Multiple pathways to bypass the enhancer requirement of sigma 54 RNA polymerase: Roles for DNA and protein determinants

Sigma 54 is a required factor for bacterial RNA polymerase to respond to enhancers and directs a mechanism that is a hybrid between bacterial and eukaryotic transcription. Three pathways were found that bypass the enhancer requirement in vitro. These rely on either deletion of the sigma 54 N terminus or destruction of the DNA consensus −12 promoter recognition element or altering solution conditions to favor transient DNA melting. Each of these allows unstable heparin-sensitive pre-initiation complexes to form that can be driven to transcribe in the absence of both enhancer protein and ATP β–γ hydrolysis. These disparate pathways are proposed to have a common basis in that multiple N-terminal contacts may mediate the interactions between the polymerase and the DNA region where melting originates. The results raise possibilities for common features of open complex formation by different RNA polymerases.

Pleiotropic Alterations in Lipid Metabolism in Yeast sac1 Mutants: Relationship to “Bypass Sec14p” and Inositol Auxotrophy

SacIp dysfunction results in bypass of the requirement for phosphatidylinositol transfer protein (Sec14p) function in yeast Golgi processes. This effect is accompanied by alterations in inositol phospholipid metabolism and inositol auxotrophy. Elucidation of how sac1 mutants effect “bypass Sec14p” will provide insights into Sec14p function in vivo. We now report that, in addition to a dramatic accumulation of phosphatidylinositol-4-phosphate, sac1 mutants also exhibit a specific acceleration of phosphatidylcholine biosynthesis via the CDP-choline pathway. This phosphatidylcholine metabolic phenotype is sensitive to the two physiological challenges that abolish bypass Sec14p in sac1 strains; i.e. phospholipase D inactivation and expression of bacterial diacylglycerol (DAG) kinase. Moreover, we demonstrate that accumulation of phosphatidylinositol-4-phosphate in sac1 mutants is insufficient to effect bypass Sec14p. These data support a model in which phospholipase D activity contributes to generation of DAG that, in turn, effects bypass Sec14p. A significant fate for this DAG is consumption by the CDP-choline pathway. Finally, we determine that CDP-choline pathway activity contributes to the inositol auxotrophy of sac1 strains in a novel manner that does not involve obvious defects in transcriptional expression of the INO1 gene.

Two modes of transvection: Enhancer action in trans and bypass of a chromatin insulator in cis

Ed Lewis introduced the term “transvection” in 1954 to describe mechanisms that can cause the expression of a gene to be sensitive to the proximity of its homologue. Transvection since has been reported at an increasing number of loci in Drosophila, where homologous chromosomes are paired in somatic tissues, as well as at loci in other organisms. At the Drosophila yellow gene, transvection can explain intragenic complementation involving the yellow2 allele (y2). Here, transvection was proposed to occur by enhancers of one allele acting in trans on the promoter of a paired homologue. In this report, we describe two yellow alleles that strengthen this model and reveal an unexpected, second mechanism for transvection. Data suggest that, in addition to enhancer action in trans, transvection can occur by enhancer bypass of a chromatin insulator in cis. We propose that bypass results from the topology of paired genes. Finally, transvection at yellow can occur in genotypes not involving y2, implying that it is a feature of yellow itself and not an attribute of one particular allele.

Mechanism of stimulation of the DNA glycosylase activity of hOGG1 by the major human AP endonuclease: bypass of the AP lyase activity step

The generation of reactive oxygen species in the cell provokes, among other lesions, the formation of 8-oxo-7,8-dihydroguanine (8-oxoG) in DNA. Due to mispairing with adenine during replication, 8-oxoG is highly mutagenic. To minimise the mutagenic potential of this oxidised purine, human cells have a specific 8-oxoG DNA glycosylase/AP lyase (hOGG1) that initiates the base excision repair (BER) of 8-oxoG. We show here that in vitro this first enzyme of the BER pathway is relatively inefficient because of a high affinity for the product of the reaction it catalyses (half-life of the complex is >2 h), leading to a lack of hOGG1 turnover. However, the glycosylase activity of hOGG1 is stimulated by the major human AP endonuclease, HAP1 (APE1), the enzyme that performs the subsequent step in BER, as well as by a catalytically inactive mutant (HAP1-D210N). In the presence of HAP1, the AP sites generated by the hOGG1 DNA glycosylase can be occupied by the endonuclease, avoiding the re-association of hOGG1. Moreover, the glycosylase has a higher affinity for a non-cleaved AP site than for the cleaved DNA product generated by HAP1. This would shift the equilibrium towards the free glycosylase, making it available to initiate new catalytic cycles. In contrast, HAP1 does not affect the AP lyase activity of hOGG1. This stimulation of only the hOGG1 glycosylase reaction accentuates the uncoupling of its glycosylase and AP lyase activities. These data indicate that, in the presence of HAP1, the BER of 8-oxoG residues can be highly efficient by bypassing the AP lyase activity of hOGG1 and thus excluding a potentially rate limiting step.

Metabolic Bypass of the Tricarboxylic Acid Cycle during Lipid Mobilization in Germinating Oilseeds1 : Regulation of NAD+-Dependent Isocitrate Dehydrogenase Versus Fumarase

Biosynthesis of sucrose from triacylglycerol requires the bypass of the CO2-evolving reactions of the tricarboxylic acid (TCA) cycle. The regulation of the TCA cycle bypass during lipid mobilization was examined. Lipid mobilization in Brassica napus was initiated shortly after imbibition of the seed and proceeded until 2 d postimbibition, as measured by in vivo [1-14C]acetate feeding to whole seedlings. The activity of NAD+-isocitrate dehydrogenase (a decarboxylative enzyme) was not detected until 2 d postimbibition. RNA-blot analysis of B. napus seedlings demonstrated that the mRNA for NAD+-isocitrate dehydrogenase was present in dry seeds and that its level increased through the 4 d of the experiment. This suggested that NAD+-isocitrate dehydrogenase activity was regulated by posttranscriptional mechanisms during early seedling development but was controlled by mRNA level after the 2nd or 3rd d. The activity of fumarase (a component of the nonbypassed section of the TCA cycle) was low but detectable in B. napus seedlings at 12 h postimbibition, coincident with germination, and increased for the next 4 d. RNA-blot analysis suggested that fumarase activity was regulated primarily by the level of its mRNA during germination and early seedling development. It is concluded that posttranscriptional regulation of NAD+-isocitrate dehydrogenase activity is one mechanism of restricting carbon flux through the decarboxylative section of the TCA cycle during lipid mobilization in germinating oilseeds.

Accuracy of lesion bypass by yeast and human DNA polymerase η

DNA polymerase η (Polη) functions in the error-free bypass of UV-induced DNA lesions, and a defect in Polη in humans causes the cancer-prone syndrome, the variant form of xeroderma pigmentosum. Both yeast and human Polη replicate through a cis-syn thymine-thymine dimer (TT dimer) by inserting two As opposite the two Ts of the dimer. Polη, however, is a low-fidelity enzyme, and it misinserts nucleotides with a frequency of ≈ 10−2 to 10−3 opposite the two Ts of the TT dimer as well as opposite the undamaged template bases. This low fidelity of nucleotide insertion seems to conflict with the role of Polη in the error-free bypass of UV lesions. To resolve this issue, we have examined the ability of human and yeast Polη to extend from paired and mispaired primer termini opposite a TT dimer by using steady-state kinetic assays. We find that Polη extends from mispaired primer termini on damaged and undamaged DNAs with a frequency of ≈ 10−2 to 10−3 relative to paired primer termini. Thus, after the incorporation of an incorrect nucleotide, Polη would dissociate from the DNA rather than extend from the mispair. The resulting primer-terminal mispair then could be subject to proofreading by a 3′→5′ exonuclease. Replication through a TT dimer by Polη then would be more accurate than that predicted from the fidelity of nucleotide incorporation alone.

Aplicação de gelatina obtida de subproduto animal como substituto parcial de gordura em spread de chocolate

O objetivo do presente estudo foi verificação da viabilidade da aplicação de gelatina de pés de frango em spread de chocolate como substituto parcial de gordura. Inicialmente apresentou-se uma revisão de literatura sobre os principais aspectos que envolvem a pesquisa. Após relatou-se a metodologia de extração e caracterização físico-química da gelatina obtida de pés de frango por meio de análises de composição centesimal, de cor, força de gel e análise de perfil de textura (TPA). Posteriormente abordou-se os efeitos da aplicação de gelatina como substituto de gordura nas propriedades físico-químicas e reológicas de spread de chocolate. Por último investigou-se a influência da concentração de gelatina e substituição de gordura na espalhabilidade, estabilidade (shelf life), custos e propriedades sensoriais dos spreads de chocolate. Para tanto, foi utilizado planejamento experimental Central Composto Rotacional e metodologia de superfície de resposta. Os resultados da extração de gelatina de subproduto de frango indicaram que as peles e tendões dos pés de frango possuem rendimento (7,83 %) e conteúdo mineral (1,92 %), apresentando alto teor proteico (84,96 %) próximo das gelatinas comerciais. Em concentração de 6,67 % a gelatina demonstrou elevada força de gel (294,78 g), comportando-se na análise de perfil de textura como um sólido. Os dados relacionados às formulações de spread de chocolate demonstraram que tanto o nível de substituição de gordura quanto a concentração de gelatina exerceram efeitos significativos (p<0,05) sobre a cor, volume, densidade e comportamento reológico dos produtos, exceto a atividade de água que foi influenciada apenas pelo primeiro fator. Sob a perspectiva reológica apenas a amostra com maior nível de substituição de gordura foi classificada como pseudoplástica. A gelatina contribuiu no aumento do teor proteico das formulações. A consistência foi significativamente (p<0,05) influenciada pelas propriedades da fase de gelatina, apresentando ampla faixa de plasticidade nas diferentes temperaturas (10, 20 e 30 °C). A consistência dos spreads aumentou em todas as temperaturas durante os 90 dias de armazenamento. Observou-se por meio da análise sensorial que os fatores em estudo provocaram alterações nos atributos sensoriais do produto suficiente para a percepção dos provadores. A formulação com 75 % de substituição de gordura seguida pelas formulações com 50 % e 0,8 % de concentração de gelatina apresentaram a maior aceitabilidade. Com o máximo de substituição de gordura chegou-se a 53 % de redução de custos. Contudo, os resultados obtidos sugerem que a aplicação de gelatina de pés de frango pode ser vantajosa, já que contribuiu com a formulação de spreads de chocolate menos calóricos e com propriedades físico-químicas e sensoriais adequadas para uma possível comercialização.

Fatores associados à quantidade e tipos de gordura disponível para consumo, presentes nos alimentos industrializados adquiridos pelas famílias paulistanas

Este trabalho examina o papel dos alimentos industrializados no acesso às gorduras. Ele analisa os determinantes socioeconâmicos da quantidade e do tipo de gordura disponível para consumo pelas famílias paulistanas, presentes nos alimentos industrializados. Essa análise envolveu uma amostra de 576 famílias no município de São Paulo, cujos dados foram coletados no período de 2008 a dezembro de 20 10, selecionada após alguns critérios excludentes. A fonte dos dados é a Pesquisa de Orçamentos Familiares da FIPE, que está em andamento desde 2008, atualizada através da ponderação do Índice de Custo de Vida da FIPE. Baseado em métodos analíticos de estatística descritiva (média, desvio-padrão, mediana), testes t de student, e métodos econométricos de regressão múltipla, alguns resultados foram encontrados. Os fatores associados aos gastos com alimentos industrializados foram renda, tamanho da família, idade e grau de instrução do chefe. Em relação à gordura total identificou-se como fatores associados renda, tamanho da família, idade do chefe, a presença de crianças na família e a proporção do gasto com alimentação com derivados de leite e derivados de carne.