Combined application of plasma mutagenesis and gene engineering leads to 5-oxomilbemycins A3/A4 as main components from Streptomyces bingchenggensis

Milbemycin oxime has been commercialized as effective anthelmintics in the fields of animal health, agriculture, and human infections. Currently, milbemycin oxime is synthesized by a two-step chemical reaction, which involves the ketonization of milbemycins A3/A4 to yield the intermediates 5-oxomilbemycins A3/A4 using CrO₃ as catalyst. Due to the low efficiency and environmental unfriendliness of the ketonization of milbemycins A3/A4, it is imperative to develop alternative strategies to produce 5-oxomilbemycins A3/A4. In this study, the atmospheric and room temperature plasma (ARTP) mutation system was first employed to treat milbemycin-producing strain Streptomyces bingchenggensis, and a mutant strain BC-120-4 producing milbemycins A3, A4, B2, and B3 as main components was obtained, which favors the construction of genetically engineered strains producing 5-oxomilbemycins. Importantly, the milbemycins A3/A4 yield of BC-120-4 reached 3,890?±?52 g/l, which was approximately two times higher than that of the initial strain BC-109-6 (1,326?±?37 g/l). The subsequent interruption of the gene milF encoding a C5-ketoreductase responsible for the ketonization of milbemycins led to strain BCJ60 (?milF) with the production of 5-oxomilbemycins A3/A4 and the elimination of milbemycins A3, A4, B2, and B3. The high 5-oxomilbemycins A3/A4 yield (3,470?±?147 g/l) and genetic stability of BCJ60 implied the potential use in industry to prepare 5-oxomilbemycins A3/A4 for the semisynthesis of milbemycins oxime.     

Genetic engineering of Streptomyces bingchenggensis to produce milbemycins A3/A4 as main components and eliminate the biosynthesis of nanchangmycin

Milbemycins A3/A4 are important 16-membered macrolides which have been commercialized and widely used as pesticide and veterinary medicine. However, similar to other milbemycin producers, the production of milbemycins A3/A4 in Streptomyces bingchenggensis is usually accompanied with undesired by-products such as C5-O-methylmilbemycins B2/B3 (α-class) and β1/β2 (β-class) together with nanchangmycin. In order to obtain high yield milbemycins A3/A4-producing strains that produce milbemycins A3/A4 as main components, milD, a putative C5-O-methyltransferase gene of S. bingchenggensis, was biofunctionally investigated by heterologous expression in Escherichia coli. Enzymatic analysis indicated that MilD can catalyze both α-class (A3/A4) and β-class milbemycins (β11) into C5-O-methylmilbemycins B2/B3 and β1, respectively, suggesting little effect of furan ring formed between C6 and C8a on the C5-O-methylation catalyzed by MilD. Deletion of milD gene resulted in the elimination of C5-O-methylmilbemycins B2/B3 and β1/β2 together with an increased yield of milbemycins A3/A4 in disruption strain BCJ13. Further disruption of the gene nanLD encoding loading module of polyketide synthase responsible for the biosynthesis of nanchangmycin led to strain BCJ36 that abolished the production of nanchangmycin. Importantly, mutant strain BCJ36 (?milD?nanLD) produced milbemycins A3/A4 as main secondary metabolites with a yield of 2312?±?47 μg/ml, which was approximately 74 % higher than that of the initial strain S. bingchenggensis BC-109-6 (1326?±?37 μg/ml).     

5-ketoreductase from <Emphasis Type="Italic">Streptomyces bingchengensis</Emphasis>: overexpression and preliminary characterization

To elucidate the biotransformation from 5-oxomilbemycins A₃ and A₄ to milbemycins A₃ and A₄ in Streptomyces bingchengensis, the C5-ketoreductase gene (milF) was cloned using PCR with the specific primer designed from homologous nucleotide sequences. The C5-ketoreductase (MilF) was heterologously expressed in E. coli BL21 (DE3) as a His-tagged fusion protein. The characterization and biotransformation function of purified MilF was verified by in vitro enzyme assay. MilF is an NADPH-dependent reductase. The biotransformation products, analyzed by LC-APCI/MS, were identified as milbemycin A₃ and milbemycin A₄. MilF is thus present in Streptomyces bingchengensis and can transform 5-oxomilbemycins A₃ and A₄ to milbemycins A₃ and A₄. These findings are significant for understanding the biosynthetic pathway of milbemycins in Streptomyces bingchengensis and pave the way to obtain a producer strain of 5-oxomilbemycins directly by targeted milF disruption.     

Evolution of Chilean colonizing populations of <Emphasis Type="Italic">Drosophila subobscura</Emphasis>: lethal genes and chromosomal arrangements

Knowledge of the frequency, distribution, and fate of lethal genes in chromosomal inversions helps to illuminate the evolution of recently founded populations. We analyze the relationship between lethal genes and inversions in two colonizing populations of D. subobscura in Chile. In the ancestral Palearctic populations of this species, lethal genes seem distributed at random on chromosomes. But in colonizing American populations, some lethal genes are associated with specific chromosomal arrangements. Some of these associated lethals were detected only during the first stages of the colonization (O ₃₊₄₊₂ ), and never thereafter, whereas others have persisted (O ₃₊₄₊₇ and O₅). However, most lethal genes in American populations have been observed only once: they have arisen by novel mutation and soon disappear. Finally, recombination between different inversions has been observed in America. However, the persistence of lethal genes associated with the heterotic inversions O ₃₊₄₊₇ and O₅ could indicate that recombination inside these inversions is rare. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Rtt107/Esc4 binds silent chromatin and DNA repair proteins using different BRCT motifs

Background  

By screening a plasmid library for proteins that could cause silencing when targeted to the HMR locus in Saccharomyces cerevisiae, we previously reported the identification of Rtt107/Esc4 based on its ability to establish silent chromatin. In this study we aimed to determine the mechanism of Rtt107/Esc4 targeted silencing and also learn more about its biological functions.     

Mapping of the <Emphasis Type="Italic">S. demissum</Emphasis> late blight resistance gene <Emphasis Type="Italic">R8</Emphasis> to a new locus on chromosome IX

The use of resistant varieties is an important tool in the management of late blight, which threatens potato production worldwide. Clone MaR8 from the Mastenbroek differential set has strong resistance to Phytophthora infestans, the causal agent of late blight. The F1 progeny of a cross between the susceptible cultivar Concurrent and MaR8 were assessed for late blight resistance in field trials inoculated with an incompatible P. infestans isolate. A 1:1 segregation of resistance and susceptibility was observed, indicating that the resistance gene referred to as R8, is present in simplex in the tetraploid MaR8 clone. NBS profiling and successive marker sequence comparison to the potato and tomato genome draft sequences, suggested that the R8 gene is located on the long arm of chromosome IX and not on the short arm of chromosome XI as was suggested previously. Analysis of SSR, CAPS and SCAR markers confirmed that R8 was on the distal end of the long arm of chromosome IX. R gene cluster directed profiling markers CDP^Sw54 and CDP^Sw55 flanked the R8 gene at the distal end (1 cM). CDP^Tm21-1, CDP^Tm21-2 and CDP^Tm22 flanked the R8 gene on the proximal side (2 cM). An additional co-segregating marker (CDP^Hero3) was found, which will be useful for marker assisted breeding and map based cloning of R8.     

Effect of the genes B and Pl on anthocyanin synthesis in maize endosperm culture

B and Pl are two genes involved in anthocyanin biosynthesis in maize (Zea mays) plant tissues. In this work the effect of B and Pl on pigment accumulation is analyzed in endosperm tissues, either cultured in vitro or scraped off from the seed. The results obtained indicate that the two genes play a different role in callus pigmentation: B exerts a qualitative change in pigment composition, while Pl controls the rate of pigment accumulation in the callus. Anthocyanin synthesis in all strains analyzed appears to be light independent. Two cases of instability in pigment production arisen in the endosperm cultures are described and discussed in relation to epigenetic variation in secondary metabolite content in plant tissue culture.Abbreviations BEAF Benzene/ethyl acetate/formic acid (40:10:5) - 2-4D 2,4-dichlorophenoxyacetic acid - Wi initial weight - Wt total weight     

Gypsy/Ty3-class retrotransposons integrated in the DNA of herring,tunicate, and echinoderms

Eight new examples of retrotransposons of the Gypsy/Ty3 class have been identified in marine species. A 525-nt pol gene-coding region was amplified using degenerate primers from highly conserved regions and has extended the range of recognition of Gypsy/Ty3 far beyond those previously known. The following matrix shows the percentage AA divergence of the translations of this segment of the pol gene coding region. Spr2 Strongylocentrotus purpuratus, sea urchin 39 Por2 Pisaster ochraceus, starfish 46 45 Cprl Clupea pallasi, herring 51 52 41 Cirl Ciona intestinalis, tunicate bar52 49 49 55 P. orchraceus, starfish 55 60 60 62 62 Spr3 S. purpuratus, sea urchin 55 61 60 63 61 24 Tgrl^* Tripneustes gratilla, sea urchin 56 61 60 63 58 26 27 Lvrl^* Lytechinus variegatus, sea urchin 57 62 60 64 62 27 10 29 Sprl^* S. purpuratus 58 61 62 65 61 15 27 30 31 Spr4 S. purpuratus 72 72 74 75 72 73 72 72 73 72 Por3 P. ochraceus The underlines separate three groups of retrotransposons that can be recognized on the basis of this amino acid sequence. The new upper group shows surprising amino acid sequence similarity among members from the DNA of herring, sea urchin, starfish, and a tunicate. For example, the herring element differs by only 41 % from the Ciona element and 46% from the sea urchin element. The group between the lines includes members close to previously known elements (marked by asterisks) and has so far been found only in sea urchins. The two upper groups differ from each other by 55–60% and yet members of both groups (e.g., Sprl and Spr2) are integrated into the DNA of one species-S. purpuratus. Below the lower underline is listed the only known representative of a very distant group, which occurs in starfish DNA. In spite of large divergence, amino acid sequence comparisons indicate that all of the elements shown in the array are members of the LTR-containing class of retrotransposons that includes Gypsy of Drosophila and Ty3 of yeast. Of all known mobile elements this class shows the closest sequence similarity to retroviruses and has the same arrangement of genes as simpler retroviruses.Correspondence to: R.J. Britten     

Improvement of milbemycin-producing <Emphasis Type="Italic">Streptomyces bingchenggensis</Emphasis> by rational screening of ultraviolet- and chemically induced mutants

Milbemycin antibiotics are produced by Streptomyces hygroscopicus subsp. aureolacrimosus and a newly isolated Streptomyces bingchenggensis, respectively. According to the biosynthetic pathway of milbemycins generated by S. hygroscopicus subsp. aureolacrimosus, a rational screening procedure with UV irradiation and N-methyl-N′-nitroso-N-nitrosoguanidine (NTG) mutation was performed to obtain high milbemycin-producing S. bingchenggensis. Aminoacetic acid (Glycine)-resistant mutants (AA^r), propionate-resistant mutants (PRP^r), streptomycin-resistant mutants (STR^r) and 2-deoxy-d-glucose-resistant mutants (DOG^r) were selected successively. A strain S. bingchenggensis BC-109-6 with AA^r, PRPr, STR^r and DOG^r was obtained and its production of milbemycin A3 and A4 reached 1,450 μg/ml, which was 80% higher than that of the ancestral strain S. bingchenggensis BC-101-4. The subculture experiments indicated that the hereditary characteristic of high productivity of S. bingchenggensis BC-109-6 was stable. The production of milbemycin A3 and A4 by S. bingchenggensis BC-109-6 in a 50-l fermentor could reach 1,380 μg/ml after 360 h batch fermentation.     

CDK4 IVS4-nt40G→A and T2D-associated obesity in Italians

Cell cycle regulators play crucial roles in the preadipocyte proliferation and adipocyte differentiation. Cyclin-dependent kinase 4 (CDK4) mediates with D-type cyclins entry of cells into cell cycle in response to external stimuli. CDK4 plays a role in body weight, adipogenesis, and beta cell proliferation. CDK4 null mice develop type 2 diabetes (T2D). Furthermore, CDK4 variants are associated with obesity-associated tumors/cancer. We aimed at identifying a role of CDK4 IVS4-nt40G → A variant in T2D-associated obesity (body mass index, BMI ≥ 30) by association tests in an Italian T2D subjects dataset. We recruited from Italy 128 unrelated T2D subjects with BMI <30 kg/m² and 54 unrelated T2D subjects with BMI ≥ 30 kg/m². We performed statistical power calculations in our dataset. DNA samples were directly sequenced with specific primers for CDK4 IVS4-nt40G → A variant. We identified a significant association of the G allele with T2D-associated obesity and of the A allele with T2D-associated BMI < 30. In our study, we found that the CDK4 IVS4-nt40GG genotype is a risk variant for T2D-associated obesity and that the AA genotype is associated with BMI < 30 in T2D. Hence, CDK4 IVS4-nt40A allele is protective and G allele confers risk for obesity in T2D patients. This study should prompt further work aiming at establishing CDK4 role in contributing to human obesity and T2D-associated obesity. J. Cell. Physiol. 221: 273–275, 2009. © 2009 Wiley-Liss, Inc.     

The Drosophila methyl-DNA binding protein MBD2/3 interacts with the NuRD complex via p55 and MI-2

Background  

Methyl-DNA binding proteins help to translate epigenetic information encoded by DNA methylation into covalent histone modifications. MBD2/3 is the only candidate gene in the Drosophila genome with extended homologies to mammalian MBD2 and MBD3 proteins, which represent a co-repressor and an integral component of the Nucleosome Remodelling and Deacetylase (NuRD) complex, respectively. An association of Drosophila MBD2/3 with the Drosophila NuRD complex has been suggested previously. We have now analyzed the molecular interactions between MBD2/3 and the NuRD complex in greater detail.     

Light-regulated Arabidopsis ACBP4 and ACBP5 encode cytosolic acyl-CoA-binding proteins that bind phosphatidylcholine and oleoyl-CoA ester

In Arabidopsis thaliana, six genes encode acyl-CoA-binding proteins (ACBPs) that show conservation of an acyl-CoA-binding domain. These ACBPs display varying affinities for acyl-CoA esters, suggesting of different cellular roles. We have recently reported that three members (ACBP4, ACBP5 and ACBP6) are subcellularly localized to the cytosol by biochemical fractionation, confocal microscopy of transgenic Arabidopsis expressing autofluorescence-tagged fusions and immuno-electron microscopy using ACBP-specific antibodies. In this study, we observed by Northern blot analysis that ACBP4 and ACBP5 mRNAs in rosettes were up-regulated by light and dampened-off in darkness, mimicking FAD7 which encodes omega-3-fatty acid desaturase, an enzyme involved in plastidial lipid metabolism. Results from in vitro binding assays indicate that recombinant ACBP4 and ACBP5 proteins bind [¹⁴C]oleoyl-CoA esters better than recombinant ACBP6, suggesting that light-regulated ACBP4 and ACBP5 encode cytosolic ACBPs that are potential candidates for the intracellular transport of oleoyl-CoA ester exported from the chloroplast to the endoplasmic reticulum for the biosynthesis of non-plastidial membrane lipids. Nonetheless, His-tagged ACBP4 and ACBP5 resemble ACBP6 in their ability to bind phosphatidylcholine suggesting that all three ACBPs are available for the intracellular transfer of phosphatidylcholine.     

The tri–μ–hydrido–bis[(η5–C5Me5)aluminum(III)] theoretical study, the assets of sandwiched M2H3 (M of 13th group elements) stability

The stability of the tri–μ–hydrido–bis[(η⁵–C₅Me₅)aluminum], Cp*₂Al₂H₃, 1 is studied at B3LYP/6–311+G(d,p), CCSD(T)//B3LYP/6–311+G(d,p) and MP4//B3LYP/6–311+G(d,p) levels. The coordination between Al₂H₃ entity and both C₅(CH₃)₅ groups is ensured by strong electrostatic and orbital interactions. The orbital analysis of the interacting fragments shows that Al₂H₃ acceptor, which keeps its tribridged structure, implies the vacant ( \texta₁￠ ) \left( {{\text{a}}_1^\prime } \right) and five antibonding (a₂^￠￠ a_2^{\prime \prime } , e′ and e″) molecular orbitals to interact with two orbitals mixtures, b₁ and e" of the donors (C₅Me₅). When we take into account the solvent effect, the computation shows that 1 seems to be stable in condensed phase with a tribridged bond between the Al atoms [Cp*Al(μ-H)₃AlCp*], whereas in the gas phase, the monobridged Cp*AlH(μ-H)AlHCp* 4 is slightly favored (4 kcal mol⁻¹). We propose that 1 could be prepared thanks to Cp*Al (2) and Cp*AlH₂ (3) reaction in acidic medium. The experimental treatment of this type of metallocenes would contribute to the development of the organometallic chemistry of 13th group elements.      

The metabolism of lactose byClostridium acetobutylicum

Summary Acetone and butanol biosynthesis byClostridium acetobutylicum ATCC 824 was affected by lactose concentration and by agitation during the fermentation. At 1% and 3% lactose concentrations acid production predominated, while butanol production predominated at 5% lactose concentration. Higher solvent production was observed in fermentors without agitation than in fermentors with agitation.