Distribute of SecBs from phylum <i>Bacteroidetes</i> in full phylogenetic tree of 3813 bacterial SecBs (left-hand column) with their detail distribution (right-hand column).

<p>The red colored branches are SecBs from phylum <i>Bacteroidetes</i>. The detailed phylogenetic tree in Newick tree format with maximum likelihood bootstrap values on all branches is available in Supplementary Materials.</p

Large-Scale Evolutionary Analyses on SecB Subunits of Bacterial Sec System

<div><p>Protein secretion systems are extremely important in bacteria because they are involved in many fundamental cellular processes. Of the various secretion systems, the Sec system is composed of seven different subunits in bacteria, and subunit SecB brings secreted preproteins to subunit SecA, which with SecYEG and SecDF forms a complex for the translocation of secreted preproteins through the inner membrane. Because of the wide existence of Sec system across bacteria, eukaryota, and archaea, each subunit of the Sec system has a complicated evolutionary relationship. Until very recently, 5,162 SecB sequences have been documented in UniProtKB, however no phylogenetic study has been conducted on a large sampling of SecBs from bacterial Sec secretion system, and no statistical study has been conducted on such size of SecBs in order to exhaustively investigate their variances of pairwise p-distance along taxonomic lineage from kingdom to phylum, to class, to order, to family, to genus and to organism. To fill in these knowledge gaps, 3,813 bacterial SecB sequences with full taxonomic lineage from kingdom to organism covering 4 phyla, 11 classes, 41 orders, 82 families, 269 genera, and 3,744 organisms were studied. Phylogenetic analysis revealed how the SecBs evolved without compromising their function with examples of 3-D structure comparison of two SecBs from <i>Proteobacteria</i>, and possible factors that affected the SecB evolution were considered. The average pairwise p-distances showed that the variance varied greatly in each taxonomic group. Finally, the variance was further partitioned into inter- and intra-clan variances, which could correspond to vertical and horizontal gene transfers, with relevance for <i>Achromobacter</i>, <i>Brevundimonas</i>, <i>Ochrobactrum</i>, and <i>Pseudoxanthomonas</i>.</p></div

Average pairwise p-distance of bacterial SecB.

<p>Blank: average pairwise p-distance is not unavailable.</p

Location of SecBs from order <i>Oceanospirillales</i> in full phylogenetic tree of 3813 bacterial SecBs (left-hand column) and in portions of phylogenetic tree (right-hand column).

<p>The accession numbers in red color are SecBs from order <i>Oceanospirillales</i>. The detailed phylogenetic tree in Newick tree format with maximum likelihood bootstrap values on all branches is available in Supplementary Materials.</p

Additional file 1: Table S1. of Predicting Crystallization Propensity of Proteins from Arabidopsis Thaliana

Presenting the 301 proteins from A. Thaliana used in this study. Table S2. Presenting the 535 characteristics of amino acids used in this study. Table S3. Presenting the amino acids and their translated amino acids. (DOC 780 kb

Locations of SecB P0AG86 from <i>Escherichia coli</i> and SecB P44853 from <i>Haemophilus influenzae</i> in phylogenetic tree composed of 3813 bacterial SecBs (A), amino acid sequence alignment of SecB P0AG86 and SecB P44853 (B), and 3-D structure alignment of SecB P0AG86 (PDB accession number 1QYN) in green color and SecB P44853 (PDB accession number 1FX3) in red color (C).

<p>The blue arrow shows the amino acid turn in SecB P44853.</p

Reactivity of a Nickel Sulfide with Carbon Monoxide and Nitric Oxide

The reactivity of the “masked” terminal nickel sulfide complex, [K­(18-crown-6)]­[(L^tBu)­Ni^II(S)] (L^tBu = {(2,6-ⁱPr₂C₆H₃)­NC­(^tBu)}₂CH), with the biologically important small molecules CO and NO, was surveyed. [K­(18-crown-6)]­[(L^tBu)­Ni^II(S)] reacts with carbon monoxide (CO) via addition across the Ni–S bond to give a carbonyl sulfide complex, [K­(18-crown-6)]­[(L^tBu)­Ni^II(<i>S</i>,<i>C</i>:η²-COS)] (<b>1</b>). Additionally, [K­(18-crown-6)]­[(L^tBu)­Ni^II(S)] reacts with nitric oxide (NO) to yield a nickel nitrosyl, [(L^tBu)­Ni­(NO)] (<b>2</b>), and a perthionitrite anion, [K­(18-crown-6)]­[SSNO] (<b>3</b>). The isolation of <b>3</b> from this reaction confirms, for the first time, that transition metal sulfides can react with NO to form the biologically important [SSNO]⁻ anion

Reversible Chalcogen-Atom Transfer to a Terminal Uranium Sulfide

The reaction of elemental S or Se with [K­(18-crown-6)]­[U­(S)­(NR₂)₃] (<b>1</b>) results in the formation of the new uranium­(IV) dichalcogenides [K­(18-crown-6)]­[U­(η²-S₂)­(NR₂)₃] (<b>2</b>) and [K­(18-crown-6)]­[U­(η²-SSe)­(NR₂)₃] (<b>5</b>). The further addition of elemental S to <b>2</b> results in the formation of [K­(18-crown-6)]­[U­(η³-S₃)­(NR₂)₃] (<b>3</b>). Complexes <b>2</b>, <b>3</b>, and <b>5</b> can be reconverted into <b>1</b> via the addition of R₃P (R = Et, Ph), concomitant with the formation of R₃PE (E = S, Se)

Synthesis of Uranium–Ligand Multiple Bonds by Cleavage of a Trityl Protecting Group

Addition of KSCPh₃ to [U­(NR₂)₃] (R = SiMe₃) in tetrahydrofuran, followed by addition of 18-crown-6, results in formation of the U­(IV) sulfide, [K­(18-crown-6)]­[U­(S)­(NR₂)₃] (<b>1</b>) and Gomberg’s dimer. Similarly, addition of KOCPh₃ to [U­(NR₂)₃] in tetrahydrofuran, followed by addition of 18-crown-6, results in formation of the U­(IV) oxide, [K­(18-crown-6)]­[U­(O)­(NR₂)₃] (<b>3</b>). Also observed in this transformation are the triphenylmethyl anion, [K­(18-crown-6)­(THF)₂]­[CPh₃] (<b>5</b>), and the U­(IV) alkoxide, [U­(OCPh₃)­(NR₂)₃] (<b>4</b>)

Synthesis of Uranium–Ligand Multiple Bonds by Cleavage of a Trityl Protecting Group

Addition of KSCPh₃ to [U­(NR₂)₃] (R = SiMe₃) in tetrahydrofuran, followed by addition of 18-crown-6, results in formation of the U­(IV) sulfide, [K­(18-crown-6)]­[U­(S)­(NR₂)₃] (<b>1</b>) and Gomberg’s dimer. Similarly, addition of KOCPh₃ to [U­(NR₂)₃] in tetrahydrofuran, followed by addition of 18-crown-6, results in formation of the U­(IV) oxide, [K­(18-crown-6)]­[U­(O)­(NR₂)₃] (<b>3</b>). Also observed in this transformation are the triphenylmethyl anion, [K­(18-crown-6)­(THF)₂]­[CPh₃] (<b>5</b>), and the U­(IV) alkoxide, [U­(OCPh₃)­(NR₂)₃] (<b>4</b>)