Structure-function analysis of Escherichia coli DNA helicase I reveals non-overlapping transesterase and helicase domains

TraI (DNA helicase I) is an Escherichia coli F plasmid-encoded protein required for bacterial conjugative DNA transfer. The protein is a sequence-specific DNA transesterase that provides the site- and strand-specific nick required to initiate DNA strand transfer and a 5' to 3' DNA helicase that unwinds the F plasmid to provide the single-stranded DNA that is transferred from donor to recipient. Sequence comparisons with other transesterases and helicases suggest that these activities reside in the N- and C-terminal regions of TraI, respectively. Computer-assisted secondary structure probability analysis identified a potential interdomain region spanning residues 304-309. Proteins encoded by segments of traI, whose N or C terminus either flanked or coincided with this region, were purified and assessed for catalytic activity. Amino acids 1-306 contain the transesterase activity, whereas amino acids 309-1504 contain the helicase activity. The C-terminal 252 amino acids of the 1756-amino acid TraI protein are not required for either helicase or transesterase activity. Protein and nucleic acid sequence similarity searches indicate that the occurrence of both transesterase- and helicase-associated motifs in a conjugative DNA transfer initiator protein is rare. Only two examples (other than R100 plasmid TraI) were found: R388 plasmid TrwC and R46 plasmid (pKM101) TraH, belonging to the IncW and IncN groups of broad host range conjugative plasmids, respectively. The most significant structural difference between these proteins and TraI is that TraI contains an additional region of approximately 650 residues between the transesterase domain and the helicase-associated motifs. This region is required for helicase activity.     

The active site of the SET domain is constructed on a knot

The SET domain contains the catalytic center of lysine methyltransferases that target the N-terminal tails of histones and regulate chromatin function. Here we report the structure of the SET7/9 protein in the absence and presence of its cofactor product, S-adenosyl-L-homocysteine (AdoHcy). A knot within the SET domain helps form the methyltransferase active site, where AdoHcy binds and lysine methylation is likely to occur. A structure-guided comparison of sequences within the SET protein family suggests that the knot substructure and active site environment are conserved features of the SET domain.     

Microhabitat distribution of protostelids in a Tropical Wet Forest in Costa Rica

A microhabitat study of protostelids was carried out in a Tropical Wet Forest at the La Selva Biological Station in Costa Rica. Nine species were recorded from sterile wheat straws placed out and then re-collected over a period of six weeks from two different litter microhabitats in an area of primary forest. All nine species were present on straws placed in the aerial litter microhabitat, but only six species were present on straws placed in the forest floor litter microhabitat. Total colonies, percent of straws colonized, and mean number of species per straw increased significantly over time. One species (Schizoplasmodiopsis pseudoendospora) typical of temperate litter was the overwhelming dominant on the forest floor litter, while Echinostelium bisporum, a species rare in temperate litter microhabitats, was the single most abundant species in the aerial litter microhabitat. Both of these species had significantly increased frequencies over time. Two species abundant in temperate aerial litter microhabitats and one species abundant in temperate forest floor litter were rare at La Selva. Our data conform to those obtained in an earlier study carried out in tropical forests in the mountains of Puerto Rico and provide additional support towards developing a model of microhabitat distribution of protostelids in terrestrial ecosystems.     

Solubilization and controlled release of a hydrophobic drug using novel micelle-forming ABC triblock copolymers

Amphiphilic ABC triblock copolymers composed of monomethoxy-capped poly(ethylene glycol) (MPEG), poly(2-(dimethylamino)ethyl methacrylate) (DMA), and poly(2-(diethylamino)ethyl methacrylate) (DEA) have been synthesized by atom transfer radical polymerization (ATRP). These copolymers dissolve molecularly in acidic aqueous media at room temperature due to protonation of the tertiary amine groups on the DMA and DEA residues. On adjusting the pH with base, micellization occurred at pH 8, with the water-insoluble, deprotonated DEA block forming the hydrophobic cores and the MPEG and DMA blocks forming the hydrophilic micellar coronas and inner shells, respectively. This pH-induced micellization has been exploited to develop a solvent-free protocol for drug loading. A model hydrophobic drug, dipyridamole (DIP), which dissolves in acid but is insoluble above pH 5.8, was incorporated into the micelles by increasing the pH of an aqueous drug/copolymer mixture to 9. Both the empty and the drug-loaded micelles were characterized by dynamic light scattering and fluorescence studies. The interaction of both pyrene and DIP with the MPEG-DMA-DEA micelles was studied by fluorescence; both compounds had relatively high partition coefficients into the micelles, 4.5 x 10(5) and 1.5 x 10(4), respectively. Intensity-average micelle diameters ranged from 20 to 90 nm, depending on the polymer composition and concentration. Shorter MPEG blocks (Mn = 2000) produced larger micelles than longer MPEG blocks (Mn = 5000) due to the shift in the hydrophilic-hydrophobic balance of the copolymer. Transmission electron microscopy studies of the drug-loaded micelles indicated spherical morphologies and reasonably uniform particle size distributions, which is in marked contrast to the needlelike morphology observed for pure DIP in the absence of the copolymer. Experiments on controlled release demonstrated that DIP-loaded MPEG-DMA-DEA micelles act as a drug carrier, giving slow release to the surrounding solution over a period of days. Rapid release can be triggered by reducing the pH to reverse the micellization.     

Productivity differences among loblolly pine genotypes are independent of individual-tree biomass partitioning and growth efficiency

Genetic differences in individual-tree biomass partitioning, growth efficiency, and stem relative growth rate (RGR) could confer intraspecific productivity differences and might strongly influence forest ecosystem carbon storage. We examined the relationship between genotype productivity (stem volume), whole-tree biomass partitioning, growth efficiency (stem wood production per unit leaf area), and stem RGR among nine different loblolly pine (Pinus taeda L.) genotypes from three different genetic groups of contrasting inherent genetic homogeneity: three open-pollinated (half-sib) families, three mass-control pollinated (full-sib) families, and three clonal varieties. We hypothesized that genotype productivity would be positively associated with increased partitioning to stem wood relative to other plant parts, higher stem RGR, and enhanced growth efficiency. After 3 years under plantation conditions, genotypes showed significant differences in stem volume, percent stem wood, percent branch wood, and partitioning to fine roots, yet no differences in stem RGR or growth efficiency. Furthermore, genotypic differences in stem volume were independent of genotypic differences in biomass partitioning, and overall, we found no evidence to support the hypothesized relationships. Even so, the observed variation in biomass partitioning has implications for forest C sequestration as genotypes which partition more biomass to long-lived biomass pools such as stems, may sequester more C. Moreover, the lack of a genetic relationship between stem volume and belowground partitioning suggests that highly productive genotypes may be planted without compromising belowground C storage.     

Diversity of Planktonic and Attached Bacterial Communities in a Phenol-Contaminated Sandstone Aquifer

Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.     

Temperature-dependent consumption and gut-residence time in the opossum shrimp Mysis relicta

Maximum daily consumption was estimated for Mysis relicta fedad libitum rations of Daphnia pulex at 4,10,15 and 18°C.Gut-residence time was also evaluated for M.relicta fed clado-ceranprey at 4, 10 and 157deg;C. Mean daily consumption (g dry weightof Daphnia g^–1 dry weight of Mysis day^–1) rangedfrom 6% at 4%C to 12% at 10°. At 18°C, Mysis feedingrate declined to 9% day1. Mean, weight-adjusted consumptionrates exhibited a ‘dome-shaped’ response in relationto water temperature. Consumption rate was highest at 10°Cand lowest at 4°C. Estimated Q₁₀ was more sensitive from4 to 10°C (Q₁₀= 3) than from 10 to 15°C (Q₁₀=1.2). Gut-residencetime for Mysis was inversely related to water temperature, implyingthat evacuation rate increases linearly with water temperature.Feeding and gut-evacuation rates become disassociated at watertemperatures >10°C. As water temperature increased above1°C, relative evacuation rate increased, whereas feedingrate declined. It is postulated that at higher water temperatures,disassociated feeding and gut-evacuation rates reduce the scopefor growth of vertically migrating Mysis and impose a physiologicalconstraint that isolates Mysis from warm, epilimnetic waterduring thermal stratification. ¹Present address: Center for Aquatic Ecology, Illinois NaturalHistory Survey, Sam Parr Biological Station, 6401 Meacham Road,Kinmundy, IL 62854, USA     

Identifying novel regulators of shoot meristem development

New organs are initiated throughout the life span of higher plants. This process occurs at the shoot meristem, which is initiated during embryogenesis and is later responsible for generating the above-ground portion of the plant. The shoot meristem can be thought of as having two zones, a central zone containing meristematic cells in an undifferentiated state, and a surrounding peripheral zone where cells enter a specific developmental pathway toward a differentiated state. Recent advances have revealed several genes that specifically regulate meristem development inArabidopsis. However, extensive mutagenesis by several labs have identified only a handful, of loci that appear to specifically regulate shoot meristem development. We have undertaken an enhancer/suppressor mutagenesis of an existing meristem mutant (clv1) and have identified novel regulators of meristem development. The extended abstract of a paper presented at the 13th International Symposium in Conjugation with Award of the International Prize for Biology “Frontier of Plant Biology”     

Modulation of insulin-like growth factor actions in L6A1 myoblasts by insulin-like growth factor binding protein (IGFBP)-4 and IGFBP-5: A dual role for IGFBP-5

We have previously shown that the insulin-like growth factors (IGFs) stimulate both proliferation and differentiation of skeletal muscle cells in culture, and that these actions in L6A1 muscle cells may be modulated by three secreted IGF binding proteins (IGFBPs), IGFBP-4, -5, and -6. Since we found that the temporal expression pattern of IGFBP-4 and IGFBP-5 differed dramatically during the transition from proliferating myoblasts to differentiated myotubes, we undertook the current study to examine the effects of purified IGFBP-4 and IGFBP-5 on IGF- stimulated actions in L6A1 muscle cells. As has been shown for other cell types, we found that IGFBP-4 had only inhibitory actions, inhibiting IGF-I and IGF-II- stimulated proliferation and differentiation. In contrast, IGFBP-5 exhibited both inhibitory and stimulatory actions. When added in the presence of 30 ng/ml IGF-I, IGFBP-5 (250 ng/ml) inhibited all markers of the early proliferative response: the tyrosine phosphorylation of the cytoplasmic signaling molecules IRS-1 and Shc, the activation of the MAP kinases, ERK1 and 2, the elevation of c-fos mRNA, the early inhibition of the elevation in myogenin mRNA, and the increase in cell number. In contrast, IGFBP-5 stimulated all aspects of the myogenic response to IGF-I: the later rise in myogenin mRNA, the elevation of creatine kinase activity, and the fusion of myoblasts into myotubes. This dual response to IGFBP-5 was greatest when it was added at a molar ratio of IGFBP-5 to IGF-I of 2:1. In contrast, when IGFBP-5 was added in the presence of IGF-II, it inhibited both proliferation and differentiation. Neither IGFBP had any effect when added in the presence of R3 IGF-I, an analog with substantially reduced affinity for IGFBPs. Our results suggest that the role of IGFBP-4 is mainly to sequester excess IGFs, and thus inhibit all actions. IGFBP-5, however, is capable of eliciting a dual response, possibly due to its unique ability to associate with the cell membrane. J. Cell. Physiol. 177:47–57, 1998. © 1998 Wiley-Liss, Inc.