Phylogenetic trees based on the partial sequences of 16S rRNA, p66 and glpQ genes.

<p>The Maximum Likelihood model was used for phylogenetic tree reconstruction of the partial A) 16S rRNA (1106 bp), B) p66 (349 bp and 355 bp for “<i>I. persulcatus</i>”-type and “<i>I. ricinus</i>”-type, respectively) and C) glpQ genes (379 bp). Only quartet puzzling support values >70% are shown. Samples sequenced in the present study are underlined.</p

<i>Borrelia miyamotoi</i> detection in ticks and estimated prevalence (%).

*<p>Not collected.</p>‡<p>P<0.0001 Fisher’s exact and Poisson probability tests.</p>§<p>P<0.05 Fisher’s exact test; P<0.001 Poisson probability test.</p

<i>Potato virus A</i> coat protein secondary structure prediction.

<p><i>Potato virus A</i> coat protein secondary structure prediction.</p

Heating-induced transition of Potyvirus Potato Virus A coat protein into β-structure

<div><p>In our previous communication, we have reported that virions of plant Potyvirus Potato Virus A (PVA) have a peculiar structure characterized by high content of disordered regions in intravirus coat protein (CP). In this report, we describe unusual properties of the PVA CP. With the help of a number of physicochemical methods, we have observed that the PVA CP just released from the virions by heating at 60–70 °C undergoes association into oligomers and transition to β- (and even cross-β-) conformation. Transition to β-structure on heating has been recently reported for a number of viral and non-viral proteins. The PVA CP isolated by LiCl method was also transformed into cross-β-structure on heating to 60 °C. Using the algorithms for protein aggregation prediction, we found that the aggregation-prone segments should be located in the central region of a PVA CP molecule. Possibly this transition mimics some functions of PVA CP in the virus life cycle in infected plants.</p></div

DSC melting curve for intact PVA virions in comparison with those of rod-shaped TMV virions and filamentous PVX virions in 10 mM phosphate buffer, pH 7.0.

<p>Melting temperatures (T_m,°C), enthalpy values (ΔH), and width at half height (W_hight/2 ) are shown in the upper right corner.</p

UV absorption (A) and far UV CD (B) spectra of PVA virions.

<p>(<b>A</b>) Directly measured UV absorption spectrum of intact PVA virions in 10 mM phosphate buffer, pH 7.0 (solid line) and scattering-corrected (dotted line) spectrum are shown. (<b>B</b>) Far UV CD spectra of intact (solid line) and 0.15% SDS-disrupted (dotted line) PVA virions in 10 mM phosphate buffer were measured in 1-mm cells at 25°C at PVA concentration of 0.14 mg/ml.</p

Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles

<p>In our previous study, we have observed that the isolated coat proteins (CP) of the Potyvirus Potato Virus A (PVA) virions exhibit an intrinsic tendency to self-associate into various multimeric forms containing some fractions of cross-β-structure. In this report, we studied the effect of solution conditions on the structure and dissociation of isolated PVA CP using a number of complementary physicochemical methods. Analysis of the structure of PVA CP in solution was performed by limited proteolysis with MALDI-TOF mass spectrometry analysis, transmission electron microscopy, intrinsic fluorescence spectroscopy, and synchrotron small angle X-ray scattering (SAXS). Overall structural characteristics of PVA CP obtained by combination of these methods and <i>ab initio</i> shape reconstruction by SAXS show that PVA CP forms large multi-subunit particles. We demonstrate that a mixture of compact virus-like particles (VLP) longer than 30 nm is assembled on dialysis of isolated CP into neutral pH buffer (at low ionic strength). Under conditions of high ionic strength (0.5 M NaCl) and high pH (pH 10.5), PVA dissociates into low compactness oval-shaped particles of approximately 30 subunits (20–30 nm). The results of limited trypsinolysis of these particles (enzyme/substrate ratio 1:100, 30 min) showed the existence of non-cleavable core-fragment, consisting of 137 amino acid residues. Trypsin treatment removed only a short N-terminal fragment in the intact virions. These particles are readily reassembled into regular VLPs by changing pH back to neutral. It is possible that these particles may represent some kind of intermediate in PVA assembly <i>in vitro</i> and <i>in vivo</i>.</p

Characteristics of purified PVA B11 virions.

<p>(<b>A</b>) PAGE; preparations were separated by discontinuous Tris-glycine 13% SDS-PAGE. For Mw determination Page Ruler Prestained Protein ladder (Fermentas SM0671) was used for Mw determination (lane M). Purified virus aliquots of 1 µg (1) and 10 µg (2) per lane were used. (<b>B</b>) Electron microscopy of sap from PVA-infected <i>N. benthamiana</i>; magnification ×20,000.</p

Intrinsic fluorescence spectra of intact and 0.15% SDS-disrupted PVA virions.

<p>Excitation by 280 nm light at 25°C. Duration of incubation in 0.15% SDS are shown in the upper right corner. Sample concentration was 0.03 mg/ml.</p

Prediction of folded and unfolded regions in isolated PVA CP was performed using the POODLE-S, Iupred, VL3H, and FoldUnfold programs.

<p>Prediction of folded and unfolded regions in isolated PVA CP was performed using the POODLE-S, Iupred, VL3H, and FoldUnfold programs.</p