Insight into the recognition mechanism of DNA cytosine-5 methyltransferases (DNMTs) by incorporation of acyclic 5-fluorocytosine (FC) nucleosides into DNA

DNA cytosine-5 methyltransferase (DNMT) catalyzes methylation at the C5 position of cytosine in the CpG sequence in double stranded DNA to give 5-methylCpG (mCpG) in the epigenetic regulation step in human cells. The entire reaction mechanism of DNMT is divided into six steps, which are scanning, recognition, flipping, loop locking, methylation, and releasing. The methylation and releasing mechanism are well-investigated; however, few reports are known about other reaction steps. To obtain insight into the reaction mechanism, we planned the incorporation of acyclic nucleosides, which make it easy to flip out the target nucleobase, into oligodeoxynucleotides (ODNs) and investigated the interaction between the ODN and DNMT. Here, we describe the design and synthesis of ODNs containing new acyclic 5-fluorocytosine nucleosides and their physiological and biological properties, including their interactions with DNMT. We found that the ODNs containing the acyclic 5-fluorocytosine nucleoside showed higher flexibility than those that contain 5-fluoro-2′-deoxycytidine. The observed flexibility of ODNs is expected to influence the scanning and recognition steps due to the decrease in helicity of the B-form.     

Erratum to: De novo sequencing and comparative analysis of expressed sequence tags from gynodioecious fig (Ficus carica L.) fruits: caprifig and common fig

Tree Genetics & Genomes - Negative correlation caused by competition among individuals and positive spatial correlation due to environmental heterogeneity may lead to biases in estimating...     

Phosphate Deficiency in Maize. I. Leaf Phosphate Status, Growth, Photosynthesis and Carbon Partitioning

Maize plants (Zea mays L.) were cultured with nutrient solutioncontaining 0.001 or 0.5 mM orthophosphate (Pi). Effects of lowphosphate (low-P) nutrition on growth, leaf phosphate status,photosynthesis, and carbon partitioning were investigated. Withlow-P treatment, the fresh weight of aerial parts decreasedby about 40% by 24 days after planting. Detailed studies ofthe effects of low-P treatment on the other characteristicsof maize leaves-were done using the middle part of the thirdleaf, counting from the base. Low-P treatment had almost noeffect on specific leaf weight or soluble protein content measured13 to 21 days after planting. Low-P treatment decreased Chicontent slightly (by 15% 19 days after planting). Twenty onedays after planting, low-P treatment had greatly decreased thelevels of leaf acid extractable Pi (by 77%) and photosynthesisrates (by 68%). The detrimental effects of low-P treatment onthe rates of photosynthesis and the amounts of acid extractablePi became progressively greater with time. There was a strongcorrelation between levels of leaf acid extractable Pi and ratesof photosynthesis. The minimum level of Pi necessary to sustainthe maximum photosynthesis rate was 0.6 mmol m^–2. Belowthis minimum content of Pi, the rate of photosynthesis decreasedsharply with decreasing Pi. To investigate the direct effectof Pi depletion on photosynthate partitioning at equivalentrates of photosynthesis, the rates in controls were reducedto almost the same as those in 18 or 19 day old low-P plants(about 50% of those in controls) by lowering light intensityand/ or ambient CO₂ concentration. The data clearly indicatesthat low-P treatment had a direct effect in lowering photosynthatepartitioning into starch. Starch mobilization during the nightwas also inhibited under low-P conditions. (Received January 7, 1991; Accepted March 5, 1991)     

Purification and characterization of a novel alcohol dehydrogenase from Leifsonia sp. strain S749: a promising biocatalyst for an asymmetric hydrogen transfer bioreduction

To find microorganisms that could reduce phenyl trifluoromethyl ketone (PTK) to (S)-1-phenyltrifluoroethanol [(S)-PTE], styrene-assimilating bacteria (ca. 900 strains) isolated from soil samples were screened. We found that Leifsonia sp. strain S749 was the most suitable strain for the conversion of PTK to (S)-PTE in the presence of 2-propanol as a hydrogen donor. The enzyme corresponding to the reaction was purified homogeneity, characterized and designated Leifsonia alcohol dehydrogenase (LSADH). The purified enzyme had a molecular weight of 110,000 and was composed of four identical subunits (molecular weight, 26,000). LSADH required NADH as a cofactor, showed little activity with NADPH, and reduced a wide variety of aldehydes and ketones. LSADH catalyzed the enantioselective reduction of some ketones with high enantiomeric excesses (e.e.): PTK to (S)-PTE (>99% e.e.), acetophenone to (R)-1-phenylethanol (99% e.e.), and 2-heptanone to (R)-2-heptanol (>99% e.e.) in the presence of 2-propanol without an additional NADH regeneration system. Therefore, it would be a useful biocatalyst.     

Genetic stability of human T lymphotropic virus type I despite antiviral pressures by CTLs

Human T lymphotropic virus type I (HTLV-I)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is an inflammatory neurological disease. Patients with HAM/TSP show high proviral load despite increased HTLV-I Tax-specific CTL. It is still unknown whether the CTL efficiently eliminate the virus in vivo and/or whether a naturally occurring variant virus becomes predominant by escaping from the CTL. To address these issues, we sequenced a large number of HTLV-I tax genes from HLA-A*02 HAM/TSP patients and estimated synonymous and nonsynonymous changes of the genes to detect positive selection pressure on the virus. We found the pressures in three of six CTL epitopes in HTLV-I Tax, where amino acid substitutions preferentially occurred. Although some of variant viruses were not recognized by the CTL, no variant viruses accumulated within 3-8 years, indicating genetic stability of HTLV-I tax gene. These results suggest that CTL eliminate the infected cells in vivo and naturally occurring variant viruses do not predominate. As Tax is a regulatory protein which controls viral replication, the amino acid substitutions in Tax may reduce viral fitness for replication. Viral fitness and host immune response may contribute to the viral evolution within the infected individuals. Furthermore, the genetic stability in the epitopes despite the antiviral pressures suggests that the three epitopes can be the candidate targets for HTLV-I vaccine development.     

Effect of concentration of compounds containing iron on the growth of Porphyromonas gingivalis

Abstract We examined the effect of the concentration of various types of iron molecules on the regulation of growth of Porphyromonas gingivalis . Bacterial growth was monitored spectrophotometrically. The hemin-depleted cells of P. gingivalis 381 were incubated in the basal medium plus test substrates such as hemoglobin, hemin, transferrin and various inorganic iron compounds. The relationship between the specific growth rate of organisms and the concentration of iron-containing compounds was determined. The value of K _s, a parameter analogous to the Michaelis-Menten constant, was estimated. P . gingivalis 381 showed a K _ss value of 3.85, 4.91 and 0.0017 μM for hemin, transferrin and hemoglobin, respectively. However, the inorganic iron compounds tested did not support growth of P. gingivalis . These findings suggest that P. gingivalis utilizes hemoglobin as an iron source much more effectively than other iron-containing compounds under an iron-limited environment.     

Antibody expression in protease-deficient strains of the methylotrophic yeast Ogataea minuta

When human antibody genes were expressed in the methylotrophic yeast Ogataea minuta, the secreted antibody became partially degraded. To suppress the degradation, a vacuolar protease-deficient strain was constructed and its antibody production was evaluated. Although antibody productivity was improved in the vacuolar protease-deficient strain, the secreted antibody still became partially degraded. Peptide sequencing revealed that the cleavage occurred in the CH1 region of the heavy chain, implying that the cleavage was caused by an aspartic protease, Yps1p. To inhibit this cleavage, Yps1p-deficient strains were constructed and their antibody production was evaluated. As a result, the partial degradation of the antibody was suppressed in the O. minuta multiple-protease-deficient strains.