Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.info:eu-repo/semantics/publishedVersio

Mechanism of Domain Closure of Sec7 Domains and Role in BFA Sensitivity

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Oxidation of oxymyoglobin by poplar plastocyanins <i style="">a</i> and <i style="">b</i>

383-388Oxidation of oxymyoglobin [MbO2 (Fe2+)] by isoplastocyanins a (PCa) and b (PCb) was experimentally investigated and the corresponding redox reaction was modeled using the physicochemical parameters of the isoforms to study the effect of the dimorphism. The kinetic curve of oxidation of MbO2 (Fe2+) by oxidized PCa [PCa(Cu2+)] and PCb [PCb(Cu2+)] and the pH-dependence of the rate constant k1 were determined. In the range of pH 4.8-9.0, PCb reacts with higher k1, compared with PCa. For example, at pH 7.0, k1(PCb) = 4 × 102 M-1s-1, whereas k1(PCa) = 2 × 102 M-1s-1. The observed values of ΔE0 for the reaction pairs Mb-PCa and Mb-PCb were -304 mV and -319 mV, respectively. The effect of the ionic strength (µ) on the rate of the electron transfer was also studied. It was found that: (i) the net charge Z1 of PCa and PCb fully corresponds to that calculated by their primary structures and Z2 of Mb corresponds to that calculated by its titration curve; (ii) the ln k as function of √¯µ was similar for both PCa and PCb; (iii) the curve of the reaction PCb Mb (pH 7.0) was shifted towards higher values of k, in agreement with the larger net negative charge of PCb; and (iv) the character of the electrostatic interactions remained unchanged by a replacement of PCa by PCb and by the change of pH from 7.0 to 4.8

Unique GMP-binding site in Mycobacterium tuberculosis guanosine monophosphate kinase.

International audienceBacterial nucleoside monophosphate (NMP) kinases, which convert NMPs to nucleoside diphosphates (NDP), are investigated as potential antibacterial targets against pathogenic bacteria. Herein, we report the biochemical and structural characterization of GMP kinase from Mycobacterium tuberculosis (GMPKMt). GMPKMt is a monomer with an unusual specificity for ATP as a phosphate donor, a lower catalytic efficiency compared with eukaryotic GMPKs, and it carries two redox-sensitive cysteines in the central CORE domain. These properties were analyzed in the light of the high-resolution crystal structures of unbound, GMP-bound, and GDP-bound GMPKMt. The latter structure was obtained in both an oxidized form, in which the cysteines form a disulfide bridge, and a reduced form which is expected to correspond to the physiological enzyme. GMPKMt has a modular domain structure as most NMP kinases. However, it departs from eukaryotic GMPKs by the unusual conformation of its CORE domain, and by its partially open LID and GMP-binding domains which are the same in the apo-, GMP-bound, and GDP-bound forms. GMPKMt also features a unique GMP binding site which is less close-packed than that of mammalian GMPKs, and in which the replacement of a critical tyrosine by a serine removes a catalytic interaction. In contrast, the specificity of GMPKMt for ATP may be a general feature of GMPKs because of an invariant structural motif that recognizes the adenine base. Altogether, differences in domain dynamics and GMP binding between GMPKMt and mammalian GMPKs should reveal clues for the design of GMPKMt-specific inhibitors

Transgenic resistance of Bulgarian potato cultivars to the Colorado potato beetle based on Bt technology

Colorado potato beetle, Leptinotarsa decemlineata Say, is the most destructive insect pest of potatoes. When the population of beetles is high, plants can be completely defoliated and commercial potato production is nearly impossible without control of the beetle. The beetles have shown a tremendous ability to develop resistance against insecticides. Previously, a biotechnology approach to control Colarado potato beetle based on the use of the synthetic Bt gene was developed. In this article, a transformation procedure for three commercial Bulgarian potato cultivars was developed and potentially commercial transgenic lines have been selected based on field resistance to Colorado potato beetles and yield. Plants were transformed with the Bacillus thuringiensis (Bt) cry3A gene using Agrobacterium-mediated transformation. 110 plants from the three cultivars were regenerated and tested by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). The Cry3A protein accumulation varied across the transgenic lines, rating from very low to 71.5 $\mu$g/g fresh weight. 21 transgenic lines expressing the Cry3A protein at levels above 10 $\mu$g/g fresh weight were tested in two successive years in filed conditions at two different locations of the country. All transgenic lines compared with the controls, nontransgenic potatoes from the respective cultivar, were consistently protected from foliar damages from all developmental stages of the beetle. The comparison of all properties of the tested transgenic lines, including variety phenotypes and tuber yield, allowed the selection of the most promising 2–3 lines per cultivar. Selected lines produced tuber amounts 80–100% higher compared with the control, non-transgenic plants. Those lines were grown for mass propagation during the third year of field experiments. The presence of the transgene in these lines was confirmed with the use of primers specific to the transgene by polymerase chain reaction (PCR). Additionally, the results from the insect bioassay showed that these lines were highly resistant to insect feeding, leading to 100% of mortality of larval populations. In summary, we generated potentially commercial potato lines highly resistant to Colorado potato beetle using Bt technology that may have a profound impact on development of sustainable agriculture in Bulgaria. This is one of the several agriculture biotechnology products entirely developed and tested in Bulgaria

Calorimetric and Crystallographic Analysis of the Oligomeric Structure of Escherichia coli GMP Kinase

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Crystallization and preliminary X-ray diffraction data of the complex between human centrin 2 and a peptide from the protein XPC

Production, crystallization and phasing procedures are reported for the complex of human centrin 2, lacking the first 25 residues, and a 17-residue peptide from the protein XPC

Structural, thermodynamic, and cellular characterization of human centrin 2 interaction with xeroderma pigmentosum group C protein.

International audienceHuman centrin 2 (HsCen2), an EF-hand calcium binding protein, plays a regulatory role in the DNA damage recognition during the first steps of the nucleotide excision repair. This biological action is mediated by the binding to a short fragment (N847-R863) from the C-terminal region of xeroderma pigmentosum group C (XPC) protein. This work presents a detailed structural and energetic characterization of the HsCen2/XPC interaction. Using a truncated form of HsCen2 we obtained a high resolution (1.8 A) X-ray structure of the complex with the peptide N847-R863 from XPC. Structural and thermodynamic analysis of the interface revealed the existence of both electrostatic and apolar inter-molecular interactions, but the binding energy is mainly determined by the burial of apolar bulky side-chains into the hydrophobic pocket of the HsCen2 C-terminal domain. Binding studies with various peptide variants showed that XPC residues W848 and L851 constitute the critical anchoring side-chains. This enabled us to define a minimal centrin binding peptide variant of five residues, which accounts for about 75% of the total free energy of interaction between the two proteins. Immunofluorescence imaging in HeLa cells demonstrated that HsCen2 binding to the integral XPC protein may be observed in living cells, and is determined by the same interface residues identified in the X-ray structure of the complex. Overexpression of XPC perturbs the cellular distribution of HsCen2, by inducing a translocation of centrin molecules from the cytoplasm to the nucleus. The present data confirm that the in vitro structural features of the centrin/XPC peptide complex are highly relevant to the cellular context