Poly(8-bromo-2'-deoxyadenylic acid): the syn/anti relationship

The synthesis of a high-molecular-weight, putatively all-syn DNA analogue, poly(8-bromo-2'-deoxyadenylic acid), is described. The syn----anti transition was shown to be both salt and temperature dependent. Conditions were found which favored 'normal' Watson-Crick pairing and duplex formation with poly(dT).     

Protein synthesis using poly(2′-halogeno-2′-deoxyadenylic acids) as messenger

Poly(2′-fluoro-2′-deoxyadenylic acid), poly(2′-chloro-2′-deoxyadenylic acid) and poly(2′-bromo-2′-deoxyadenylic acid) are used as messenger RNAs in protein synthesizing systems in vitro. All polynucleotides were active as messengers and [¹⁴C]lysine was incorporated into polypeptides. The initial velocity of polylysine formation was greater using poly(2′-fluoro-2′-deoxyadenylic acid) as messenger than in the case of poly(rA), and all synthetic messengers lived longer in the protein synthetic system.     

Incorporation of 5-bromo-2′deoxyuridine (BUdR) in Dictyostelium discoideum DNA

The modality of incorporation of 5-bromo-2′deoxyuridine (BUdR) in the DNA of Dictyostelium discoideum was studied after one generation of growth of the amoebae in the presence of different concentrations of the drug. The analog was incorporated following the semiconservative pattern of DNA replication. BUdR incorporation in monosubstituted DNA has been measured both by CsCl isopycnic centrifugation or by base analysis chromatography; substitution of thymidine by its analog reaches a maximal value of 30% (60% in the substituted strand). Up to 20% substitution it is proportional to the drug concentration in the growth medium. In these conditions, thymidine substitution is higher in repetitive sequences of the DNA than in unique sequences; the percent of increase of thymidine substitution in repetitive fractions versus total DNA is inversely proportional to thymidine substitution in total DNA.     

The binding of Ni2+ to adenylyl-3',5'-adenosine and to poly(adenylic acid)

Studies of the binding of Ni²⁺ to adenylyl-3',5'-adenosine (ApA) at pH 6-0 by ultraviolet spectrophotometry indicate the formation of a 1:1 complex in the presence of a large excess of metal ion. At 25 °C. and ionic strength μ = 0.5 M, the stability constant of Ni(ApA) is evaluated to be K = 2.6 (±0.6) M^?1. The low stability is taken as evidence that the predominant complex species is one in which the ApA acts as a monodentate ligand, mainly through the adenine group. The rate constants for complex formation and dissociation, k_f = 1430 M^?1 s^?1 and k_b = 665 s^?1 (25°C. μ = 0.5M). determined by the temperature-jump relaxation technique, are consistent with this interpretation. The binding strength of Ni²⁺ to poly(adenylic acid) [poly(A)] has been studied at pH 7.0 using murexide as an indicator of the concentration of free Ni²⁺. Within the concentration range [Ni²⁺ = 1 × 10^?5 × 10^?3 M the data can be represented in the form of a linear Scatchard plot. i.e., the process can be described as the binding of Ni²⁺ to one class of independent binding sites. The number of binding sites per monomer is 0.26, and the stability constant K = 8.2×10³ M^?1 (25°C μ = 0.1 M). In kinetic studies of the reaction of Ni²⁺ with poly(A), two relaxation effects due to complex formation were detected, one with a concentration-independent time constant of about 0.4 ms, the other with a concentration-dependent time constant in the millisecond range. The concentration dependence of the longer relaxation time can be accounted for by a three-step mechanism which consists of a fast second-order association reaction followed by two first-order steps. There is evidence, however, that the overall process is more complicated than expressed by the three-step mechanism.     

Cyclic 3′,5′-AMP phosphodiesterase in Physarum polycephalum: II. Kinetic properties

The effect of several inhibitors of the enzyme cyclic 3′,5′-AMP phosphodiesterase as chemoattractants in Physarum polycephalum was examined. Of the compounds tested, 4-(3-butoxy-4-methoxybenzyl)-2-imidazolidinone (Roche 20-1724/001) and 1-ethyl-4-(isopropylidinehydrazino)-1H-pyrazolo-(3,4-b)-pyridine-5-carboxylic acid ethyl ester, hydrochloride (Squibb 20009) were the most potent attractants. 3-Isobutyl-1-methyl xanthine, theophylline, and morin (a flavanoid) were moderate attractants and sometimes gave negative chemotaxis at high concentrations. Cyclic 3′,5′-AMP was an effective, but not potent attractant. A repellent effect following the positive chemotactic action was sometimes observed with cyclic 3′,5′-AMP at concentrations as high as 1 · 10⁻² M. Dibutyryl cyclic AMP appeared to be a somewhat more potent attractant than cyclic 3′,5′-AMP. The 8-thiomethyl and 8-bromoderivatives of cyclic AMP, which are poorly hydrolyzed by the phosphodiesterase, were not attractants in Physarum. Possible participation of cyclic 3′,5′-AMP in the directional movement in P. polycephalum is discussed.     

Inhibition of replicative DNA synthesis in nuclei of Strongylocentrotus intermedium urchin embryo by 2′,3′-dideoxy-3′-aminonucleoside 5′-triphosphates

2′,3′-Dideoxy-3′-aminonucleoside 5′-triphosphates have been shown to be inhibitors of replicative DNA synthesis in isolated nuclei of sea urchin embryo. These compounds inhibit the Okazaki fragment synthesis. The effect of 2′,3′-dideoxy-3′-aminothymidine 5′-triphosphate and arabinothymidine 5′-triphosphate is reversible when adding the corresponding substrate for DNA synthesis, 2′-deoxythymidine 5′-triphosphate.     

2′-hydroxymethyl abscisic acid: A major catabolite of (±)-abscisic acid in leaves of Hordeum vulgare L.

Radioactive (±)-abscisic acid (ABA), supplied via the transpiration stream to light-grown leaves of Hordeum vulgare was catabolized to 2′-hydroxymethyl ABA. Identification was made by capillary gas chromatography-mass spectrometry (GC-MS).     

L-乳酸的发酵生产和聚L-乳酸的化学加工

L-乳酸广泛应用于食品、医药、日化和工业等各个领域。近年来随着石化资源的不断紧缺,众多化学合成的高分子材料的生产受到了限制。以生物质资源为基础的L-乳酸因此被大量用于加工生产成聚L-乳酸等环境友好型生物可降解材料。正是由于L-乳酸需求量的增大,如何高效低成本地生产L-乳酸显得尤为重要。系统综述了L-乳酸生产菌株的选育,用于L-乳酸发酵生产的廉价资源的开发利用,L-乳酸的发酵生产和L-乳酸的分离纯化等方面的研究进展。目前研究的热点和难点正是基于上述四个部分:菌种方面,以可以高效代谢利用廉价底物,且营养需求低的选育目标获得了多个优良的生产菌种,然而具备综合代谢优势的菌种还有待进一步选育;发酵底物方面,已开发利用多种廉价,来源丰富且易于菌种代谢并高效转化成乳酸的底物,但是对这些底物工业规模应用还有待进一步研究;发酵工艺方面,建立了环境友好型,劳动强度低的发酵工艺,然而实际应用中仍然存在成本高的问题;后提取方面,通过选育低营养需求的生产菌种和采用新型发酵工艺有效地简化了后提取过程,但是实际应用方面仍受发酵工艺成本高的制约。最后对聚L-乳酸的化学加工以及聚L-乳酸的生物降解进行了探讨并提出了一些建议。     

Poly (glutamic acid)--an emerging biopolymer of commercial interest

Poly (γ-glutamic acid) (PGA) is water-soluble, anionic, biodegradable, and edible biopolymer produced by Bacillus subtilis. It has multifarious potential applications in foods, pharmaceuticals, healthcare, water treatment and other fields. The production of PGA has already been established on the industrial scale. Various studies regarding the fermentative production, downstream processing and characterization of PGA have been reported in the literature. This review provides updated information on fermentative production of PGA by various bacterial strains and effect of fermentation conditions and media component on production of PGA in submerged as well as solid state fermentation. Information on the application of genetic engineering for enhancement of yield of PGA, kinetic studies for production of PGA in submerged fermentation and recovery and purification of PGA is included. An attempt has also been made to review the current and potential applications of PGA. This review may contribute to further development of this commercially and academically interesting biopolymer.     

Poly (I:C) therapy decreases cerebral ischaemia/reperfusion injury via TLR3‐mediated prevention of Fas/FADD interaction

Toll‐like receptor (TLR)‐mediated signalling plays a role in cerebral ischaemia/reperfusion (I/R) injury. Modulation of TLRs has been reported to protect against cerebral I/R injury. This study examined whether modulation of TLR3 with poly (I:C) will induce protection against cerebral I/R injury. Mice were treated with or without Poly (I:C) (n = 8/group) 1 hr prior to cerebral ischaemia (60 min.) followed by reperfusion (24 hrs). Poly (I:C) pre‐treatment significantly reduced the infarct volume by 57.2% compared with untreated I/R mice. Therapeutic administration of Poly (I:C), administered 30 min. after cerebral ischaemia, markedly decreased infarct volume by 34.9%. However, Poly (I:C)‐induced protection was lost in TLR3 knockout mice. In poly (I:C)‐treated mice, there was less neuronal damage in the hippocampus compared with untreated I/R mice. Poly (I:C) treatment induced IRF3 phosphorylation, but it inhibited NF‐κB activation in the brain. Poly (I:C) also decreased I/R‐induced apoptosis by attenuation of Fas/FasL‐mediated apoptotic signalling. In addition, Poly (I:C) treatment decreased microglial cell caspase‐3 activity. In vitro data showed that Poly (I:C) prevented hypoxia/reoxygenation (H/R)‐induced interaction between Fas and FADD as well as caspase‐3 and ‐8 activation in microglial cells. Importantly, Poly (I:C) treatment induced co‐association between TLR3 and Fas. Our data suggest that Poly (I:C) decreases in cerebral I/R injury via TLR3 which associates with Fas, thereby preventing the interaction of Fas and FADD, as well as microglial cell caspase‐3 and ‐8 activities. We conclude that TLR3 modulation by Poly (I:C) could be a potential approach for protection against ischaemic stroke.     

Effect of polyamines on the uptake of poly (2′-fluoro-2′-deoxyuridylic acid) by a mammalian cell line

VERO cells can take up poly(dUfl)¹ from the medium. The uptake involves surface adsorption and, most probably, intracellular penetration. Part of the poly(dUfl) is hydrolyzed during incubation with the cells but the hydrolysis products are not incorporated into de novo synthesized nucleic acids. The uptake is reduced by serum and stimulated by polycationic ionenes. The magnitude of stimulation depends on the structure of the ionene and the treatment regimen.     

Poly(ADP-ribose): PARadigms and PARadoxes

Poly(ADP-ribosyl)ation (PARylation) is a posttranslational protein modification (PTM) catalyzed by members of the poly(ADP-ribose) polymerase (PARP) enzyme family. PARPs use NAD⁺ as substrate and upon cleaving off nicotinamide they transfer the ADP-ribosyl moiety covalently to suitable acceptor proteins and elongate the chain by adding further ADP-ribose units to create a branched polymer, termed poly(ADP-ribose) (PAR), which is rapidly degraded by poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribosylhydrolase 3 (ARH3). In recent years several key discoveries changed the way we look at the biological roles and mode of operation of PARylation. These paradigm shifts include but are not limited to (1) a single PARP enzyme expanding to a PARP family; (2) DNA-break dependent activation extended to several other DNA dependent and independent PARP-activation mechanisms; (3) one molecular mechanism (covalent PARylation of target proteins) underlying the biological effect of PARPs is now complemented by several other mechanisms such as protein–protein interactions, PAR signaling, modulation of NAD⁺ pools and (4) one principal biological role in DNA damage sensing expanded to numerous, diverse biological functions identifying PARP-1 as a real moonlighting protein. Here we review the most important paradigm shifts in PARylation research and also highlight some of the many controversial issues (or paradoxes) of the field such as (1) the mostly synergistic and not antagonistic biological effects of PARP-1 and PARG; (2) mitochondrial PARylation and PAR decomposition, (3) the cross-talk between PARylation and signaling pathways (protein kinases, phosphatases, calcium) and the (4) divergent roles of PARP/PARylation in longevity and in age-related diseases.     

重组大肠杆菌转化甘油合成聚3-羟基丙酸-co-乳酸

聚羟基脂肪酸酯作为性质优良的生物塑料,引起了广泛的关注。由于聚羟基脂肪酸合成酶PhaC特异性较强,难以通过生物合成方法获得含乳酸单体聚合物。为了实现乳酸的聚合,PhaC的筛选至关重要。以甘油为底物,通过引入Klebsiella pneumoniae的甘油脱水酶DhaB123及其激活因子GdrAB以及Salmonella typhimurium LT2的丙醛脱氢酶基因PduP,获得3-羟基丙酰辅酶A;通过引入Megasphaera elsdenii DSM 20460的丙酰辅酶A转移酶PCT,获得乳酰辅酶A;并对3种不同聚羟基脂肪酸合成酶的作用进行考察。在Pseudomonas putida的原始酶PhaC1或者PhaC2的作用下,不能实现乳酸的聚合;而在双位点突变(Ser325Thr和Gln481Lys)的PhaC1(STQK)存在条件下,重组菌可以利用甘油合成聚3-羟基丙酸-co-乳酸。经过对溶氧、有机氮源等发酵条件的优化,聚3-羟基丙酸-co-乳酸的产量可以达到0.22g/L,占细胞干重的3.2%,是含乳酸单体聚合物生物合成研究的一次有益尝试。     

Site binding as a local equilibrium. Mn2+ binding to poly(acrylic acid) as a function of the degree of ionization

Mn2+ binding to poly(acrylic acid) at different degrees of ionization, alpha, has been studied from the frequency dependence of the water protons' relaxation rates T1(-1) and T2(-1). Site binding is treated as an equilibrium with the concentration of free ions at the immediate vicinity (CIV) of the polyion. The CIV is calculated as the solution of the Poisson-Boltzmann equation at the surface of the cylindrical polyion. A single value of K is shown to fit the results at all values of alpha. The amount of site binding is higher than the total amount of condensed divalent counterions predicted for a finite polyion concentration in the presence of monovalent counterions by Manning's theory.     

费氏中华根瘤菌合成羟基丁酸和羟基己酸共聚体的研究

进行了费氏中华根瘤菌(Sinorhizobium fredii)合成羟基丁酸和羟基己酸共聚体[P(HB-HH)]的研究,通过摇瓶正交试验优化了培养基成分、培养条件和癸酸盐调控条件,采用发酵罐分批发酵和两阶段补料分批发酵方式及两步加盐法研究了P(HB-HH)的高密度发酵技术参数。经55h发酵,P(HB-HH)产量可以达到17.55g/L,其中HH单体含量占共聚体的20.6%,该共聚体的分子量约为1.4×105D。结果表明S.fredii的生产性状优良,有可能通过该菌株的高密度发酵与代谢调控实现P(HB-HH)的工业化生产。     

重组肺炎克雷伯氏菌转化甘油为聚3-羟基丙酸

聚3-羟基丙酸[Poly(3-hydroxypropionate),P3HP]是一种生物可降解及生物相容的新型聚羟基脂肪酸酯。目前已鉴定的生物均不能天然合成P3HP。采用PCR克隆鼠伤寒沙门氏菌的丙醛脱氢酶(Pdu P)基因及罗尔斯通氏菌的聚羟基脂肪酸酯合成酶(Pha C)基因,构建共表达载体,转化肺炎克雷伯氏菌后获得两株重组菌。以甘油为唯一碳源进行摇瓶发酵,pdu P和pha C共用tac启动子的工程菌K.p(p ET-tac-pdu P-pha C)产生0.054 g/L的P3HP,而pdu P和pha C各自独用tac启动子的工程菌K.p(p ET-tac-pdu P-tac-pha C)产生0.091 g/L的P3HP。     

Poly(ADP-ribose) protects vascular smooth muscle cells from oxidative DNA damage

Vascular smooth muscle cells (VSMCs) undergo death during atherosclerosis, a widespread cardiovascular disease. Recent studies suggest that oxidative damage occurs in VSMCs and induces atherosclerosis. Here, we analyzed oxidative damage repair in VSMCs and found that VSMCs are hypersensitive to oxidative damage. Further analysis showed that oxidative damage repair in VSMCs is suppressed by a low level of poly (ADP-ribosyl)ation (PARylation), a key post-translational modification in oxidative damage repair. The low level of PARylation is not caused by the lack of PARP-1, the major poly(ADP-ribose) polymerase activated by oxidative damage. Instead, the expression of poly(ADP-ribose) glycohydrolase, PARG, the enzyme hydrolyzing poly(ADP-ribose), is significantly higher in VSMCs than that in the control cells. Using PARG inhibitor to suppress PARG activity facilitates oxidative damage-induced PARylation as well as DNA damage repair. Thus, our study demonstrates a novel molecular mechanism for oxidative damage-induced VSMCs death. This study also identifies the use of PARG inhibitors as a potential treatment for atherosclerosis. [BMB Reports 2015; 48(6): 354-359]     

HMGN1 Protein Regulates Poly(ADP-ribose) Polymerase-1 (PARP-1) Self-PARylation in Mouse Fibroblasts

In mammalian cells, the nucleosome-binding protein HMGN1 (high mobility group N1) affects the structure and function of chromatin and plays a role in repair of damaged DNA. HMGN1 affects the interaction of DNA repair factors with chromatin and their access to damaged DNA; however, not all of the repair factors affected have been identified. Here, we report that HMGN1 affects the self-poly(ADP-ribosyl)ation (i.e., PARylation) of poly(ADP-ribose) polymerase-1 (PARP-1), a multifunctional and abundant nuclear enzyme known to recognize DNA lesions and promote chromatin remodeling, DNA repair, and other nucleic acid transactions. The catalytic activity of PARP-1 is activated by DNA with a strand break, and this results in self-PARylation and PARylation of other chromatin proteins. Using cells obtained from Hmgn1(-/-) and Hmgn1(+/+) littermate mice, we find that in untreated cells, loss of HMGN1 protein reduces PARP-1 self-PARylation. A similar result was obtained after MMS treatment of these cells. In imaging experiments after low energy laser-induced DNA damage, less PARylation at lesion sites was observed in Hmgn1(-/-) than in Hmgn1(+/+) cells. The HMGN1 regulation of PARP-1 activity could be mediated by direct protein-protein interaction as HMGN1 and PARP-1 were found to interact in binding assays. Purified HMGN1 was able to stimulate self-PARylation of purified PARP-1, and in experiments with cell extracts, self-PARylation was greater in Hmgn1(+/+) than in Hmgn1(-/-) extract. The results suggest a regulatory role for HMGN1 in PARP-1 activation.     

Kinetics of molecular weight reduction of poly(glutamic acid) by in situ depolymerization in cell-free broth of Bacillus subtilis

Poly(glutamic acid) (PGA) is a water soluble, biodegradable biopolymer that is produced by microbial fermentation. Recent research has shown that poly(glutamic acid) can be used in drug delivery applications for the controlled release of paclitaxel (Taxol) in cancer treatment. The molecular weight of microbial poly(glutamic acid) is generally larger than what is required for drug delivery. As such, molecular weight reduction is a necessary step in producing poly(glutamic acid) for this application. Poly(glutamic acid) produced by Bacillus subtilis IFO 3335 was subjected to in situ depolymerization in the cell-free fermentation broth. Molecular weight reduction was measured, and an empirical kinetic model was used to correlate the experimental data. The kinetic rate constant, k, was found to be 6.92 × 10⁻⁶ h⁻¹ at pH 7.0 and 37 °C, which were the optimum depolymerization conditions.     

The relationship between the fatty acid profiles of the yolk and the embryonic tissue lipids: A comparison between the lesser black backed gull (Larus fuscus) and the pheasant (Phasianus colchicus)

Although substantial information is available regarding the fatty acid composition of lipids of the yolk and of the developing tissues of the chicken embryo, there is little knowledge on this topic for other avian species. The aim of the present study was to compare the yolk and embryonic tissue fatty acid profiles for a species selecting its food in the wild (the lesser black backed gull) with one fed on a standard commercial diet (the commercially reared pheasant). The fatty acid compositions of the yolk lipids were determined, and major differences were observed between the two species. In particular, the phospholipid of the gull yolk was enriched in 20:4n-6 and 22:6n-3 (18.8 and 7.1%, respectively, by weight of total fatty acids) in comparison with the pheasant (4.0 and 4.1%, respectively). The fatty acid compositions of the embryonic tissues were determined using eggs incubated in the laboratory. For the liver and heart, the fatty acid composition of the lipids in the two species reflected the initial yolk composition, with the gull tissue lipids generally containing higher proportions of 20:4n-6 and 22:6n-3 than those of the pheasant. In contrast, the fatty acid profiles of the brain phospholipid were essentially identical in the two species, with 20:4n-6 and 22:6n-3 comprising approximately 9 and 17%, respectively, of total fatty acids in both cases.