Crystal structures of Drosophila mutant translin and characterization of translin variants reveal the structural plasticity of translin proteins

Translin protein is highly conserved in eukaryotes. Human translin binds both ssDNA and RNA. Its nucleic acid binding site results from a combination of basic regions in the octameric structure. We report here the first biochemical characterization of wild-type Drosophila melanogaster (drosophila) translin and a chimeric translin, and present 3.5 A resolution crystal structures of drosophila P168S mutant translin from two crystal forms. The wild-type drosophila translin most likely exists as an octamer/decamer, and binds to the ssDNA Bcl-CL1 sequence. In contrast, ssDNA binding-incompetent drosophila P168S mutant translin exists as a tetramer. The structures of the mutant translin are identical in both crystal forms, and their C-terminal residues are disordered. The chimeric protein, possessing two nucleic acid binding motifs of drosophila translin, the C-terminal residues of human translin, and serine at position 168, attains the octameric state and binds to ssDNA. The present studies suggest that the oligomeric status of translin critically influences the DNA binding properties of translin proteins.     

Biofuel alternatives to ethanol: pumping the microbial well

Engineered microorganisms are currently used for the production of food products, pharmaceuticals, ethanol fuel and more. Even so, the enormous potential of this technology has yet to be fully exploited. The need for sustainable sources of transportation fuels has generated a tremendous interest in technologies that enable biofuel production. Decades of work have produced a considerable knowledge-base for the physiology and pathway engineering of microbes, making microbial engineering an ideal strategy for producing biofuel. Although ethanol currently dominates the biofuel market, some of its inherent physical properties make it a less than ideal product. To highlight additional options, we review advances in microbial engineering for the production of other potential fuel molecules, using a variety of biosynthetic pathways.     

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution

Lupins are important grain legume crops that form a critical part of sustainable farming systems, reducing fertilizer use and providing disease breaks. It has a basal phylogenetic position relative to other crop and model legumes and a high speciation rate. Narrow‐leafed lupin (NLL; Lupinus angustifolius L.) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten‐free. We report the draft genome assembly (609 Mb) of NLL cultivar Tanjil, which has captured >98% of the gene content, sequences of additional lines and a dense genetic map. Lupins are unique among legumes and differ from most other land plants in that they do not form mycorrhizal associations. Remarkably, we find that NLL has lost all mycorrhiza‐specific genes, but has retained genes commonly required for mycorrhization and nodulation. In addition, the genome also provided candidate genes for key disease resistance and domestication traits. We also find evidence of a whole‐genome triplication at around 25 million years ago in the genistoid lineage leading to Lupinus. Our results will support detailed studies of legume evolution and accelerate lupin breeding programmes.     

DNA adducts and liver DNA replication in rats during chronic exposure to N-nitrosodimethylamine (NDMA) and their relationships to the dose-dependence of NDMA hepatocarcinogenesis

Exposure of rats to the hepatocarcinogen N-nitrosodimethylamine (NDMA) (0.2-2.64 ppm in the drinking water) for up to 180 days resulted in rapid accumulation of N7- and O6-methylguanine in liver and white blood cell DNA, maximum adduct levels being reached within 1-7 days, depending on the dose. The levels of both adducts remained constant up to treatment day 28, subsequently declining slowly to about 40% of maximal levels for the liver and 60% for white blood cells by day 180. In order to elucidate the role of DNA replication in NDMA hepatocarcinogenesis, changes in liver cell labeling index (LI) were also measured on treatment days 21, 120 and 180. Although the time- and dose-dependence of the observed effects were complex, a clear trend towards increased rates of hepatocyte LI, as indicated by BrdU incorporation, with increasing NDMA doses was evident, particularly above 1 ppm, a concentration above which NDMA hepatocarcinogenicity is known to increase sharply. In contrast, no increase in Kupffer cell DNA replication was found at any of the doses employed, in accordance with the low susceptibility of these cells to NDMA-induced carcinogenesis. No significant increase in the occurrence of necrotic or apoptotic cells was noted under the treatment conditions employed. These results suggest that, in addition to the accumulation of DNA damage, alterations in hepatocyte DNA replication during the chronic NDMA exposure may influence the dose-dependence of its carcinogenic efficacy.     

Chemical induction of physiological changes during adventitious root formation and bud break in grapevine cuttings

The effects of some terpenoids (isopatchoulenone-rich fraction ofCyperus scariosus oil, C16-guaianolide and thymol), anauxin (IBA) and a combination of terpenoids and IBA were investigated onrooting, sprouting and accompanying biochemical changes in grapevine cuttingsvar. perlette. Treatment of cuttings for 24 h before planting insand pots caused stimulatory effects in terms of number of primary roots,lengthof longest primary root and shoot length, with a concomitant increase in totaldry weight of roots and shoots over control at 60 days after planting stage.Theactivities of peroxidase, polyphenol oxidase and the content of total phenolsdeclined in comparison with the control, hence sparing IAA resulted in enhancedcontents for the induction of adventitious roots. Different terpenoidtreatmentsalso significantly enhanced the chl a, chl b and total chl content in leaves.The levels of total soluble sugars, reducing sugars and proteins also alteredwith these terpenoids. C.S. oil and C16-guaianolide exhibited a better responsein combination with 100 g ml^–1 IBA, whichsuggests its synergistic effect.     

Ring A-seco mosquito larvicidal limonoids from Turraea wakefieldii

Five novel limonoids, 1-5, were isolated from the root bark of Turraea wakefieldii and were characterized as tecleaninoid derivatives. This is the first report of the natural occurrence of tecleanin-type limonoids with a five-membered-ring A-seco structure for which we propose the name neotecleanins. The relative stereochemical structures of compounds 1-5 were established on the basis of NMR spectroscopy. The absolute stereochemical structure of 5 was confirmed by X-ray diffraction methods. In mosquito larvicidal assays, compounds 1, 2 and 4 showed dose-dependent larvicidal activity against larvae of Anopheles gambiae s.s.     

Effects of exogenous vitamin E supplementation on the levels of oxidants and antioxidants in chronic obstructive pulmonary disease

Oxidative stress has been recognized as a central feature of smoke induced chronic obstructive pulmonary disease (COPD). Imbalance between oxidant and antioxidant enzymes is also an established fact in these patients. But studies in regard to stable COPD patients and effect of vitamin E supplementation are lacking. Thirty patients with COPD were included in the study. Their baseline clinical examination, spirometry, plasma malondialdehyde (MDA), alpha-tocopherol and red blood cell superoxide dismutase (SOD) levels were mea sured. Twenty healthy non-smokers who were matched for age and sex served as controls. All the above parameters were repeated after 12 weeks of supplementation with 400 IU of vitamin E daily. The mean malondialdehyde levels in the patients at baseline were higher than controls (5.91 +/- 1.23 nmol/ml vs 4.55 +/- 1.51 nmol/ml, P = 0 001), so also was plasma alpha-tocopherol levels (P < 0 001), while SOD levels were lower in the patients compared to controls (1692 +/- 259 units g/Hb vs 2451 +/- 131 units g/Hb, P < 0 001). Exogenous vitamin E (400 IU per day) supplementation did not bring about any significant change in plasma alpha-tocopherol and SOD levels. The Pearson s co-efficient of correlation between the levels of MDA, vitamin E, SOD; and spirometric measurements were not significant either on day 1 or after 12 weeks of vitamin E supplementation. The present study shows that initially the plasma lipid peroxide (MDA) levels are high and antioxidants (alpha-tocopherol and SOD) are low in patients with COPD. Exogenous supplementation with vitamin E does not have any significant effect on the spirometric measurements though it brings down the levels of MDA showing attenuation of further damage. However, inclusion of larger number of patients and supple mentation with vitamin E for longer periods may throw more light on free radical injury and protective effects of antioxidants.     

Lipid peroxidation and antioxidant defence status during larval development and metamorphosis of giant prawn,Macrobrachium rosenbergii

In the present communication we studied the involvement of reactive oxygen species and alteration in antioxidant defence status during larval development and metamorphosis of giant prawn, Macrobrachium rosenbergii. Overall results indicate that there was a decline in endogenous lipid peroxidation level during larval development. Activity of superoxide dismutase was the lowest in early larval stages (Zoea-I and II) and thereafter increased in V and VI stages, followed by a decrease in the subsequent larval stages. Catalase and glutathione peroxidase did not exhibit specific pattern of changes during development. Reduced glutathione content exhibited an incremental increase during larval progression until metamorphosis. Ascorbic acid content of the larval tissue remained unaltered during development but a sharp fall was marked in its content in the post-larvae. Hence it is concluded that early larvae face high oxidative stress as evident from the high content of thiobarbituric acid reactive substances. This may be due to direct exposure of larvae to ambient oxygen of the water as well as their low antioxidant potential. However, during development with the augmentation in antioxidant reserve of the larval tissues a diminution in the oxidative stress was recorded. Thus it is presumed that antioxidant defences play an important role in providing protection to the developing larvae from oxidative assault during larval progression and metamorphosis.     

raiIR genes are part of a quorum-sensing network controlled by cinI and cinR in Rhizobium leguminosarum

Analysis of N-acyl-L-homoserine lactones (AHLs) produced by Rhizobium leguminosarum bv. viciae indicated that there may be a network of quorum-sensing regulatory systems producing multiple AHLs in this species. Using a strain lacking a symbiosis plasmid, which carries some of the quorum-sensing genes, we isolated mutations in two genes (raiI and raiR) that are required for production of AHLs. The raiIR genes are located adjacent to dad genes (involved in D-alanine catabolism) on a large indigenous plasmid. RaiR is predicted to be a typical LuxR-type quorum-sensing regulator and is required for raiI expression. The raiR gene was expressed at a low level, possibly from a constitutive promoter, and its expression was increased under the influence of the upstream raiI promoter. Using gene fusions and analysis of AHLs produced, we showed that expression of raiI is strongly reduced in strains carrying mutations in cinI or cinR, genes which determine a higher-level quorum-sensing system that is required for normal expression of raiIR. The product of CinI, N-(3-hydroxy-7-cis tetradecenoyl) homoserine lactone, can induce raiR-dependent raiI expression, although higher levels of expression are induced by other AHLs. Expression of raiI in a strain of Agrobacterium that makes no AHLs resulted in the identification of N-(3-hydroxyoctanoyl)-L-homoserine lactone (3OH,C(8)-HSL) as the major product of RaiI, although other AHLs that comigrate with N-hexanoyl-, N-heptanoyl-, and N-octanoyl-homoserine lactones were also made at low levels. The raiI gene was strongly induced by 3OH,C(8)-HSL (the product of RaiI) but could also be induced by other AHLs, suggesting that the raiI promoter can be activated by other quorum-sensing systems within a network of regulation which also involves AHLs determined by genes on the symbiotic plasmid. Thus, the raiIR and cinIR genes are part of a complex regulatory network that influences AHL biosynthesis in R. leguminosarum.     

The distribution of cofilin and DNase I in vivo

Actin is the principal component of the cytoskeleton, a structure that can be disassembled and reassembled in a matter of seconds in vivo. The state of assembly of actin in vivo is primarily regulated by one or more actin binding proteins (ABPs). Typically, the actions of ABPs have been studied one by one, however, we propose that multiple ABPs, acting cooperatively, may be involved in the control of actin filament length. Cofilin and DNase I are two ABPs that have previously been demonstrated to form a ternary complex with actin in vitro. This is the first report to demonstrate their co-localisation in vivo, and differences in their distributions. Our observations strongly suggest a physiological role for higher order complexes of actin in regulation of cytoskeletal assembly during processes such as cell division.