Domain Movement within a Gene: A Novel Evolutionary Mechanism for Protein Diversification

A protein function is carried out by a specific domain localized at a specific position. In the present study, we report that, within a gene, a specific amino acid sequence can move between a certain position and another position. This was discovered when the sequences of restriction-modification systems within the bacterial species Helicobacter pylori were compared. In the specificity subunit of Type I restriction-modification systems, DNA sequence recognition is mediated by target recognition domain 1 (TRD1) and TRD2. To our surprise, several sequences are shared by TRD1 and TRD2 of genes (alleles) at the same locus (chromosomal location); these domains appear to have moved between the two positions. The gene/protein organization can be represented as x-(TRD1)-y-x-(TRD2)-y, where x and y represent repeat sequences. Movement probably occurs by recombination at these flanking DNA repeats. In accordance with this hypothesis, recombination at these repeats also appears to decrease two TRDs into one TRD or increase these two TRDs to three TRDs (TRD1-TRD2-TRD2) and to allow TRD movement between genes even at different loci. Similar movement of domains between TRD1 and TRD2 was observed for the specificity subunit of a Type IIG restriction enzyme. Similar movement of domain between TRD1 and TRD2 was observed for Type I restriction-modification enzyme specificity genes in two more eubacterial species, Streptococcus pyogenes and Mycoplasma agalactiae. Lateral domain movements within a protein, which we have designated DOMO (domain movement), represent novel routes for the diversification of proteins

Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

<p>Abstract</p> <p>Background</p> <p>The genome of <it>Helicobacter pylori</it>, an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. The high incidence of stomach cancer in East Asia might be related to bacterial genotype. We used newly developed comparative methods to follow the evolution of East Asian <it>H. pylori </it>genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains.</p> <p>Results</p> <p>A phylogenetic tree of concatenated well-defined core genes supported divergence of the East Asian lineage (hspEAsia; Japanese and Korean) from the European lineage ancestor, and then from the Amerind lineage ancestor. Phylogenetic profiling revealed a large difference in the repertoire of outer membrane proteins (including <it>oipA</it>, <it>hopMN</it>, <it>babABC</it>, <it>sabAB </it>and <it>vacA-2</it>) through gene loss, gain, and mutation. All known functions associated with molybdenum, a rare element essential to nearly all organisms that catalyzes two-electron-transfer oxidation-reduction reactions, appeared to be inactivated. Two pathways linking acetyl~CoA and acetate appeared intact in some Japanese strains. Phylogenetic analysis revealed greater divergence between the East Asian (hspEAsia) and the European (hpEurope) genomes in proteins in host interaction, specifically virulence factors (<it>tipα</it>), outer membrane proteins, and lipopolysaccharide synthesis (human Lewis antigen mimicry) enzymes. Divergence was also seen in proteins in electron transfer and translation fidelity (<it>miaA, tilS</it>), a DNA recombinase/exonuclease that recognizes genome identity (<it>addA</it>), and DNA/RNA hybrid nucleases (<it>rnhAB</it>). Positively selected amino acid changes between hspEAsia and hpEurope were mapped to products of <it>cagA</it>, <it>vacA</it>, <it>homC </it>(outer membrane protein), <it>sotB </it>(sugar transport), and a translation fidelity factor (<it>miaA</it>). Large divergence was seen in genes related to antibiotics: <it>frxA </it>(metronidazole resistance), <it>def </it>(peptide deformylase, drug target), and <it>ftsA </it>(actin-like, drug target).</p> <p>Conclusions</p> <p>These results demonstrate dramatic genome evolution within a species, especially in likely host interaction genes. The East Asian strains appear to differ greatly from the European strains in electron transfer and redox reactions. These findings also suggest a model of adaptive evolution through proteome diversification and selection through modulation of translational fidelity. The results define <it>H. pylori </it>East Asian lineages and provide essential information for understanding their pathogenesis and designing drugs and therapies that target them.</p

A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI)

Genome comparison and genome context analysis were used to find a putative mobile element in the genome of Photorhabdus luminescens, an entomopathogenic bacterium. The element is composed of 16-bp direct repeats in the terminal regions, which are identical to a part of insertion sequences (ISs), a DNA methyltransferase gene homolog, two genes of unknown functions and an open reading frame (ORF) (plu0599) encoding a protein with no detectable sequence similarity to any known protein. The ORF (plu0599) product showed DNA endonuclease activity, when expressed in a cell-free expression system. Subsequently, the protein, named R.PluTI, was expressed in vivo, purified and found to be a novel type IIF restriction enzyme that recognizes 5′-GGCGC/C-3′ (/ indicates position of cleavage). R.PluTI cleaves a two-site supercoiled substrate at both the sites faster than a one-site supercoiled substrate. The modification enzyme homolog encoded by plu0600, named M.PluTI, was expressed in Escherichia coli and shown to protect DNA from R.PluTI cleavage in vitro, and to suppress the lethal effects of R.PluTI expression in vivo. These results suggested that they constitute a restriction–modification system, present on the putative mobile element. Our approach thus allowed detection of a previously uncharacterized family of DNA-interacting proteins

多糖ゲルによる糖質加水分解酵素のアフィニティ-クロマトグラフィ-

Soluble starch, pectic acid and alginic acid were cross-linked by polyacrylamide. Several enzymes, including commercially available specimen and food material sources, were examined for their specificities to the polysaccharide gels. α-Amylase showed high affinity for the starch-gel in the presence of 3M ammonium sulfate and eluted with the buffer solution containing no ammonium sulfate. Pectinase and alginate-lyase bound to the pectin-gel and the alginate-gel, respectively. On the other hand, galactanase form the common bean (Phaseolus vulgaris L) bound to the starch-gel ; however, trehalase did not bound to this gel. Highly purified alginate-lyase was obtained by the current affinity chromatography method. Based on these results, relationship between the chemical structure of the polysaccharide-gels and the substrate specificity of the enzymes was discussed

エリンギ(Pleurotus eryngii)のトレハラーゼ : 酵素の分布、精製および性質について

Trehalase activity in a homogenized preparation from the fruit body of king oyster mushroom (eryngii), Pleurotus eryngii was studied in detail. Distribution of trehalose and trehalase activity was higher in the cap (pileus) fraction than in the other positions such as stalk (stipe). The tretalase peak 1 was purified by the Sephacryl S-200 and Toyopearl HW-55 column chromatography. Electorophoretic analysis of trehalase gave values of molecular weight of 36~37kDa, and oligomeric forms and blycoprotein forms of trehalase were suggested by the band patterns of resulting gels. Optimum conditons of pH and temperature were determined to be pH5.0 and 30℃, respectively. Trehalase peak 1 showed higher reactivity to α-, α-trehalose, whereas peak 2 enzyme showed higher activity to β-,β-trehalose, methyl-β-glucoside, and cellobiose, indicating that this enzyme might have a substrate specificity such asβ-glucosidase

Purification and properties of a novel enzyme from Bacillus spp. T-3040, which catalyses the conversion of dextran to cyclic isomaltooligosaccharides

AbstractA novel enzyme, cycloisomaltooligosaccharide glucanotransferase (CITase), catalyzes the conversion of dextran to cyclic isomaltooligosaccharides by intramolecular transglucosylation (cyclization reaction). CITase was purified to homogeneity from the culture filtrate of Bacillus sp. T-3040 isolated from soil. The Mr of the enzyme was estimated to be 98,000 by SDS-PAGE. The enzyme catalyzed the cyclization reaction and gave three cyclic isomaltooligosaccharides (cycloisomalto-heptaose, -octaose, and -nonaose) at a total yield of about 20%. Coupling and disproportionation reactions were also observed. These results showed that this enzyme is a multi-functional enzyme which catalyzes intramolecular and intermolecular transglucosylation

Changes in linkage pattern of glucan products induced by substitution of Lys residues in the dextransucrase

AbstractDextransucrase S (DSRS) is the only active glucansucrase that has been found in Leuconostoc mesenteroides NRRL B-512F strain. Native DSRS produces mainly 6-linked glucopyranosyl residue (Glcp), while Escherichia coli recombinant DSRS was observed to produce a glucan consisting of 70% 6-linked Glcp and 15% 3,6-Glcp. Lys residues were introduced at the N-terminal end of the core domain by site-directed mutagenesis. In glucans produced by the one-point mutants T350K and S455K, the amount of 6-linked Glcp was increased to about 85% of the total glucan produced, more similar in structure to native B-512F dextran. The double mutant T350K/S455K produced adhesive, water-insoluble glucan with 77% 6-linked Glcp, 8% 3,6-linked Glcp and 4% 2,6-linked Glcp. The T350K/S455K mutant exhibited a 10-fold increase in glucosyltransferase activity over those of the parental DSRS-His6 and its T350K and S455K mutants. This is the first report demonstrating a change in the properties of a dextransucrase or a related glucosyltransferase through simple site-directed mutagenesis to create 2,6-linked Glcp