FEBS Journal

The identification of nucleotide sequences flanking already characterized genome regions can be pursued by several genome walking (GW) strategies. Several GW methods have been developed in the last 20 years, including the recent coupling with Next Generation Sequencing technologies. This review focuses on the use of GW strategies in several aspects of the study of eukaryotic genomes

The AMPK/SNF1/SnRK1-mediated responses across species show remarkable similarities, indicating that the cross-species structural conservation of the kinase complex reflects the remarkable functional conservation. Although intensive research has already been performed on the AMPK/SNF1/SnRK1 kinase complexes, several fundamental issues still await to be clarified. In this review, we highlight these issues and focus on the structure, function and regulation

From ITC analysis, chitin oligosaccharide binding to a family GH19 chitinase from Bryum coronatum was found to be driven by favorable enthalpy changes with unfavorable entropy changes. The longer the chain length of the oligosaccharide tested (3–6), the larger the negative values of the binding free energy changes. The analysis provided new insight into the binding mode of GH19 enzymes

To identify a possible biological role of the prion protein, we performed a protein-binding screen of naturally occurring metabolites. Using a combination of NMR, fluorescence and SPR we identified thiamine as a specific prion ligand (K_D∼ 60 μm). This is one of the first endogenous prion ligands to be identified and may suggest a new physiological function for this protein

Expression of an ATP binding cassette protein, LmrC, in Lactococcus lactis led to an increase in resistance to ribosomally active antibiotics. However, LmrC function did not cause this resistance. Rather, a cellular stress response induced by the expression of LmrC was responsible. A model in which the induction of cellular stress responses leads to antibiotic resistance is presented

Nonmuscle myosin IIs (NM IIs) are known to be involved in cell migration, division and adhesion. We report that expression of NM IIs is increased in 3-methylcholanthrene (3MC) induced mouse tumor. Treatment of 3MC initiates dedifferentiation of C2C12-myotube in our in vitro study. Dedifferentiation of muscle fibers along with fibroblast transformation could be cellular pathways for 3MC induced tumor formation in mice

Cyanobacterial NAD(P)-reducing reversible hydrogenases comprise five subunits (HoxE/F/U/Y/H). Upon hoxE deletion, the Synechocystis PCC6803 hydrogenase became unable to catalyze H₂ production or uptake in interaction with NADH/NAD⁺. However, activation of the electron transfer-independent H⁺/D exchange reaction by NADPH was still observed, whereas activation by NADH was lost. These data suggest different mechanisms for diaphorase-mediated electron transfer and catalytic site activation

Homology modelled structure of the βB2B3-crystallin heterodimer based on data obtained by ion mobility and radical probe mass spectrometry

Kinetic model for electron flux through a dual-flavin enzyme. Computer simulations of the kinetic model, along with experimentally-determined measures of the K_Ahq and the cytochrome c (Cyt c) reductase activity, provide rate estimates for the protein conformational opening and closing steps (k_1,k₃, k₋₁, k₋₃) and the interflavin electron transfer step (k₂) that enable catalysis by dual-flavin enzymes

Potato tuber storage proteins were obtained from vacuoles isolated from field-grown starch potato tubers cv. Kuras. Proteome analysis demonstrated an abundance of molecular forms of six abundant super families, Kunitz and carboxy protease inhibitors, protease inhibitors 1 and 2, patatins and lipoxygenases

We characterized the promoter region of the human chromosome 7 open reading frame 24 gene (C7orf24) to explore its transcriptional regulatory mechanism. A luciferase reporter gene assay demonstrated that the three proximal CCAAT boxes are essential for C7orf24 gene transcription. Moreover, we revealed that NF-Ys bind to the three CCAAT boxes and play a central role in C7orf24 gene expression

We identified key amino acid residues of HSA involved in 4Z,15Z-bilirubin-IXα (4Z,15Z-BR) binding using phage display analysis and point mutation techniques. From various binding assays and photoconversion experiments, whilst both Lys195 and Lys199 in subdomain IIA are important for the high affinity binding of 4Z,15Z-BR, Lys199 plays a more prominent role in the elimination of 4Z,15Z-BR

The Saccharomyces cerevisiae vacuolar ABC-transporter Ycf1p is involved in selenite toxicity. Using secretory vesicles isolated from a sec6-4 mutant, we establish that the glutathione-conjugate selenodiglutathione is a high-affinity substrate of this ABC-transporter and that oxidized glutathione is also efficiently transported. Finally, we show that the presence of Ycf1p impairs the GSH/GSSG ratio of cells subjected to a selenite stress

As inhibitors of chitin synthase, nikkomycins have attracted interest as potential antibiotics. However, information on the biosynthetic reactions leading to these peptide nucleosides is still very limited. In order to elucidate the last step of the biosynthesis of the aminohexuronic building block of nikkomycins, we have identified a pyridoxal-5-phosphate dependent aminotransferase

Onconase, an antitumoral ribonuclease, is a much poorer catalyst than its relative, ribonuclease A. We determine a low-temperature, atomic-resolution crystal structure that clarifies deficiencies in its active site. Peptide backbone displacements, anisotropic atomic displacement parameters and an elastic network model reveal collective motion that had previously eluded detection. Differences in conformational equilibria could contribute to onconase’s reduced ribonucleolytic activity

Mobilization of hematopoietic stem and progenitor cells (HSPCs) from the bone marrow to the peripheral blood is utilized in clinical HSPC transplantation protocols. Aminoglycoside-polyarginine conjugates (APACs) induce mobilization of white blood cells and preferentially immature hematopoietic progenitor cells in mice. Administration of AMD3100 with each one of the APACs revealed additional HPC mobilization, accompanied by a significant elevation in plasma CXCL12 levels