Differences in the solution structures of the parallel beta-helical pectate lyases as determined by limited proteolysis

The pectate lyase family of proteins has been shown to fold into a novel domain motif, the right-handed parallel beta-helix. As a means of gaining insight to the solution structure of the pectate lyases, the enzymes were subjected to limited proteolytic digestion by the endoproteases AspN, GluC and trypsin. The effects of proteolytic cleavage on enzymatic activity were determined, and the early products of proteolysis were identified by capillary electrophoresis, MALDI-TOF mass spectrometry and HPLC. A single peptide bond between Lys158 and Asp159 in pectate lyase B (PLb) was cleaved by both AspN and trypsin, with no detectable hydrolysis of PLb by GluC. Pectate lyase E (PLe) was hydrolyzed by trypsin between Lys164 and Asp165, a bond on an analogous loop structure found to be susceptible to proteolytic attack in PLb. AspN and GluC preferentially hydrolyzed peptide bonds (at Asp127 and Glu124, respectively) on another loop extending from the central beta-helical core of PLe. A single beta-strand of the central cylinder of the pectate lyase C (PLc) molecule was susceptible to all three proteases used. These data demonstrate that the most susceptible peptide bonds to proteolytic scission within the native enzymes lie on or near one of the three parallel beta-sheets that compose the core domain motif Despite the proximity of the proteolytic cleavages to the catalytic sites of the enzymes, significant retention of lyase activity was observed after partial proteolysis, indicating preservation of functional tertiary structure in the proteolytic products.     

Molecular diversity among marine picophytoplankton as revealed by psbA analyses

Photosynthetic microorganisms play a crucial role in the marine environment. In vast areas of the oceans, marine primary productivity is performed by cells smaller than 2-3 micro m (picoplankton). Here, we report on molecular analyses of the conserved photosynthetic psbA gene (coding for protein D1 of photosystem II reaction centre) as a diversity indicator of naturally occurring marine oxygenic picophytoplankton. The psbA genes proved to be good indicators of the presence of a wide variety of photosynthetic marine microbial groups, including new cyanobacterial groups and eukaryotic algae (prasinophytes). Furthermore, using environmental bacterial artificial chromosome (BAC) libraries, we were able to correlate psbA genes with small subunit rRNAs and, therefore, to confirm their phylogenetic affiliation.     

Cancer mortality risk among workers at the Mayak nuclear complex

At present, direct data on risk from protracted or fractionated radiation exposure at low dose rates have been limited largely to studies of populations exposed to low cumulative doses with resulting low statistical power. We evaluated the cancer risks associated with protracted exposure to external whole-body gamma radiation at high cumulative doses (the average dose is 0.8 Gy and the highest doses exceed 10 Gy) in Russian nuclear workers. Cancer deaths in a cohort of about 21,500 nuclear workers who began working at the Mayak complex between 1948 and 1972 were ascertained from death certificates and autopsy reports with follow-up through December 1997. Excess relative risk models were used to estimate solid cancer and leukemia risks associated with external gamma-radiation dose with adjustment for effects of plutonium exposures. Both solid cancer and leukemia death rates increased significantly with increasing gamma-ray dose (P < 0.001). Under a linear dose-response model, the excess relative risk for lung, liver and skeletal cancers as a group (668 deaths) adjusted for plutonium exposure is 0.30 per gray (P < 0.001) and 0.08 per gray (P < 0.001) for all other solid cancers (1062 deaths). The solid cancer dose-response functions appear to be nonlinear, with the excess risk estimates at doses of less than 3 Gy being about twice those predicted by the linear model. Plutonium exposure was associated with increased risks both for lung, liver and skeletal cancers (the sites of primary plutonium deposition) and for other solid cancers as a group. A significant dose response, with no indication of plutonium exposure effects, was found for leukemia. Excess risks for leukemia exhibited a significant dependence on the time since the dose was received. For doses received within 3 to 5 years of death the excess relative risk per gray was estimated to be about 7 (P < 0.001), but this risk was only 0.45 (P = 0.02) for doses received 5 to 45 years prior to death. External gamma-ray exposures significantly increased risks of both solid cancers and leukemia in this large cohort of men and women with occupational radiation exposures. Risks at doses of less than 1 Gy may be slightly lower than those seen for doses arising from acute exposures in the atomic bomb survivors. As dose estimates for the Mayak workers are improved, it should be possible to obtain more precise estimates of solid cancer and leukemia risks from protracted external radiation exposure in this cohort.     

Visualizing genetic influences on human brain functions

, in this issue of Cell, integrate genetics and functional brain imaging by showing that variation in the human brain-derived neurotrophic factor (BDNF) gene is associated with variation in episodic memory ability and in hippocampal neurochemistry and function.     

Quantitative determination of the enantiomers of methadone and its metabolite (EDDP) in human saliva by enantioselective liquid chromatography with mass spectrometric detection

A sensitive enantioselective liquid chromatographic assay with mass spectrometric detection (LC-MS) has been developed and validated for the simultaneous determination of saliva concentrations of (R)- and (S)-methadone (Met) and (R)- and (S)-2-ethylidene-1,5-dimethyl-3,3-diphenyl-pyrrolidine (EDDP, a primary metabolite of Met). Saliva specimens were collected using Salivette devices (Sarsedt), and centrifuged; collected saliva was then spiked with deuterated internal standards, D3-Met and D3-EDDP, and directly injected into the LC-MS. Enantioselective separations were achieved on a liquid chromatographic chiral stationary phase (CSP) based upon immobilized alpha(1)-acid glycoprotein (AGP) using a mobile phase composed of acetonitrile: ammonium acetate buffer (10mM, pH 7.0) in a ratio of 18:82 (v/v), a flow rate of 0.9 ml/min and a temperature of 25 degrees C. Under these conditions, enantioselective separations were observed for methadone (alpha=1.30) and EDDP (alpha=1.17) within 15 min. Met, EDDP, D3-Met and D3-EDDP were detected using selected ion monitoring at m/z 310.20, 278.20, 313.20 and 281.20, respectively. Linear relationships between peak height ratio and drug-enantiomer concentrations were obtained for methadone in the range of 5.0-600.0 ng/ml, and for EDDP from 0.5 to 15.0 ng/ml per enantiomer with correlation coefficients better than 0.9994, where lower limit of quantification (LLOQ) for Met was 5 ng/ml and for EDDP 0.5 ng/ml. Acceptable intra- and inter-day precision of the method (CVs<4.0%) and accuracy (CVs<4.0%) were obtained. These findings demonstrate the accuracy and precision of the method used to successfully analyze saliva obtained from patients enrolled in a methadone-maintenance program.     

Use of UV absorbance To monitor furans in dilute acid hydrolysates of biomass

A simple method based on UV spectra was developed for the estimation of total furans (furfural and hydroxymethylfurfural) in hemicellulose hydrolysates. UV spectra of hemicellulose hydrolysate contained a single dominant peak at around 278 nm. Approximately two-thirds of this peak can be attributed to furan absorbance (furfural and hydroxymethylfurfural). At 284 nm, both furfural and hydroxymethylfurfural have equal absorbance on a weight basis. A comparison of HPLC determinations for different samples of hydrolysate was used to develop a simple equation that allows the accurate prediction of total furans based on the difference in absorbance at 284 and 320 nm. This method may prove useful for quality control applications during the production of biomass syrups using a dilute acid hydrolysis process and during treatments for the amelioration of toxins. Although furans represent only a portion of the toxins present in hemicellulose hydrolysates, the abundance of furans appears to serve as a useful marker to predict relative toxicity.     

Increased sensitivity to chromatid aberration induction by bleomycin and neocarzinostatin results from alterations in a DNA damage response pathway

DNA damage response pathways coordinate the cellular response to DNA damage. To investigate the roles of tumor suppressor genes in these pathways, human lymphoblastoid cells (wild-type, p53-/-, ATM-/-) were treated for 1 h with 0-3 microg/ml of the radiomimetic compound bleomycin (BLM), and cells treated in G(2) were analyzed for chromatid aberrations. BLM-induced aberration frequencies were significantly increased, to the greatest extent in the ATM-/- cells and, to a lesser extent, in the p53-/- cells compared to wild-type cells. These observations are consistent with p53 and ATM acting in a damage response pathway activated by DNA strand breaks. The consequences of disrupting this pathway were further investigated by studies using wortmannin, a PI-3 kinase and DNA repair inhibitor. Wortmannin significantly increased the BLM-induced aberration frequencies in all but the ATM-/- cells, elevating the sensitivity of p53-/- cells to ATM-/- levels and that of wild-type cells to intermediate levels. These differential sensitivities suggest that the ATM phenotype is the result of dual cellular defects, one involving p53 and the other a wortmannin-sensitive component. Similar studies in Brca1+/- and Brca2+/- human lymphoblasts showed no increased sensitization to BLM in the absence of inhibitor, and differential sensitization by wortmannin. To determine if there was any substrate specificity for p53- and ATM-mediated DNA damage responses, chromatid aberrations were assessed in wild-type, p53-/-, and ATM-/- cells exposed to 0-0.4 microg/ml neocarzinostatin (NCS) for 1 h. In contrast to results with BLM, the p53-/- cells exhibited a low sensitivity to NCS-induced aberrations, similar to wild-type, while ATM-/- cells remained highly sensitive. This suggests that the response to BLM- and NCS-induced lesions involves different mechanisms.     

Eating the evidence? Manduca sexta larvae can not disrupt specific jasmonate induction in Nicotiana attenuata by rapid consumption

As feeding by the tobacco specialist Manduca sexta L. is known to result in significantly higher jasmonate (JA) concentrations in Nicotiana plants than do mechanical simulations of the larval damage, we investigated whether M. sexta, which is known to rapidly consume large quantities of leaf material, can impair this “recognition” response by consuming the leaf tissue before it can respond with amplified JA levels. We report that oral secretions (OS) from M. sexta, but not from the cabbage specialist Pieris rapae, amplified the wound-induced JA response of Nicotiana attenuata Torr. Ex Wats., regardless of larval diet, instar and molting stage, and were still active after boiling and when diluted to 1/1000. The largest JA response occurred within 40 min in tissues adjacent to the OS application site. When 3 mm of leaf tissue immediately adjacent to the OS application site was excised within 40 s, the signal that elicits JA amplification was found to travel rapidly into the leaf, beyond the mandibular reach of the larvae. We conclude that M. sexta is not able to consume the evidence of feeding activity. Received: 16 July 1999 / Accepted: 12 August 1999