Proton and cadmium adsorption by the archaeon Thermococcus zilligii: Generalising the contrast between thermophiles and mesophiles as sorbents

Adsorption by microorganisms can play a significant role in the fate and transport of metals in natural systems. Surface complexation models (SCMs) have been applied extensively to describe metal adsorption by mesophilic bacteria, and several recent studies have extended this framework to thermophilic bacteria. We conduct acid-base titrations and batch experiments to characterise proton and Cd adsorption onto the thermophilic archaeon Thermococcus zilligii. The experimental data and the derived SCMs indicate that the archaeon displays significantly lower overall sorption site density compared to previously studied thermophilic bacteria such Anoxybacillus flavithermus, Geobacillus stearothermophilus, G. thermocatenulatus, and Thermus thermophilus. The thermophilic bacteria and archaea display lower sorption site densities than the mesophilic microorganisms that have been studied to date, which points to a general pattern of total concentration of cell wall adsorption sites per unit biomass being inversely correlated to growth temperature

Binding of the Bacillus subtilis LexA protein to the SOS operator

The Bacillus subtilis LexA protein represses the SOS response to DNA damage by binding as a dimer to the consensus operator sequence 5′-CGAACN(4)GTTCG-3′. To characterize the requirements for LexA binding to SOS operators, we determined the operator bases needed for site-specific binding as well as the LexA amino acids required for operator recognition. Using mobility shift assays to determine equilibrium constants for B.subtilis LexA binding to recA operator mutants, we found that several single base substitutions within the 14 bp recA operator sequence destabilized binding enough to abolish site-specific binding. Our results show that the AT base pairs at the third and fourth positions from the 5′ end of a 7 bp half-site are essential and that the preferred binding site for a LexA dimer is 5′-CGAACATATGTTCG-3′. Binding studies with LexA mutants, in which the solvent accessible amino acid residues in the putative DNA binding domain were mutated, indicate that Arg-49 and His-46 are essential for binding and that Lys-53 and Ala-48 are also involved in operator recognition. Guided by our mutational analyses as well as hydroxyl radical footprinting studies of the dinC and recA operators we docked a computer model of B.subtilis LexA on the preferred operator sequence in silico. Our model suggests that binding by a LexA dimer involves bending of the DNA helix within the internal 4 bp of the operator

La riscoperta del linguaggio - Conversazione con Tengan Daisuke

Five new orbitides, cyclolinopeptides <b>21</b>–<b>25</b>, were identified in flaxseed oil (<i>Linum usitatissimum</i>) extracts. Their HPLC-ESIMS quasimolecular ion peaks at <i>m</i>/<i>z</i> 1097.7 (<b>21</b>), 1115.6 (<b>22</b>), 1131.6 (<b>23</b>), 1018.6 (<b>24</b>), and 1034.6 (<b>25</b>) [M + H]⁺ corresponded to the molecular formulae C₅₉H₈₉N₁₀O₁₀, C₅₈H₈₇N₁₀O₁₀S, C₅₈H₈₇N₁₀O₁₁S, C₅₃H₈₀N₉O₉S, and C₅₃H₈₀N₉O₁₀S, respectively. Their structures were elucidated by extensive HPLC-ESIMS/MS analyses, and their presence was confirmed by precursor proteins identified in flax genomic DNA sequence data. The amino acid sequences of these orbitides were confirmed as [1–10-NαC]-GILVPPFFLI, [1–10-NαC]-GMLIPPFFVI, [1–10-NαC]-G<i>O</i>LIPPFFVI, [1–9-NαC]-GMLVFPLFI, and [1–9-NαC]-G<i>O</i>LVFPLFI for cyclolinopeptides <b>21</b>–<b>25</b>, respectively. Previously reported orbitides, [1–9-NαC]-ILVPPFFLI (<b>1</b>), [1–9-NαC]-MLIPPFFVI (<b>2</b>), [1–9-NαC]-<i>O</i>LIPPFFVI (<b>3</b>), [1–8-NαC]-MLVFPLFI (<b>7</b>), and [1–8-NαC]-<i>O</i>LVFPLFI (<b>8</b>), were also present in flaxseed oil. The precursors of orbitides <b>21</b>, <b>22</b>, and <b>24</b> also produced orbitides <b>1</b>, <b>2</b>, and <b>7</b> by alternative cyclization. Cyclolinopeptides <b>3</b>, <b>8</b>, <b>23</b>, and <b>25</b> contain MetO (<i>O</i>) and are not directly encoded, but are products of post-translational modification of the Met present in <b>2</b>, <b>7</b>, <b>22</b>, and <b>24</b>, respectively. Sufficient cyclolinopeptide <b>23</b> was isolated for characterization via 1D (¹H and ¹³C) and 2D (NOESY and HMBC) NMR spectroscopy. These compounds have been named as cyclolinopeptides U, V, W, X, and Y for <b>21</b>, <b>22</b>, <b>23</b>, <b>24</b>, and <b>25</b>, respectively