Comparative genomic analysis of bacteriophage EP23 infecting <Emphasis Type="Italic">Shigella sonnei</Emphasis> and <Emphasis Type="Italic">Escherichia coli</Emphasis>

Bacteriophage EP23 that infects Escherichia coli and Shigella sonnei was isolated and characterized. The bacteriophage morphology was similar to members of the family Siphoviridae. The 44,077 bp genome was fully sequenced using 454 pyrosequencing. Comparative genomic and phylogenetic analyses showed that EP23 was most closely related to phage SO-1, which infects Sodalis glossinidius and phage SSL-2009a, which infects engineered E. coli. Genomic comparison indicated that EP23 and SO-1 were very similar with each other in terms of gene order and amino acid similarity, even though their hosts were separated in the level of genus. EP23 and SSL-2009a displayed high amino acid similarity between their genes, but there was evidence of several recombination events in SSL-2009a. The results of the comparative genomic analyses further the understanding of the evolution and relationship between EP23 and its bacteriophage relatives.     

Altering PI3K—Akt signalling in zebrafish embryos affects PTEN phosphorylation and gastrulation

Background information. PTEN (phosphatase and tensin homologue deleted on chromosome 10) is a negative regulator of the PI3K (phosphoinositide 3‐kinase)–Akt (also called protein kinase B) signalling pathway and is essential for embryogenesis, but its function in early vertebrate embryos is unclear. Results. To address how PTEN functions in early embryos, we overexpressed one of the four zebrafish PTEN isoforms at the 1–2‐cell stage. Overexpression of Ptena454 alters phospho‐Akt levels and impairs cell movements associated with gastrulation. Heat shocking embryos increases phospho‐Akt levels and lowers phospho‐Ptena454 levels. Inhibiting CK2 (protein kinase CK2) activity reduces phospho‐Pten levels and augments the effects due to Ptena454 overexpression. Low phospho‐Akt and corresponding low phospho‐GSK‐3 (glycogen synthase kinase‐3) and high phospho‐Pten levels accompany wortmannin or LY294002 treatment, which inhibit PI3K activity. Conclusions. These results suggest that Ptena454 regulation is correlated to changes in phospho‐Akt levels. We propose a model in which homoeostasis in rapidly dividing and migrating embryonic cells depends on a counterbalance between pro‐survival signalling employing CK2 and GSK‐3 and the pro‐apoptotic activity of Ptena454.     

Microarray-based global differential expression profiling of P450 monooxygenases and regulatory proteins for signal transduction pathways in the white rot fungus <Emphasis Type="Italic">Phanerochaete chrysosporium</Emphasis>

Whole genome sequencing of the model white rot basidiomycete Phanerochaete chrysosporium has revealed the largest P450 contingent known to date in fungi, along with related phase I and phase II metabolic genes and signaling cascade genes. As a part of their functional characterization, genome-wide expression profiling under physiologically distinct conditions, nutrient-limited (ligninolytic) and nutrient-rich (non-ligninolytic), was investigated using a custom-designed 70-mer oligonucleotide microarray developed based on 190 target genes and 23 control genes. All 150 P450 genes were found to be expressible under the test conditions, with 27 genes showing differential expression based on a >twofold arbitrary cut-off limit. Of these, 23 P450 genes were upregulated (twofold to ninefold) in defined high-nitrogen cultures whereas four genes were upregulated (twofold to twentyfold) in defined low-nitrogen cultures. Furthermore, tandem P450 member genes in ten of the 16 P450 genomic clusters showed nonassortative regulation of expression reflecting their functional diversity. Full-length cDNAs for two of the high-nitrogen upregulated genes pc-hn1 (CYP5035A1) and pc-hn2 (CYP5036A1) and partial cDNA for a low-nitrogen upregulated gene pc-ln1 (CYP5037A1) were cloned and characterized. The study provided first molecular evidence for the presence of active components of the cAMP- and MAP kinase-signaling pathways in a white rot fungus; four of these components (cpka and ste-12 of cAMP pathway and two MAP kinases, mps1 and sps1) were significantly upregulated (fourfold to eightfold) under nutrient-limited conditions, implying their likely role in the regulation of gene expression involved in secondary metabolism and biodegradation processes under these conditions.     

Formation of complexes between microsomal cytochrome P-450-Fe(II) and nitrosoarenes obtained by oxidation of arylhydroxylamines or reduction of nitroarenes in situ.

A cytochrome P-450 complex exhibiting a Soret peak at 454 nm is formed by direct interaction of nitrosobenzene with NADPH-reduced rat liver microsomes in anaerobic conditions, by reaction of phenylhydroxylamine with aerobic microsomes or during nitrobenzene reduction by NADPH-reduced or dithionite-reduced microsomes. In the latter conditions, the complex formation is only transient as it is unstable to dithionite. Analogous reactions with myoglobin lead to the previously described myoglobin-Fe(II)-nitrosobenzene complex which has similar properties to those of the 454-nm-absorbing cytochrome P-450 complex. This analogy, together with the various conditions of its formation, strongly indicates that it is a cytochrome-P-450-Fe(II)-nitrosobenzene complex. The corresponding complex with the 4-chloro-nitrosobenzene ligand is formed in similar conditions. Cytochrome P-450-Fe(II) complexes with nitrosoarenes seem less stable than the previously described complexes with nitrosoalkanes.     

A major invasion of transposable elements accounts for the large size of the <Emphasis Type="Italic">Blumeria graminis</Emphasis> f.sp. <Emphasis Type="Italic">tritici</Emphasis> genome

Powdery mildew of wheat (Triticum aestivum L.) is caused by the ascomycete fungus Blumeria graminis f.sp. tritici. Genomic approaches open new ways to study the biology of this obligate biotrophic pathogen. We started the analysis of the Bg tritici genome with the low-pass sequencing of its genome using the 454 technology and the construction of the first genomic bacterial artificial chromosome (BAC) library for this fungus. High-coverage contigs were assembled with the 454 reads. They allowed the characterization of 56 transposable elements and the establishment of the Blumeria repeat database. The BAC library contains 12,288 clones with an average insert size of 115 kb, which represents a maximum of 7.5-fold genome coverage. Sequencing of the BAC ends generated 12.6 Mb of random sequence representative of the genome. Analysis of BAC-end sequences revealed a massive invasion of transposable elements accounting for at least 85% of the genome. This explains the unusually large size of this genome which we estimate to be at least 174 Mb, based on a large-scale physical map constructed through the fingerprinting of the BAC library. Our study represents a crucial step in the perspective of the determination and study of the whole Bg tritici genome sequence.     

A 14-mer Hsp70 peptide stimulates natural killer (NK) cell activity

Compared with normal cells, tumor cell lines exhibit an unusual plasma membrane localization of heat shock protein 70 (Hsp70). This tumor-selective Hsp70 membrane expression has been found to correlate with an increased sensitivity to lysis mediated by human natural killer (NK) cells that transiently adhere to plastic following cytokine stimulation. A human Hsp70-specific monoclonal antibody (mAb) detects membrane-bound Hsp70 on viable tumor cells and blocks the immune response of NK cells against Hsp70-expressing tumor cells. By peptide scanning (pep-scan) analysis, the epitope of this mAb was mapped as the C-terminal-localized 8-mer NLLGRFEL (NLL, amino acids [aa] 454-461). Most interestingly, similar to full-length Hsp70 protein, the N-terminal-extended 14-mer peptide TKDNNLLGRFELSG (TKD, aa 450-463) was able to stimulate the cytolytic and proliferative activity of NK cells at concentrations equivalent to full-length Hsp70 protein. Blocking studies revealed that an excess of the 14-mer peptide TKDNNLLGRFELSG inhibits the cytolytic activity of NK cells similar to that of Hsp70 protein. In comparison, other TKD-related peptides, including the 8-mer antibody epitope NLLGRFEL (aa 454-461), the 12-mer TKDNNLLGRFEL (aa 450-461), the 13-mer C-terminal-extended peptide NLLGRFELSGIPP (aa 454-466), the 14-mer TKD-equivalent sequences of Hsp70hom TKDNNLLGRFELTG (aa 450-463), Hsc70 TKDNNLLGKFELTG (aa 450-463), and DnaK AADNKSLGQFNLDG (aa 447-460) failed to activate NK activity.     

The Morphology of Three Loxophyllum Species (Ciliophora,Pleurostomatida) from Southern China,L. lembum sp. n., L. vesiculosum sp. n. and L. perihoplophorum Buddenbrock, 1920, with Notes on the Molecular Phylogeny of Loxophyllum

Two new pleurostomatid ciliates, Loxophyllum lembum sp. n., L. vesiculosum sp. n., and the poorly known L. perihoplophorum Buddenbrock, 1920, isolated from brackish waters in coastal regions of southern China, are described following observations of live cells and protargol‐impregnated specimens. Loxophyllum lembum sp. n. is distinguished by a combination of characters including two macronuclear nodules, 6–9 contractile vacuoles along the ventral margin, 11–14 right and 6–8 left kineties and the presence of cortical granules. Loxophyllum vesiculosum sp. n. differs from its congeners mainly by the unique distribution of contractile vacuoles, several of which lie along the dorsal margin and one on the ventral margin, and 15–21 right and 6–8 left kineties. Loxophyllum perihoplophorum is characterized by its large cell size (350–450 μm long in vivo), 3–5 contractile vacuoles along the dorsal margin in the posterior region of the body, and 19–23 right and 7–9 left kineties. An improved diagnosis of L. perihoplophorum is provided. The SSU rDNA sequence of L. perihoplophorum is reported for the first time and its molecular phylogeny is analyzed. Maximum likelihood and Bayesian inference analyses of SSU rDNA sequence data recover the monophyly both of the order Pleurostomatida and of the genus Loxophyllum.     

A gene from the fungal plant pathogen Nectria haematococca that encodes the phytoalexin-detoxifying enzyme pisatin demethylase defines a new cytochrome P450 family

The gene PDAT9 from the fungus Nectria haematococca encodes pisatin demethylase, an enzyme that detoxifies the phytoalexin pisatin, an antimicrobial compound produced by pea in response to infection by this plant pathogen. PDAT9 was found to contain an open reading frame (ORF) encoding 515 amino acids and four introns of 52–58 nucleotides each within its coding region. The amino acid sequence F-G-A-G-S-R-S-C-I-G, indicative of the fifth ligand binding site present in all cytochrome P454s, occurs as residues 446 to 455, confirming that PDAT9 is a cytochrome P450. The deduced amino acid sequence is distinct from all other reported cytochrome P-450s, and PDAT9 has been assigned to a new cytochrome P450 family, CYP57. A 1.3 kb SacI fragment of the PDAT9 ORF that lacked the fifth ligand binding site, hybridized to unique DNA fragments in N. haematococca isolates known to possess PDA genes that encode different whole cell phenotypes for pisatin demethylating activity. These genes were also tentatively identified as cytochrome P450s by the hybridization of the same fragments to separate subclones of PDAT9, one of which contained the fifth ligand sequence. That probe also hybridized to DNA other than that attributed to pisatin demethylase genes; these other DNAs are presumed to represent other cytochrome P450s.     

Isotopic reconstruction of human diet and animal husbandry practices during the Classical-Hellenistic, imperial, and Byzantine periods at Sagalassos, Turkey

An isotopic reconstruction of human dietary patterns and livestock management practices (herding, grazing, foddering, etc.) is presented here from the sites of Düzen Tepe and Sagalassos in southwestern Turkey. Carbon and nitrogen stable isotope ratios were determined from bone collagen extracted from humans (n = 49) and animals (n = 454) from five distinct time periods: Classical‐Hellenistic (400–200 BC), Early to Middle Imperial (25 BC–300 AD), Late Imperial (300–450 AD), Early Byzantine (450–600 AD), and Middle Byzantine (800–1200 AD). The humans had protein sources that were based on C₃ plants and terrestrial animals. During the Classical‐Hellenistic period, all of the domestic animals had δ¹³C and δ¹⁵N signatures that clustered together; evidence that the animals were herded in the same area or kept in enclosures and fed on similar foods. The diachronic analysis of the isotopic trends in the dogs, cattle, pigs, sheep, and goats highlighted subtle but distinct variations in these animals. The δ¹³C values of the dogs and cattle increased (reflecting C₄ plant consumption) during the Imperial and Byzantine periods, but the pigs and the goats displayed little change and a constant C₃ plant‐based diet. The sheep had a variable δ¹³C pattern reflecting periods of greater and lesser consumption of C₄ plants in the diet. In addition, the δ¹⁵N values of the dogs, pigs, cattle, and sheep increase substantially from the Classical‐Hellenistic to the Imperial periods reflecting a possible increase in protein consumption, but the goats showed a decrease. Finally, these isotopic results are discussed in the context of zooarcheological, archeobotanical, and trace element evidence. Am J Phys Anthropol 149:157–171, 2012. © Wiley Periodicals, Inc.     

7,8-benzoflavone binding to human cytochrome P450 3A4 reveals complex fluorescence quenching,suggesting binding at multiple protein sites

Human cytochrome P450 (P450) 3A4 is involved in the metabolism of one-half of marketed drugs and shows cooperative interactions with some substrates and other ligands. The interaction between P450 3A4 and the known allosteric effector 7,8-benzoflavone (α-naphthoflavone, αNF) was characterized using steady-state fluorescence spectroscopy. The binding interaction of P450 3A4 and αNF effectively quenched the fluorescence of both the enzyme and ligand. The Hill Equation and Stern–Volmer fluorescence quenching models were used to evaluate binding of ligand to enzyme. P450 3A4 fluorescence was quenched by titration with αNF; at the relatively higher [αNF]/[P450 3A4] ratios in this experiment, two weaker quenching interactions were revealed (K_d 1.8–2.5 and 6.5 μM). A range is given for the stronger interaction since αNF quenching of P450 3A4 fluorescence changed the protein spectral profile: quenching of 315 nm emission was slightly more efficient (K_d 1.8 μM) than the quenching of protein fluorescence at 335 and 355 nm (K_d 2.5 and 2.1 μM, respectively). In the reverse titration, αNF fluorescence was quenched by P450 3A4; at the lower [αNF]/[P450 3A4] ratios here, two strong quenching interactions were revealed (K_d 0.048 and 1.0 μM). Thus, four binding interactions of αNF to P450 3A4 are suggested by this study, one of which may be newly recognized and which could affect studies of drug oxidations by this important enzyme.     

Crystallization and preliminary X-ray diffraction analysis of bovine seminal plasma PDC-109, a protein composed of two fibronectin type II domains

PDC-109 is a 13 kDa glycoprotein and the major phosphorylcholine- and heparin-binding protein of bull seminal plasma. It is built by an acidic 23-residue N-terminal sequence followed by a tandem of fibronectin type II domains. Full-length PDC-109 was crystallized in complex with o-phosphorylcholine by vapor diffusion in sitting drops. Crystals grew to maximal size of 0.5 × 0.3 × 0.2 mm³, diffract x-rays beyond 2.6 Å resolution, and belong to space group P321 with unit cell dimensions a = b = 93.6 Å, c = 52.7 Å. Proteins 28:454–456, 1997. © 1997 Wiley-Liss, Inc.     

A Novel Calcium Binding Site in the Slow Vacuolar Cation Channel TPC1 Senses Luminal Calcium Levels

Cytosolic calcium homeostasis is pivotal for intracellular signaling and requires sensing of calcium concentrations in the cytosol and accessible stores. Numerous Ca²⁺ binding sites have been characterized in cytosolic proteins. However, little is known about Ca²⁺ binding inside organelles, like the vacuole. The slow vacuolar (SV) channel, encoded by Arabidopsis thaliana TPC1, is regulated by luminal Ca²⁺. However, the D454/fou2 mutation in TPC1 eliminates vacuolar calcium sensitivity and increases store calcium content. In a search for the luminal calcium binding site, structure modeling indicated a possible coordination site formed by residues Glu-450, Asp-454, Glu-456, and Glu-457 on the luminal side of TPC1. Each Glu residue was replaced by Gln, the modified genes were transiently expressed in loss-of-TPC1-function protoplasts, and SV channel responses to luminal calcium were recorded by patch clamp. SV channels lacking any of the four negatively charged residues appeared altered in calcium sensitivity of channel gating. Our results indicate that Glu-450 and Asp-454 are directly involved in Ca²⁺ binding, whereas Glu-456 and Glu-457 are probably involved in connecting the luminal Ca²⁺ binding site to the channel gate. This novel vacuolar calcium binding site represents a potential tool to address calcium storage in plants.     

Multiplicity of n‐heptane oxidation pathways catalyzed by cytochrome P450

Modeling, mutagenesis, and kinetic studies have demonstrated that the substrate‐binding site of cytochrome P450 is composed of multiple interactive regions that are capable of simultaneously binding two or more xenobiotics. Substrate molecules can interact with each other after docking. Thus, substrates can compete for the activated oxygen–ferrous complex or alter the spatial orientation of other molecules. Cytochrome P450 is a unique enzyme that produces n‐heptane metabolites of different oxidation states. Metabolism of n‐heptane was investigated with rat liver microsomes and a reconstituted rat liver system. Ethanol, n‐propanol, and n‐butanol molecules interacted with the n‐heptane molecule and resulted in cytochrome P450 spectral changes as well as alterations in the n‐heptane metabolic profile. The observed modifications in the biotransformation of n‐heptane indicated that there are three distinct pathways for oxidation of n‐heptane to heptanols, heptanones, and one‐side oxygen‐oriented heptanediones. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:287–294, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20291     

Translocation of antibiotic resistance markers of a plasmid-free Streptococcus pyogenes (group A) strain into different streptococcal hemolysin plasmids

Summary Wild-type strain A454 (Streptococcus pyogenes) transferred en bloc its erythromycin (Em) and tetracycline (Tc) resistance markers into several plasmid-free streptococcal recipients. No plasmid DNA was detected in either the wild-type or the transconjugant strains. Crosses were performed between A454 and S. faecalis Rec⁺ or Rec^- recipients carrying hemolysin-bacteriocin plasmids, pIP964 or pAD1. The Em Tc-resistant transconjugants obtained harbored either the parental plasmid or an Em Tc resistance plasmid derived from pIP964 or pAD1. The restriction endonuclease analysis of 12 derivative plasmids showed insertions of various sizes into different fragments of pIP964 or pAD1. A454 and the Em Tc-resistant plasmid-free transconjugants were found to contain two EcoRI DNA fragments, that shared homology with ³²P-labeled pIP1077, one of the Em Tc resistance derivative plasmids, but not with ³²P-labeled pIP964. No homology was detected between pIP1077 and the cellular DNA of the antibiotic-susceptible recipients.Previously Thea Horodniceanu     

Grateloupia Serra sp. nov. H. W. Wang & Y. Lou (Halymeniaceae,Rhodophyta): a new species previously confused with Grateloupia asiatica in China

A new Grateloupia species from Luxun park, Qingdao Province, North China, was discovered during recent investigations and named Grateloupia serra H. W. Wang &; Y. Lou sp. nov. Morphological observations showed that: (1) the thalli were purple to dark red, cartilaginous and mucilaginous in texture, 15–45?cm in height; (2) the surface of thalli was covered with numerous proliferous branchlets and proliferous branchlets that were dentate when on the main axes; (3) the thalli were 450–550?µm thick, a cortex consisted of 6–8 layers of oblong or rounded cells and a medulla covered by compact medullary filaments; (4) the carpogonial branch was 6-celled and the auxiliary-cell branch was 5-celled, they were typical Grateloupia-type; (5) the internal structure of mature tetrasporangia were cruciately divided, oblong or square in shape. The morphological differences were supported by molecular analyses based on ribulose-1, 5-bisphosphate carboxylase/oxygenase gene (rbcL) sequences. Sequences of four G. serra sp. nov. samples were embedded into the Grateloupia clade and showed no pairwise divergence.     

Structural peculiarities of linear megaplasmid,pLMA1, from <Emphasis Type="Italic">Micrococcus luteus</Emphasis> interfere with pyrosequencing reads assembly

Different strains of Micrococcus luteus, isolated from high-altitude Argentinean wetlands, were recently reported to harbour the linear plasmids pLMA1, pLMH5 and pLMV7, all of which with 5′-covalently attached terminal proteins. The link between pLMA1 and the host’s erythromycin resistance as well as further presumptive qualities prompted us to perform a detailed characterization. When the 454 technology was applied for direct sequencing of gel-purified pLMA1, assembly of the reads was impossible. However, combined Sanger/454 sequencing of cloned pLMA1 fragments, covering altogether 23 kb of the 110-kb spanning plasmid, allowed numerous sequence repeats of varying in lengths to be identified thus rendering an explanation for the above 454 assembly failure. A large number of putative transposase genes were identified as well. Furthermore, a region with five putative iteron sequences is possibly involved in pLMA1 replication.     

Identification and characterization of <Emphasis Type="Italic">gerPI</Emphasis> and <Emphasis Type="Italic">gerPII</Emphasis> involved in epoxidation and hydroxylation of dihydrochalcolactone in <Emphasis Type="Italic">Streptomyces</Emphasis> species KCTC 0041BP

The macrolide antibiotics are biosynthesized by initial assembly of a macrolactone ring, followed by a series of post-polyketide (PKS) modifications. In general, the additional hydroxyl or epoxy groups are installed by cytochrome P450 enzymes, improving the bioactivity profile through structural diversification of natural products. The biosynthetic gene cluster for the 16-membered macrolide antibiotic dihydrochalcomycin (DHC) has been cloned from Streptomyces sp. KCTC 0041BP. Three cytochrome P450 genes are found in the DHC biosynthetic gene (ger) cluster. Two P450 enzymes were characterized from this cluster. Disruption of gerPI accumulated predominantly 12,13-de-epoxydihydrochalcomycin while disruption of gerPII accumulated 8-dehydroxy-12,13-de-epoxydihydrochalcomycin; DHC production was abolished in both cases. The results suggest that GerPII P450 catalyzes hydroxylation at the C₈ position followed by an epoxidation reaction catalyzed by GerPI P450 at the C₁₂–C₁₃ position.     

Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454 pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size‐fractioned plankton samples collected in the Bay of Naples. One group‐specific primer set targeting the LSU rDNA D1/D2 region was designed to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8–3 or 3–20 μm) and two sampling depths [subsurface, at 1 m, or deep chlorophyll maximum (DCM) at 23 m]. 454 reads were identified using a database covering the entire Haptophyta diversity currently sequenced. Our data set revealed several hundreds of Haptophyte clusters. However, most of these clusters could not be linked to taxonomically known sequences: considering OTUs_97% (clusters build at a sequence identity level of 97%) on our global data set, less than 1% of the reads clustered with sequences from cultures, and less than 12% clustered with reference sequences obtained previously from cloning and Sanger sequencing of environmental samples. Thus, we highlighted a large uncharacterized environmental genetic diversity, which clearly shows that currently cultivated species poorly reflect the actual diversity present in the natural environment. Haptophyte community appeared to be significantly structured according to the depth. The highest diversity and evenness were obtained in samples from the DCM, and samples from the large size fraction (3–20 μm) taken at the DCM shared a lower proportion of common OTUs_97% with the other samples. Reads from the species Chrysoculter romboideus were notably found at the DCM, while they could be detected at the subsurface. The highest proportion of totally unknown OTUs_97% was collected at the DCM in the smallest size fraction (0.8–3 μm). Overall, this study emphasized several technical and theoretical barriers inherent to the exploration of the large and largely unknown diversity of unicellular eukaryotes.