The DNA deaminase activity of human APOBEC3G is required for Ty1, MusD, and human immunodeficiency virus type 1 restriction

Human APOBEC3G and several other APOBEC3 proteins have been shown to inhibit the replication of a variety of retrotransposons and retroviruses. All of these enzymes can deaminate cytosines within single-strand DNA, but the overall importance of this conserved activity in retroelement restriction has been questioned by reports of deaminase-independent mechanisms. Here, three distinct retroelements, a yeast retrotransposon, Ty1, a murine endogenous retrovirus, MusD, and a lentivirus, human immunodeficiency virus type 1 (HIV-1), were used to evaluate the relative contributions of deaminase-dependent and -independent mechanisms. Although human APOBEC3G can restrict the replication of all three of these retroelements, APOBEC3G lacking the catalytic glutamate (E259Q) was clearly defective. This phenotype was particularly clear in experiments with low levels of APOBEC3G expression. In contrast, purposeful overexpression of APOBEC3G-E259Q was able to cause modest to severe reductions in the replication of Ty1, MusD, and HIV-1(ΔVif). The importance of these observations was highlighted by data showing that CEM-SS T-cell lines expressing near-physiologic levels of APOBEC3G-E259Q failed to inhibit the replication of HIV-1(ΔVif), whereas similar levels of wild-type APOBEC3G fully suppressed virus infectivity. Despite the requirement for DNA deamination, uracil DNA glycosylase did not modulate APOBEC3G-dependent restriction of Ty1 or HIV-1(ΔVif), further supporting prior studies indicating that the major uracil excision repair system of cells is not involved. In conclusion, the absolute requirement for the catalytic glutamate of APOBEC3G in Ty1, MusD, and HIV-1 restriction strongly indicates that DNA cytosine deamination is an essential part of the mechanism.     

Kinetic parameters of nitrate uptake by different catch crop species: effects of low temperatures or previous nitrate starvation

The pollution of aquifers by NO^?₃ in temperate environments is aggravated by farming practices that leave the ground bare during winter. The use of catch crops during this time may decrease nitrate loss from the soil. Nitrate uptake by several catch crop species (Brassica napus L., Sinapis alba L., Brassica rapa L., Raphanus sativus L., Trifolium alexandrinum L., Trifolium incarnatum L., Phacelia tanacetifolia Benth., Lolium perenne L., Lolium multiflorum Lam. and Secale cereale L.) was here studied in relation to transpiration rate and low temperatures applied to the whole plant or to roots only. The Michaelis constant (K_m), maximum uptake rate (V_max), time of induction and contributions of inducible and constitutive mechanisms were estimated from measurements of NO^?₃ depletion in the uptake medium. There were large differences between species, with K_m (μM) values ranging between 5.12 ± 0.64 (Trifolium incarnatum) and 36.4 ± 1.97 (Lolium perenne). Maximum NO^?₃ uptake rates expressed per unit root weight were influenced by ageing, temperature and previous NO^?₃ nutrition. They were also closely correlated with water flow through the roots and with shoot/root ratio of these species. The combined results from all species and treatments showed that V_max increased with shoot/root ratio, suggesting a regulatory role for the shoots in NO^?₃ uptake. Overall, the results showed a great diversity in NO^?₃ uptake characteristics between species in terms of kinetic parameters, contribution of the constitutive system (100% of total uptake in ryegrass, nil in Fabaceae) and time of induction.     

Seasonal pattern of accumulation and effects of low temperatures on storage compounds in Trifolium repens

The seasonal pattern of concentrations of nitrogen, starch and vegetative storage protein (VSP) in stolons of Trifolium repens L. grown in the field were studied. Two different genotypes, cv. Aran and cv. Rivendel, differing in their morphology (stolon thickness and branching rate) but with similar growth rates, were used. Maximum concentrations of starch were found in summer whereas hydrolysis of starch took place throughout winter, suggesting that C storage is more important for winter survival than for promotion of early spring growth. On the other hand, VSP and nitrogen accumulated in autumn and early winter and then decreased when growth was resumed during early spring. For both cultivars, an inverse relationship was found between VSP concentration in stolons and mean air temperature, suggesting that VSP accumulation may be triggered by low temperature. Further experiments with plants grown under different regimes of temperature and daylength, suggested that VSP synthesis is stimulated by low root temperatures, with a slight synergistic effect of short daylength.
The effects of root temperature on growth, N₂ fixation, NH₄⁺ uptake and N allocation within Trifolium repens L., were studied under controlled conditions. The shoot growth rate was greatly reduced when root temperatures were lowered from 12 to 6°C, while the rate of stolon growth was less affected. Low root temperatures inhibited N2 fixation more than it did NH₄⁺ uptake, but the relative allocation of N to stolons was increased. Lowering root temperature also increased the accumulation of VSP in stolons. These results are discussed in terms of the mechanism associated with low temperature stimulation of VSP accumulation and its coupling with changes in the source/sink relations for allocation of N, between growth and storage.     

Changes in NO3− and K+ uptake by four species in flowing solution culture in response to increased irradiance

Net rates of NO₃^? and K⁺ uptake were compared for oilseed rape (Brassica napus L. cv. Jet neuf), perennial ryegrass (Lolium perenne L. cv. S23), Italian ryegrass (Lolium multiflorum Lam. cv. Augusta) and wheat (Triticum aestivum L. cv. Fen-man) in flowing solution culture during a 4-day sequence of low-low-high-high natural irradiance. Concentrations of NO₃^? (10 μM) and K⁺ (2.5 μM) in solutions were maintained automatically and hourly variation in net uptake of these ions was measured. During the 2 days of low irradiance (<1 MJ m^?2 day^?1) the uptake rates of both ions by all species were low at <1 mmol NO₃^?, m^?2 h^?1 and <0.4 mmol K⁺ m^?2 h^?1. Uptake increased in each species during the first day of high irradiance (7.90 MJ m^?2 day^?1) to >4 mmol NO₃^? m^?2 h^?1 and >1.4 mmol K⁺ m^?1 h^?1. These higher rates were maintained throughout the following night. The lag-time between maximum irradiance and the onset of the highest acceleration in uptake was greater for NO₃^? (5–8 h) than for K⁺ (≤1 h) in rape, wheat and Italian ryegrass. Uptake of NO₃^?, by perennial ryegrass showed an almost constant acceleration for 18 h following maximum irradiance. In all species the measured maximum inflows (uptake rate per unit root length) of both ions were greater than theoretical maximum potential inflows to a non-competing infinite-sink root in soil, by factors of 7 and 36, respectively, for NO₃^? and K⁺, averaged over all species.     

Morphological compatibility of white clover and perennial ryegrass cultivars grown under two nitrate levels in flowing solution culture

The effects of nitrate (NO3-) supply on shoot morphology, vertical distribution of shoot and root biomass and total nitrogen (N) acquisition by two perennial ryegrass (Lolium perenne L.) cultivars (AberElan and Preference) and two white clover (Trifolium repens L.) cultivars (Grasslands Huia and AberHerald) were studied in flowing nutrient culture. Cultivars were grown from seed as monocultures and the clovers inoculated with Rhizobium. The 6-week measurement period began on day 34 (grasses) and day 56 (clovers) when the NO3- supply was adjusted to either 2 mmol m-3 (low nitrogen, LN) or 50 mmol m-3 (high nitrogen, HN). These treatments were subsequently maintained automatically. Plants were harvested at intervals to measure their morphology and N content. Cultivars of both species differed significantly in several aspects of their response to NO3- supply. In the grasses, the LN treatment increased the root : shoot ratio of AberElan but did not affect the distribution of root length in the root profile. In contrast, this treatment changed the root distribution of Preference compared with HN, resulting in a larger proportion of root length being distributed further down the root profile. The morphology of white clover Grasslands Huia was for the most part unaffected by the level of NO3- supply. In contrast, AberHerald exhibited different growth strategies, with LN plants increasing their stolon weight per unit length at the expense of leaf production, leaf area and stolon length, whereas HN plants showed reduced stolon thickness, greater leaf area production and stolon length per plant. Cultivars with different morphological/physiological strategies in response to NO3- supply may be of value in the construction of 'compatible mixtures' aimed at reducing oscillations in sward clover content by extending the range of conditions that allow balanced coexistence of species to occur.     

Short-term changes in xylem N compounds in Lolium perenne following defoliation

Previous studies have indicated that an increased asparagine to glutamine ratio (Asn : Gln) occurs in the xylem fluid of Lolium perenne 24 h after defoliation. However, the absolute changes in Asn and Gln leading to the increased Asn : Gln ratio are unknown. The present study tested the hypotheses that: (1) defoliation-induced changes in xylem amino acid composition occur in L perenne within the first 24 h following defoliation, irrespective of phasing with respect to the diurnal light/dark cycle; and (2) the increase in Asn : Gln ratio in the xylem fluid of L perenne following defoliation is due to an increase in Asn content. Plants of L perenne L. 'Aurora' were grown in flowing solution culture for 40 d. Plants were then either left intact, defoliated at the end of the light period or defoliated at the end of the dark period. 15N-labelled NO3- was supplied following defoliation to discriminate between the recovery of N absorbed prior to, and following, defoliation. Xylem samples were collected over the subsequent 24 h period with amino acids speciated by GC-MS. There was support for the first hypothesis: increased Asn : Gln ratios occurred within the first 24 h, irrespective of the phasing of defoliation with respect to light/dark cycles. The second hypothesis was not supported: the concentration of all amino acids in the xylem exudate declined after defoliation, and the increased Asn : Gln ratio was accounted for by a disproportionately large reduction in Gln levels. Low concentrations of amino acids in the xylem of defoliated plants precluded accurate discrimination of their nitrogen content into pre- and post-defoliation sources.     

Inhibition of N2 fixation by white clover (Trifolium repens L.) at low concentrations of NO inf3 sup− in flowing solution culture

The impact of sustained low external concentrations of NO ₃ ^– (0, 10, 100 and 1000 mmol m^–3) on plant growth and the relative acquisition of N through N₂ fixation and NO ₃ ^– uptake by established, nodulated white clover (Trifolium repens L. cv. Blanca) was studied over 28 days in flowing solution culture. Nitrogen fixation was measured by N difference and ¹⁵N dilution methods. Plants supplied with NO ₃ ^– achieved higher relative growth rates (% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGabmiEayaara% aaaa!3702!\[\bar x\]=0.091 d^–1) compared with control plants dependent on N₂ fixation (0.073 d^–1). Nitrate plants showed progressive increases in shoot: root d.w. ratios from 4 to 6.5–7.6 between days 0–28, compared with 5.1 on day 28 for control plants. Increases in both nodule d.w. and numbers per plant were inhibited after day seven at all concentrations of NO ₃ ^– . The severity of inhibition of N₂ fixation increased with increasing NO ₃ ^– concentration and with time. The total amounts of N₂ fixed per plant between days 0–7 after supplying 10, 100 and 1000 mmol m^–3 NO ₃ ^– , respectively, were 37–39, 28–30 and 0–13%, of the total N acquired. Between days 7–28 the proportional contributions of N₂ fixation to total N acquisition declined to 3, 0.5 and 0%, respectively, in these treatments. The corresponding mean specific rates of N₂ fixation between days 0–7 were, respectively, 5.4, 3.2, and 2.0 mmol N d^–1 g^–1 nodule d.w., compared with 7.9 mmol N d^–1 g^–1 nodule d.w. for zero NO ₃ ^– plants. There was no evidence of a transitory increase in N₂ fixation following the addition of NO ₃ ^– , even at the lowest supply concentration.     

Diurnal variation in the simultaneous uptake and 'sink' allocation of NH4+ and NO3- by Lolium perenne in flowing solution culture

Perennial ryegrass (Lolium perenne L.) was grown in flowingsolution culture under artificial illumination with a 10 h lightperiod. The diurnal fluctuations in the net uptake of and from a 20 mmol m^–3 NH₄NO₃ supply were measured (i) fromthe amounts of these ions supplied automatically to maintainconcentrations in solution, and (ii) by ¹⁵N pulse-labellingthroughout the diurnal cycle. Diurnal variation in leaf extension,translocation and allocation of assimilated C (¹⁴CO₂ pulse-labelling)and N (¹⁵N pulse and steadystate labelling) were also followed.The apparent ‘sinkstrength’ of different organsfor recently assimilated C and N was calculated from the concentrationof label recovered in the tissues. Ammonium and showed qualitatively similar diurnal patterns ofnet uptake, with minimum and maximum rates, respectively, atthe start and end of the photoperiod; but uptake showed a proportionately steeper declineduring the dark period. This trend was mirrored by the decreasein translocation of N from roots to shoots during the dark,concurrent with an increase in the relative allocation of -N to expanding leaves and young tillers,and in -N to older expanded leaves. Overall the apparent ‘sink-strength’ ofexpanding leaves for N declined during the dark period. Pulse-chasesof ¹⁴CO₂ fed to the youngest fully expanded leaf at the startand end of the photoperiod showed that translocation of ¹⁴Cto the roots continued throughout the dark period, but thatthe apparent rate was halved after 9 h of darkness. The resultswere interpreted as contrary to the ‘carbohydrate supplylimitation’ hypothesis for the dark-related decline inN uptake, but compatible with regulation by ‘sink-strength’for N. Key words: Nitrate, ammonium, diurnal variation, perennial ryegrass, translocation     

Effects of temperature on parameters of root growth relevant to nutrient uptake: Measurements on oilseed rape and barley grown in flowing nutrient solution

Summary Effects of root temperature on the growth and morphology of roots were measured in oilseed rape (Brassica napus L.) and barley (Hordeum vulgare L.). Plants were grown in flowing solution culture and acclimatized over several weeks to a root temperature of 5°C prior to treatment at a range of root temperatures between 3 and 25°C, with common shoot temperature. Root temperature affected root extension, mean radius, root surface area, numbers and lengths of root hairs. Total root length of rape plants increased with temperature over the range 3–9°C, but was constant at higher temperatures. Root length of barley increased with temperature in the range 3–25°C, by a factor of 27 after 20 days. Root radii had a lognormal distribution and their means decreased with increasing temperature from 0.14 mm at 3°C to 0.08 mm at 25°C. The density of root hairs on the root surface increased by a factor of 4 in rape between 3 and 25°C, but in barley the highest density was at 9°C. The contribution of root hairs to total root surface area was relatively greater in rape than in barley. The changes in root system morphology may be interpreted as adaptive responses to temperature stress on nutrient uptake, providing greater surface area for absorption per unit root weight or length.