- than late-sown crop, but no significant relationship between conversion efficiency and quantum yield was found in either treatment.     

CO2 and water vapour exchange in four alpine herbs at two altitudes and under varying light and temperature conditions

CO₂ and water vapour exchange rates of four alpine herbs namely: Rheum emodi, R. moorcroftianum, Megacarpaea polyandra and Rumex nepalensis were studied under field conditions at 3600 m (natural habitat) and 550 m altitudes. The effect of light and temperature on CO₂ and water vapour exchange was studied in the plants grown at lower altitude. In R. moorcroftianum and R. nepalensis, the average photosynthesis rates were found to be about three times higher at 550 m as compared to that under their natural habitat. However, in M. polyandra, the CO₂ exchange rates were two times higher at 3600 m than at 550 m but in R. emodi, there were virtually no differences at the two altitudes. These results indicate the variations in the CO₂ exchange rates are species specific. The change in growth altitude does not affect this process uniformly.The transpiration rates in R. emodi and M. polyandra were found to be very high at 3600 m compared to 550 m and are attributed to overall higher stomatal conductance in plants of these species, grown at higher altitude. The mid-day closure of stomata and therefore, restriction of transpirational losses of water were observed in all the species at 550 m altitude. In addition to the effect of temperature and relative humidity, the data also indicate some endogenous rhythmic control of stomatal conductance.The temperature optima for photosynthesis was close to 30°C in M. polyandra and around 20°C in the rest of the three species. High temperature and high light intensity, as well as low temperature and high light intensity, adversely affect the net rate of photosynthesis in these species.Both light compensation point and dark respiration rate increased with increasing temperature.The effect of light was more prominent on photosynthesis than the effect of temperature, however, on transpiration the effect of temperature was more prominent than the effect of light intensity.No definite trends were found in stomatal conductance with respect to light and temperature. Generally, the stomatal conductance was highest at 20°C.The study reveals that all these species can easily be cultivated at relatively lower altitudes. However, proper agronomical methodology will need to be developed for better yields.     

A theoretical and experimental analysis of the qP and qN coefficients of chlorophyll fluorescence quenching and their relation to photochemical and nonphotochemical events

The initial (F₀), maximal (F_M) and steady-state (F_S) levels of chlorophyll fluorescence emitted by intact pea leaves exposed to various light intensities and environmental conditions, were measured with a modulated fluorescence technique and were analysed in the context of a theory for the energy fluxes within the photochemical apparatus of photosynthesis. The theoretically derived expressions of the fluorescence signals contain only three terms, X=J₂p_2F/(1–G), Y=T/(1–G) and V, where V is the relative variable fluorescence, J₂ is the light absorption flux in PS II, p_2F is the probability of fluorescence from PS II, G and T are, respectively, the probabilities for energy transfer between PS II units and for energy cycling between the reaction center and the chlorophyll pool: F₀=X, F_M=X/(1–Y) and F_S=X(1+(YV/(1–Y))). It is demonstrated that the amplitudes of the previously defined coefficients of chlorophyll fluorescence quenching, q_P and q_N, reflect, not just photochemical (q_P) or nonphotochemical (q_N) events as implied in the definitions, but both photochemical and nonphotochemical processes of PS II deactivation. The coefficient q_P is a measure of the ratio between the actual macroscopic quantum yield of photochemistry in PS II (41-1) in a given light state and its maximal value measured when all PS II traps are open (41-2) in that state, with 41-3 and 41-4. When the partial connection between PS II units is taken into consideration, 1-q_P is nonlinearily related to the fraction of closed reaction centers and is dependent on the rate constants of all (photochemical as well as nonphotochemical) exciton-consuming processes in PS II. On the other hand, 1-q_N equals the (normalized) ratio of the rate constant of photochemistry (k_2b) to the combined rate constant (k_N) of all the nonphotochemical deactivation processes excluding the rate constant k₂₂ of energy transfer between PS II units. It is demonstrated that additional (qualitative) information on the individual rate constants, k_N-k₂₂ and k_2b, is provided by the fluorescence ratios 1/F_M and (1/F₀)–(1/F_M), respectively. Although, in theory, 41-5 is determined by the value of both k_2b and k_N-k₂₂, experimental results presented in this paper show that, under various environmental conditions, 41-6 is modulated largely through changes in k _N, confirming the idea that PS II quantum efficiency is dynamically regulated in vivo by nonphotochemical energy dissipation.Abbreviations Chl chlorophyll - F₀, F_M and F_S initial, maximal and steady-state levels of modulated Chl fluorescence emitted by light-adapted leaves - PS I and II photosystem I and II - q_P and q_N (previously defined) photochemical and nonphotochemical components of Chl fluorescence quenching     

PHOTOSYNTHETIC QUANTUM EFFICIENCIES OF PHYTOPLANKTON FROM PERENNIALLY ICE COVERED ANTARCTIC LAKES1

A recently introduced approach far estimating the photosynthetic quantum efficiency (φ) of a freshwater or marine phytoplankton community has been applied for the first time to high latitude polar ecosystems, namely four lakes of southern Victoria Land, Antarctica. Values for φ at various depths ranged from 0.0022–0.1560 when calculated using a recommended mean extinction coefficient for phytoplankton (i.e. k?_c= 0.016). By contrast, φ ranged from 0.0037–0.0760 when calculated using an empirically estimated value for k?_c of 0.0328. If the recommended k?_c= 0.016 more closely approaches an accurate estimate, then the φ valves indicate that the phytoplankton convert light to organic carbon more efficiently than elsewhere. However, if the empirically derived k?_c= 0.0328 more closely approaches an accurate estimate, then the φ values indicate the phytoplankton trap light more efficiently than elsewhere. Although we have not resolved whether light conversion (φ) or light trapping are more efficient, the results show that the phytoplankton of these Antarctic lakes are well adapted to performing photosynthesis under extremely low light conditions.