The PRA1 gene family in Arabidopsis

Prenylated Rab acceptor 1 (PRA1) domain proteins are small transmembrane proteins that regulate vesicle trafficking as receptors of Rab GTPases and the vacuolar soluble N-ethylmaleimide-sensitive factor attachment receptor protein VAMP2. However, little is known about PRA1 family members in plants. Sequence analysis revealed that higher plants, compared with animals and primitive plants, possess an expanded family of PRA1 domain-containing proteins. The Arabidopsis (Arabidopsis thaliana) PRA1 (AtPRA1) proteins were found to homodimerize and heterodimerize in a manner corresponding to their phylogenetic distribution. Different AtPRA1 family members displayed distinct expression patterns, with a preference for vascular cells and expanding or developing tissues. AtPRA1 genes were significantly coexpressed with Rab GTPases and genes encoding vesicle transport proteins, suggesting an involvement in the vesicle trafficking process similar to that of their animal counterparts. Correspondingly, AtPRA1 proteins were localized in the endoplasmic reticulum, Golgi apparatus, and endosomes/prevacuolar compartments, hinting at a function in both secretory and endocytic intracellular trafficking pathways. Taken together, our data reveal a high functional diversity of AtPRA1 proteins, probably dealing with the various demands of the complex trafficking system.     

One-dimensional 13C NMR and HPLC-1H NMR techniques for observing carbon-13 and deuterium labelling in biosynthetic studies

For several decades isotope labelling techniques have been the indispensable tools used to unravel pathways of secondary product biosynthesis. NMR spectroscopy, together with mass spectrometry, is the most effective measuring technique used in the analysis of metabolites enriched with stable isotopes. ²H and ¹³C are the NMR-detectable nuclides which have been most frequently employed in plant secondary metabolite synthesis. Examples from the biosynthesis of phenylpropanoids, phenylphenalenones, and glucosinolates are used when discussing some aspects of one-dimensional NMR analysis of metabolites selectively labelled with ²H and ¹³C. Besides direct NMR detection of ¹³C-enriched metabolites, special emphasis is placed on indirect detection of ¹³C and ²H, especially by HPLC-¹H NMR coupling, to analyse the isotopomer pattern of compounds in low concentration. The examples discussed in this paper were obtained from studies with Anigozanthos preissii (root cultures) (Haemodoraceae) and Eruca sativa (Brassicaceae).     

Tilt and Rotation Angles of a Transmembrane Model Peptide as Studied by Fluorescence Spectroscopy

In this study the membrane orientation of a tryptophan-flanked model peptide, WALP23, was determined by using peptides that were labeled at different positions along the sequence with the environmentally sensitive fluorescent label BADAN. The fluorescence properties, reflecting the local polarity, were used to determine the tilt and rotation angles of the peptide based on an ideal α-helix model. For WALP23 inserted in dioleoylphosphatidylcholine (DOPC), an estimated tilt angle of the helix with respect to the bilayer normal of 24° ± 5° was obtained. When the peptides were inserted into bilayers with different acyl chain lengths or containing different concentrations of cholesterol, small changes in tilt angle were observed as response to hydrophobic mismatch, whereas the rotation angle appeared to be independent of lipid composition. In all cases, the tilt angles were significantly larger than those previously determined from ²H NMR experiments, supporting recent suggestions that the relatively long timescale of ²H NMR measurements may result in an underestimation of tilt angles due to partial motional averaging. It is concluded that although the fluorescence technique has a rather low resolution and limited accuracy, it can be used to resolve the discrepancies observed between previous ²H NMR experiments and molecular-dynamics simulations.     

Enzymatic surface modification and functionalization of PET: A water contact angle,FTIR, and fluorescence spectroscopy study

The purpose of this study was to investigate the changes induced by a lypolytic enzyme on the surface properties of polyethylene terephthalate (PET). Changes in surface hydrophilicity were monitored by means of water contact angle (WCA) measurements. Fourier Transform Infrared spectroscopy (FTIR) in the Attenuated Total Reflectance mode (ATR) was used to investigate the structural and conformational changes of the ethylene glycol and benzene moieties of PET. Amorphous and crystalline PET membranes were used as substrate. The lipolytic enzyme displayed higher hydrolytic activity towards the amorphous PET substrate, as demonstrated by the decrease of the WCA values. Minor changes were observed on the crystalline PET membrane. The effect of enzyme adhesion was addressed by applying a protease after‐treatment which was able to remove the residual enzyme protein adhering to the surface of PET, as demonstrated by the behavior of WCA values. Significant spectral changes were observed by FTIR–ATR analysis in the spectral regions characteristic of the crystalline and amorphous PET domains. The intensity of the crystalline marker bands increased while that of the amorphous ones decreased. Accordingly, the crystallinity indexes calculated as band intensity ratios (1,341/1,410 cm^?1 and 1,120/1,100 cm^?1) increased. Finally, the free carboxyl groups formed at the surface of PET by enzyme hydrolysis were esterified with a fluorescent alkyl bromide, 2‐(bromomethyl)naphthalene (BrNP). WCA measurements confirmed that the reaction proceeded effectively. The fluorescence results indicate that the enzymatically treated PET films are more reactive towards BrNP. FTIR analysis showed that the surface of BrNP‐modified PET acquired a more crystalline character. Biotechnol. Bioeng. 2009;103: 845–856. © 2009 Wiley Periodicals, Inc.     

Automated measurement of permethylated serum N-glycans by MALDI–linear ion trap mass spectrometry

The use of N-glycan mass spectrometry for clinical diagnostics requires the development of robust high-throughput profiling methods. Still, structural assignment of glycans requires additional information such as MS² fragmentation or exoglycosidase digestions. We present a setting which combines a MALDI ionization source with a linear ion trap analyzer. This instrumentation allows automated measurement of samples thanks to the crystal positioning system, combined with MSⁿ sequencing options. 2,5-Dihydroxybenzoic acid, commonly used for the analysis of glycans, failed to produce the required reproducibility due to its non-homogeneous crystallization properties. In contrast, α-cyano-4-hydroxycinnamic acid provided a homogeneous crystallization pattern and reproducibility of the measurements. Using serum N-glycans as a test sample, we focused on the automation of data collection by optimizing the instrument settings. Glycan structures were confirmed by MS² analysis. Although sample processing still needs optimization, this method provides a reproducible and high-throughput approach for measurement of N-glycans using a MALDI–linear ion trap instrument.     

Synthesis of Lewis X epitopes on plant N-glycans

Glycoproteins from tobacco line xFxG1, in which expression of a hybrid β-(1→4)-galactosyltransferase (GalT) and a hybrid α-(1→3)-fucosyltransferase IXa (FUT9a) is combined, contained an abundance of hybrid N-glycans with Lewis X (Le^X) epitopes. A comparison with N-glycan profiles from plants expressing only the hybrid β-(1→4)-galactosyltransferase suggested that the fucosylation of the LacNAc residues in line xFxG1 protected galactosylated N-glycans from endogenous plant β-galactosidase activity.     

Molybdenum complexes with O,N,S donor ligands as models for active sites in oxotransferases and hydroxylases

A series of homologous mononuclear dioxomolybdenum complexes were prepared and fully characterized with structurally related thiosemicarbazone ligands supplying a tridentate O,N,S donor set to the central metal atom. The ligands are derived from the prototype 2-hydroxybenzaldehyde-4-triphenylmethylthiosemicarbazone (H₂L). Within this series the crystal structures of 11 complex compounds [MoO₂(LRⁿ)(dmf)] and [MoO₂(LRⁿ)(MeOH)] were determined showing characteristic differences in the gross structural properties of the central metal core. From the variation of substituents in this ligand library the influences of electronic ligand effects on the spectroscopic, electrochemical, and functional properties of these biomimetic model complexes for molybdenum-containing oxotransferases are reported.     

Functional dissection of human and mouse POT1 proteins

The single-stranded telomeric DNA binding protein POT1 protects mammalian chromosome ends from the ATR-dependent DNA damage response, regulates telomerase-mediated telomere extension, and limits 5'-end resection at telomere termini. Whereas most mammals have a single POT1 gene, mice have two POT1 proteins that are functionally distinct. POT1a represses the DNA damage response, and POT1b controls 5'-end resection. In contrast, as we report here, POT1a and POT1b do not differ in their ability to repress telomere recombination. By swapping domains, we show that the DNA binding domain of POT1a specifies its ability to repress the DNA damage response. However, no differences were detected in the in vitro DNA binding features of POT1a and POT1b. In contrast to the repression of ATR signaling by POT1a, the ability of POT1b to control 5'-end resection was found to require two regions in the C terminus, one corresponding to the TPP1 binding domain and a second representing a new domain located between amino acids (aa) 300 and 350. Interestingly, the DNA binding domain of human POT1 can replace that of POT1a to repress ATR signaling, and the POT1b region from aa 300 to 350 required for the regulation of the telomere terminus is functionally conserved in human POT1. Thus, human POT1 combines the features of POT1a and POT1b.