RNA and DNA binding properties of HIV-1 Vif protein: a fluorescence study

The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Some "non-permissive" cell lines cannot sustain replication of Vif(-) HIV-1 virions. In these cells, Vif counteracts the natural antiretroviral activity of the DNA-editing enzymes APOBEC3G/3F. Moreover, Vif is packaged into viral particles through a strong interaction with genomic RNA in viral nucleoprotein complexes. To gain insights into determinants of this binding process, we performed the first characterization of Vif/nucleic acid interactions using Vif intrinsic fluorescence. We determined the affinity of Vif for RNA fragments corresponding to various regions of the HIV-1 genome. Our results demonstrated preferential and moderately cooperative binding for RNAs corresponding to the 5'-untranslated region of HIV-1 (5'-untranslated region) and gag (cooperativity parameter omega approximately 65-80, and K(d) = 45-55 nM). In addition, fluorescence spectroscopy allowed us to point out the TAR apical loop and a short region in gag as primary strong affinity binding sites (K(d) = 9.5-14 nM). Interestingly, beside its RNA binding properties, the Vif protein can also bind the corresponding DNA oligonucleotides and their complementary counterparts with an affinity similar to the one observed for the RNA sequences, while other DNA sequences displayed reduced affinity. Taken together, our results suggest that Vif binding to RNA and DNA offers several non-exclusive ways to counteract APOBEC3G/3F factors, in addition to the well documented Vif-induced degradation by the proteasome and to the Vif-mediated repression of translation of these antiviral factors.     

An Interspecific Backcross of Lycopersicon Esculentum X L. Hirsutum: Linkage Analysis and a Qtl Study of Sexual Compatibility Factors and Floral Traits

A BC(1) population of the self-compatible tomato Lycopersicon esculentum and its wild self-incompatible relative L. hirsutum f. typicum was used for restriction fragment length polymorphism linkage analysis and quantitative trait loci (QTL) mapping of reproductive behavior and floral traits. The self-incompatibility locus, S, on chromosome 1 harbored the only QTL for self-incompatibility indicating that the transition to self-compatibility in the lineage leading to the cultivated tomato was primarily the result of mutations at the S locus. Moreover, the major QTL controlling unilateral incongruity also mapped to the S locus, supporting the hypothesis that self-incompatibility and unilateral incongruity are not independent mechanisms. The mating behavior of near-isogenic lines carrying the L. hirsutum allele for the S locus on chromosome 1 in an otherwise L. esculentum background support these conclusions. The S locus region of chromosome 1 also harbors most major QTL for several floral traits important to pollination biology (e.g., number and size of flowers), suggesting a gene complex controlling both genetic and morphological mechanisms of reproduction control. Similar associations in other flowering plants suggest that such complex may have been conserved since early periods of plant evolution or else reflect a convergent evolutionary process.     

The conversion of the corn/soybean ecosystem to no-till agriculture may result in a carbon sink

Mitigating or slowing an increase in atmospheric carbon dioxide concentration ([CO₂]) has been the focus of international efforts, most apparent with the development of the Kyoto Protocol. Sequestration of carbon (C) in agricultural soils is being advocated as a method to assist in meeting the demands of an international C credit system. The conversion of conventionally tilled agricultural lands to no till is widely accepted as having a large-scale sequestration potential. In this study, C flux measurements over a no-till corn/soybean agricultural ecosystem over 6 years were coupled with estimates of C release associated with agricultural practices to assess the net biome productivity (NBP) of this no-till ecosystem. Estimates of NBP were also calculated for the conventionally tilled corn/soybean ecosystem assuming net ecosystem exchange is C neutral. These measurements were scaled to the US as a whole to determine the sequestration potential of corn/soybean ecosystems, under current practices where 10% of agricultural land devoted to this ecosystem is no-tilled and under a hypothetical scenario where 100% of the land is not tilled. The estimates of this analysis show that current corn/soybean agriculture in the US releases ∼7.2 Tg C annually, with no-till sequestering ∼2.2 Tg and conventional-till releasing ∼9.4 Tg. The complete conversion of land area to no till might result in 21.7 Tg C sequestered annually, representing a net C flux difference of ∼29 Tg C. These results demonstrate that large-scale conversion to no-till practices, at least for the corn/soybean ecosystem, could potentially offset ca. 2% of annual US carbon emissions.     

Will photosynthesis of maize (Zea mays) in the US Corn Belt increase in future [CO2] rich atmospheres? An analysis of diurnal courses of CO2 uptake under free‐air concentration enrichment (FACE)

The C₄ grass Zea mays (maize or corn) is the third most important food crop globally in terms of production and demand is predicted to increase 45% from 1997 to 2020. However, the effects of rising [CO₂] upon C₄ plants, and Z. mays specifically, are not sufficiently understood to allow accurate predictions of future crop production. A rainfed, field experiment utilizing free‐air concentration enrichment (FACE) technology in the primary area of global corn production (US Corn Belt) was undertaken to determine the effects of elevated [CO₂] on corn. FACE technology allows experimental treatments to be imposed upon a complete soil–plant–atmosphere continuum with none of the effects of experimental enclosures on plant microclimate. Crop performance was compared at ambient [CO₂] (354 μ mol mol^?1) and the elevated [CO₂] (549 μmol mol^?1) predicted for 2050. Previous laboratory studies suggest that under favorable growing conditions C₄ photosynthesis is not typically enhanced by elevated [CO₂]. However, stomatal conductance and transpiration are decreased, which can indirectly increase photosynthesis in dry climates. Given the deep soils and relatively high rainfall of the US Corn Belt, it was predicted that photosynthesis would not be enhanced by elevated [CO₂]. The diurnal course of gas exchange of upper canopy leaves was measured in situ across the growing season of 2002. Contrary to the prediction, growth at elevated [CO₂] significantly increased leaf photosynthetic CO₂ uptake rate (A) by up to 41%, and 10% on average. Greater A was associated with greater intercellular [CO₂], lower stomatal conductance and lower transpiration. Summer rainfall during 2002 was very close to the 50‐year average for this site, indicating that the year was not atypical or a drought year. The results call for a reassessment of the established view that C₄ photosynthesis is insensitive to elevated [CO₂] under favorable growing conditions and that the production potential of corn in the US Corn Belt will not be affected by the global rise in [CO₂].     

Aminoglycoside binding to the HIV-1 RNA dimerization initiation site: thermodynamics and effect on the kissing-loop to duplex conversion

Owing to a striking, and most likely fortuitous, structural and sequence similarity with the bacterial 16 S ribosomal A site, the RNA kissing-loop complex formed by the HIV-1 genomic RNA dimerization initiation site (DIS) specifically binds 4,5-disubstituted 2-deoxystreptamine (2-DOS) aminoglycoside antibiotics. We used chemical probing, molecular modeling, isothermal titration calorimetry (ITC) and UV melting to investigate aminoglycoside binding to the DIS loop–loop complex. We showed that apramycin, an aminoglycoside containing a bicyclic moiety, also binds the DIS, but in a different way than 4,5-disubstituted 2-DOS aminoglycosides. The determination of thermodynamic parameters for various aminoglycosides revealed the role of the different rings in the drug–RNA interaction. Surprisingly, we found that the affinity of lividomycin and neomycin for the DIS (K_d ~ 30 nM) is significantly higher than that obtained in the same experimental conditions for their natural target, the bacterial A site (K_d ~ 1.6 µM). In good agreement with their respective affinity, aminoglycoside increase the melting temperature of the loop–loop interaction and also block the conversion from kissing-loop complex to extended duplex. Taken together, our data might be useful for selecting new molecules with improved specificity and affinity toward the HIV-1 DIS RNA.     

Physiology of the Rhizobium-legume association: I—The presence of bacterial DNA within the plant root

Summary Rhizobium deoxyribonucleic acid has been detected within Vicia faba root cells by in situ hybridization and autoradiography after exposure of root apexes to Rhizobium viable cells. Reannealed regions are localized into the cortex cells; the presence of bacterial DNA is specific for the root tissue; labelled regions were not detectable within apexes exposed to non-nodulating strains or to bacteria other than Rhizobium; Rhizobium DNA was not detectable in tissues of plants other than its leguminous host. re]19750313     

Luteibacter rhizovicinus MIMR1 promotes root development in barley (Hordeum vulgare L.) under laboratory conditions

In order to preserve environmental quality, alternative strategies to chemical-intensive agriculture are strongly needed. In this study, we characterized in vitro the potential plant growth promoting (PGP) properties of a gamma-proteobacterium, named MIMR1, originally isolated from apple shoots in micropropagation. The analysis of the 16S rRNA gene sequence allowed the taxonomic identification of MIMR1 as Luteibacter rhizovicinus. The PGP properties of MIMR1 were compared to Pseudomonas chlororaphis subsp. aurantiaca DSM 19603^T, which was selected as a reference PGP bacterium. By means of in vitro experiments, we showed that L. rhizovicinus MIMR1 and P. chlororaphis DSM 19603^T have the ability to produce molecules able to chelate ferric ions and solubilize monocalcium phosphate. On the contrary, both strains were apparently unable to solubilize tricalcium phosphate. Furthermore, the ability to produce 3-indol acetic acid by MIMR1 was approximately three times higher than that of DSM 19603^T. By using fluorescent recombinants of strains MIMR1 and DSM 19603^T, we also demonstrated that both bacteria are able to abundantly proliferate and colonize the barley rhizosphere, preferentially localizing on root tips and in the rhizoplane. Finally, we observed a negative effect of DSM 19603^T on barley seed germination and plant growth, whereas MIMR1, compared to the control, determined a significant increase of the weight of aerial part (+22 %), and the weight and length of roots (+53 and +32 %, respectively). The results obtained in this work make L. rhizovicinus MIMR1 a good candidate for possible use in the formulation of bio-fertilizers.