Structural reorganization of the interleukin-7 signaling complex.

We report here an unliganded receptor structure in the common gamma-chain (γ(c)) family of receptors and cytokines. The crystal structure of the unliganded form of the interleukin-7 alpha receptor (IL-7Rα) extracellular domain (ECD) at 2.15 Å resolution reveals a homodimer forming an "X" geometry looking down onto the cell surface with the C termini of the two chains separated by 110 Å and the dimer interface comprising residues critical for IL-7 binding. Further biophysical studies indicate a weak association of the IL-7Rα ECDs but a stronger association between the γ(c)/IL-7Rα ECDs, similar to previous studies of the full-length receptors on CD4(+) T cells. Based on these and previous results, we propose a molecular mechanism detailing the progression from the inactive IL-7Rα homodimer and IL-7Rα-γ(c) heterodimer to the active IL-7-IL-7Rα-γ(c) ternary complex whereby the two receptors undergo at least a 90° rotation away from the cell surface, moving the C termini of IL-7Rα and γ(c) from a distance of 110 Å to less than 30 Å at the cell surface. This molecular mechanism can be used to explain recently discovered IL-7- and γ(c)-independent gain-of-function mutations in IL-7Rα from B- and T-cell acute lymphoblastic leukemia patients. The mechanism may also be applicable to other γ(c) receptors that form inactive homodimers and heterodimers independent of their cytokines.

Biophysical characterization of glycosaminoglycan-IL-7 interactions using SPR.

Glycosaminoglycans (GAGs) interact with a number of cytokines and growth factors thereby playing an essential role in the regulation of many physiological processes. These interactions are important for both normal signal transduction and the regulation of the tissue distribution of cytokines/growth factors. In the present study, we employed surface plasmon resonance (SPR) spectroscopy to dissect the binding interactions between GAGs and murine and human forms of interleukin-7 (IL-7). SPR results revealed that heparin binds with higher affinity to human IL-7 than murine IL-7 through a different kinetic mechanism. The optimal oligosaccharide length of heparin for the interactions to human and murine IL-7 involves a sequence larger than a tetrasaccharide. These results further demonstrate that while IL-7 is principally a heparin/heparan sulfate binding protein, it also interacts with dermatan sulfate, chondroitin sulfates C, D, and E, indicating that this cytokine preferentially interacts with GAGs having a higher degree of sulfation.

Aicardi-Goutieres syndrome gene and HIV-1 restriction factor SAMHD1 is a dGTP-regulated deoxynucleotide triphosphohydrolase.

The SAMHD1 protein is an HIV-1 restriction factor that is targeted by the HIV-2 accessory protein Vpx in myeloid lineage cells. Mutations in the SAMHD1 gene cause Aicardi-Goutières syndrome, a genetic disease that mimics congenital viral infection. To determine the physiological function of the SAMHD1 protein, the SAMHD1 gene was cloned, recombinant protein was produced, and the catalytic activity of the purified enzyme was identified. We show that SAMHD1 contains a dGTP-regulated deoxynucleotide triphosphohydrolase. We propose that Vpx targets SAMHD1 for degradation in a viral strategy to control cellular deoxynucleotide levels for efficient replication.

Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.

BACKGROUND: In Escherichia coli, cytotoxic DNA methyl lesions on the N1 position of purines and N3 position of pyrimidines are primarily repaired by the 2-oxoglutarate (2-OG) iron(II) dependent dioxygenase, AlkB. AlkB repairs 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) lesions, but it also repairs 1-methylguanine (1-meG) and 3-methylthymine (3-meT) at a much less efficient rate. How the AlkB enzyme is able to locate and identify methylated bases in ssDNA has remained an open question. METHODOLOGY/PRINCIPAL FINDINGS: We determined the crystal structures of the E. coli AlkB protein holoenzyme and the AlkB-ssDNA complex containing a 1-meG lesion. We coupled this to site-directed mutagenesis of amino acids in and around the active site, and tested the effects of these mutations on the ability of the protein to bind both damaged and undamaged DNA, as well as catalyze repair of a methylated substrate. CONCLUSIONS/SIGNIFICANCE: A comparison of our substrate-bound AlkB-ssDNA complex with our unliganded holoenzyme reveals conformational changes of residues within the active site that are important for binding damaged bases. Site-directed mutagenesis of these residues reveals novel insight into their roles in DNA damage recognition and repair. Our data support a model that the AlkB protein utilizes at least two distinct conformations in searching and binding methylated bases within DNA: a "searching" mode and "repair" mode. Moreover, we are able to functionally separate these modes through mutagenesis of residues that affect one or the other binding state. Finally, our mutagenesis experiments show that amino acid D135 of AlkB participates in both substrate specificity and catalysis.

Inhibition of Listeria monocytogenes in Cold-process (Smoked) Salmon by Sodium Lactate.

Comminuted raw salmon containing various concentrations and combinations of sodium lactate, sodium chloride, and sodium nitrite was inoculated with 10 Listeria monocytogenes cells per g (150 cells/15-g sample), vacuum-packaged in oxygen-impermeable film and stored at 5 or 10°C. Samples were examined for growth of L. monocytogenes and total aerobic microorganisms at specific intervals for up to 50 d. Sodium lactate exhibited a concentration-dependent antilisterial effect that was enhanced by nitrite and/or increased concentrations of NaCl. At 5°C, total inhibition of L monocytogenes was achieved for up to 50 d by 2% sodium lactate in combination with 3% water-phase NaCl. At 10°C, total inhibition was achieved for up to 35 d by 3% sodium lactate in combination with 3% water-phase NaCl, or by 2% sodium lactate in combination with 125 ppm sodium nitrite and 3% water-phase NaCl. Sodium lactate and the other additives also inhibited growth of the aerobic microflora but to a lesser degree than L. monocytogenes .

Comparison of Selective Direct Plating Media for Enumeration and Recovery of L. monocytogenes from Cold-process (smoked) Fish.

Three selective media were evaluated for direct plating recovery and enumeration of Listeria monocytogenes in the presence of high levels of a variety of microorganisms occurring on cold-process (smoked) salmon products. Sliced salmon was brined to contain either no added salt, 3, or 5% water-phase NaCl, or 3 or 5% NaCl plus 140 ppm NaNO2. The slices were packaged in oxygen-permeable film or sealed under vacuum in oxygen-impermeable film, and stored at 10°C or 5°C until total microbial loads reached 106 to 109 CFU/g. Oxford formulation of Listeria selective agar and Lee's modification of Listeria selective agar achieved quantitative recovery of 102 cells per ml of L. monocytogenes strain Scott A in the presence of diluted slurries of these fish containing 104 to 108 CFU/ml of background organisms. A modification of lithium chloride-phenylethanol-moxalactam agar containing an iron-esculin indicator system sometimes failed because of interfering growth by the background microflora.