Mapping of the entomocidal fragment of Spodoptera -specific Bacillus thuringiensis toxin CryIC

 Insecticidal CryI protoxins of Bacillus thuringiensis are activated by proteolysis in the midgut of insects. A conservation of proteolytic cleavage sites in the CryI proteins facilitates the expression of active toxins in transgenic plants to obtain protection from various insects. However, the engineering of CryIC toxins has, thus far, failed to yield applicable resistance to armyworms of Spodoptera species representing common insect pests worldwide. To improve the production of recombinant CryIC toxins, we established a CryIC consensus sequence by comparative analysis of three cryIC genes and tested the stability and protease sensitivity of truncated CryIC toxins in Escherichia coli and in vitro. In contrast to previous data, the boundaries of trypsin-resistant CryIC core toxin were mapped to amino acid residues I28 and R627. Proteolysis of the truncated CryIC proteins showed that Spodoptera midgut proteases may further shorten the C-terminus of CryIC toxin to residue A615. However, C-terminal truncation of CryIC to residue L614, and a mutation causing amino acid replacement I610T, abolished the insecticidal activity of CryIC toxin to S. littoralis larvae, as well as its resistance to trypsin and Spodoptera midgut proteases. Because no CryIC toxin carrying a proteolytically processed N-terminus could be stably expressed in bacteria, our data indicate that, in contrast to other CryI poteins, an entomocidal fragment located between amino acid positions 1 and 627 is required for stable production of recombinant CryIC toxins. Received: 15 April 1996/Accepted: 10 July 1996     

A Novel p53 Mutant Found in Iatrogenic Urothelial Cancers Is Dysfunctional and Can Be Rescued by a Second-site Global Suppressor Mutation

Exposure to herbal remedies containing the carcinogen aristolochic acid (AA) has been widespread in some regions of the world. Rare A→T TP53 mutations were recently discovered in AA-associated urothelial cancers. The near absence of these mutations among all other sequenced human tumors suggests that they could be biologically silent. There are no cell banks with established lines derived from human tumors with which to explore the influence of the novel mutants on p53 function and cellular behavior. To investigate their impact, we generated isogenic mutant clones by integrase-mediated cassette exchange at the p53 locus of platform (null) murine embryonic fibroblasts and kidney epithelial cells. Common tumor mutants (R248W, R273C) were compared with the AA-associated mutants N131Y, R249W, and Q104L. Assays of cell proliferation, migration, growth in soft agar, apoptosis, senescence, and gene expression revealed contrasting outcomes on cellular behavior following introduction of N131Y or Q104L. The N131Y mutant demonstrated a phenotype akin to common tumor mutants, whereas Q104L clone behavior resembled that of cells with wild-type p53. Wild-type p53 responses were restored in double-mutant cells harboring N131Y and N239Y, a second-site rescue mutation, suggesting that pharmaceutical reactivation of p53 function in tumors expressing N131Y could have therapeutic benefit. N131Y is likely to contribute directly to tumor phenotype and is a promising candidate biomarker of AA exposure and disease. Rare mutations thus do not necessarily point to sites where amino acid exchanges are phenotypically neutral. Encounter with mutagenic insults targeting cryptic sites can reveal specific signature hotspots.     

Survival and population growth of a long-lived threatened snake species, Drymarchon couperi (Eastern Indigo Snake)

Demographic data provide a basis for understanding the life history and ecology of species, factors which are vital for informing conservation efforts; however, little is known regarding the population ecology of most snake species, including the threatened Eastern Indigo Snake (Drymarchon couperi). We used 11 years (1999–2009) of capture-mark-recapture (CMR) and 2.5 years (2003–2005) of radiotelemetry data from southeastern Georgia, USA, in a CMR modeling framework to estimate apparent survival, capture and transition probabilities, and evaluate factors influencing these parameters. The model-averaged estimate of overall apparent annual survival probability was 0.700 (±0.030 SE) and is comparable to that obtained from known fate analysis (radiotelemetry) at the same site. Body size positively influenced survival, regardless of sex. Capture probability differed seasonally by sex, suggesting lower capture probability for females in fall and males in winter. There was no evidence for effect of precipitation or site-specific differences in survival. Model averaged estimate of annual adult survival estimated using multistate CMR models was 0.738 ± 0.030 and 0.515 ± 0.189 for subadults. We estimated population growth rate (λ) and elasticity (proportional sensitivity) of λ to vital rates using a stage-structured matrix population model. Population growth rate ranged from 0.96 to 1.03 depending on the value of the probability of transitioning from subadult to adult stage. The λ was proportionally most sensitive to changes in adult survival rate, followed by subadult survival. Our results suggest that protecting adult snakes and their habitats would result in the highest likelihood of long-term population stability and growth.     

Identification and characterization of a novel polysaccharide deacetylase C (PdaC) from Bacillus subtilis

Cell wall metabolism and cell wall modification are very important processes that bacteria use to adjust to various environmental conditions. One of the main modifications is deacetylation of peptidoglycan. The polysaccharide deacetylase homologue, Bacillus subtilis YjeA (renamed PdaC), was characterized and found to be a unique deacetylase. The pdaC deletion mutant was sensitive to lysozyme treatment, indicating that PdaC acts as a deacetylase. The purified recombinant and truncated PdaC from Escherichia coli deacetylated B. subtilis peptidoglycan and its polymer, (-GlcNAc-MurNAc[-L-Ala-D-Glu]-)(n). Surprisingly, RP-HPLC and ESI-MS/MS analyses showed that the enzyme deacetylates N-acetylmuramic acid (MurNAc) not GlcNAc from the polymer. Contrary to Streptococcus pneumoniae PgdA, which shows high amino acid sequence similarity with PdaC and is a zinc-dependent GlcNAc deacetylase toward peptidoglycan, there was less dependence on zinc ion for deacetylation of peptidoglycan by PdaC than other metal ions (Mn(2+), Mg(2+), Ca(2+)). The kinetic values of the activity toward B. subtilis peptidoglycan were K(m) = 4.8 mM and k(cat) = 0.32 s(-1). PdaC also deacetylated N-acetylglucosamine (GlcNAc) oligomers with a K(m) = 12.3 mM and k(cat) = 0.24 s(-1) toward GlcNAc(4). Therefore, PdaC has GlcNAc deacetylase activity toward GlcNAc oligomers and MurNAc deacetylase activity toward B. subtilis peptidoglycan.     

Modulation of gain-of-function α6*-nicotinic acetylcholine receptor by β3 subunits

We previously have shown that β3 subunits either eliminate (e.g. for all-human (h) or all-mouse (m) α6β4β3-nAChR) or potentiate (e.g. for hybrid mα6hβ4hβ3- or mα6mβ4hβ3-nAChR containing subunits from different species) function of α6*-nAChR expressed in Xenopus oocytes, and that nAChR hα6 subunit residues Asn-143 and Met-145 in N-terminal domain loop E are important for dominant-negative effects of nAChR hβ3 subunits on hα6*-nAChR function. Here, we tested the hypothesis that these effects of β3 subunits would be preserved even if nAChR α6 subunits harbored gain-of-function, leucine- or valine-to-serine mutations at 9' or 13' positions (L9'S or V13'S) in their second transmembrane domains, yielding receptors with heightened functional activity and more amenable to assessment of effects of β3 subunit incorporation. However, coexpression with β3 subunits potentiates rather than suppresses function of all-human, all-mouse, or hybrid α6((L9'S or V13'S))β4*- or α6(N143D+M145V)(L9'S)β2*-nAChR. This contrasts with the lack of consistent function when α6((L9'S or V13'S)) and β2 subunits are expressed alone or in the presence of wild-type β3 subunits. These results provide evidence that gain-of-function hα6hβ2*-nAChR (i.e. hα6(N143D+M145V)(L9'S)hβ2hβ3 nAChR) could be produced in vitro. These studies also indicate that nAChR β3 subunits can be assembly partners in functional α6*-nAChR and that 9' or 13' mutations in the nAChR α6 subunit second transmembrane domain can act as gain-of-function and/or reporter mutations. Moreover, our findings suggest that β3 subunit coexpression promotes function of α6*-nAChR.     

Conserved Ser/Arg-rich motif in PPZ orthologs from fungi is important for its role in cation tolerance

PPZ1 orthologs, novel members of a phosphoprotein phosphatase family of phosphatases, are found only in fungi. They regulate diverse physiological processes in fungi e.g. ion homeostasis, cell size, cell integrity, etc. Although they are an important determinant of salt tolerance in fungi, their physiological role remained unexplored in any halotolerant species. In this context we report here molecular and functional characterization of DhPPZ1 from Debaryomyces hansenii, which is one of the most halotolerant and osmotolerant species of yeast. Our results showed that DhPPZ1 knock-out strain displayed higher tolerance to toxic cations, and unlike in Saccharomyces cerevisiae, Na(+)/H(+) antiporter appeared to have an important role in this process. Besides salt tolerance, DhPPZ1 also had role in cell wall integrity and growth in D. hansenii. We have also identified a short, serine-arginine-rich sequence motif in DhPpz1p that is essential for its role in salt tolerance but not in other physiological processes. Taken together, these results underscore a distinct role of DhPpz1p in D. hansenii and illustrate an example of how organisms utilize the same molecular tool box differently to garner adaptive fitness for their respective ecological niches.     

Incorporating species losses and gains into a fish-based index for stream bioassessment increases the detection of anthropogenic disturbances

The taxonomic completeness index (ratio of observed to expected species; O/E) is widely used in stream bioassessment programs to infer ecological impairment. However, its sensitivity to detecting anthropogenic disturbances may be reduced by (1) the modelling procedure used to determine the expected species at a site (2) the inability of the index to account for assemblage shifts through species gains as well as losses; and (3) the frequent use of a threshold that only allows assessment of the absence of prevalent species. We used a version of the BC biotic index (an adaptation of Bray-Curtis distance) that incorporated alien and translocated species into the observed component, and generated expected native species probabilities using single species ensemble models (‘BC_A’). Sensitivity analysis, bivariate correlations and multiple linear regression analyses were used to test whether BC_A better detected anthropogenic disturbances than the standard BC (i.e. without alien and translocated species) and O/E₅₀ derived from the same models. We also tested three additional fish biotic indices currently used in the Ecosystem Health Monitoring Program in Southeast Queensland, Australia. Of the indices tested, BC_A explained the greatest amount of variance in anthropogenic disturbance variables, followed by BC and the proportional sample abundance of alien species. The BC_A index was 18% more sensitive to detecting non-reference conditions, 20% more responsive to an anthropogenic disturbance gradient, and had twice the number of significant bivariate correlations with disturbance variables than the O/E₅₀ index derived from the same underlying predictive model. We suggest that the improved performance of BC_A relative to O/E₅₀ lies in its ability to detect the addition of alien, translocated, and some native species whose traits allow them to persist or thrive in degraded conditions, and the inclusion of low prevalence taxa that may be sensitive to mild levels of disturbance. Given that generation of the BC_A index requires no further information than already provided by traditional multivariate predictive models, we recommend its inclusion into bioassessment programs that use multivariate fish based indices.     

Targeted modification of mammalian genomes

The stable and site-specific modification of mammalian genomes has a variety of applications in biomedicine and biotechnology. Here we outline two alternative approaches that can be employed to achieve this goal: homologous recombination (HR) or site-specific recombination. Homologous recombination relies on sequence similarity (or rather identity) of a piece of DNA that is introduced into a host cell and the host genome. In most cell types, the frequency of homologous recombination is markedly lower than the frequency of random integration. Especially in somatic cells, homologous recombination is an extremely rare event. However, recent strategies involving the introduction of DNA double-strand breaks, triplex forming oligonucleotides or adeno-associated virus can increase the frequency of homologous recombination.

Site-specific recombination makes use of enzymes (recombinases, transposases, integrases), which catalyse DNA strand exchange between DNA molecules that have only limited sequence homology. The recognition sites of site-specific recombinases (e.g. Cre, Flp or ΦC31 integrase) are usually 30–50 bp. In contrast, retroviral integrases only require a specific dinucleotide sequence to insert the viral cDNA into the host genome. Depending on the individual enzyme, there are either innumerable or very few potential target sites for a particular integrase/recombinase in a mammalian genome. A number of strategies have been utilised successfully to alter the site-specificity of recombinases. Therefore, site-specific recombinases provide an attractive tool for the targeted modification of mammalian genomes.     

Papain Does Not Cleave Operator-Bound Lambda Repressor: Structural Characterization of the Carboxy Terminal Domain and the Hinge

Abstract

The circular dichroism spectra of three different purified carboxy terminal fragments 93–236, 112–236 and 132–236 of the bacteriophage γ cI repressor have been measured and compared with those of the intact repressor and the amino terminal fragment 1–92. All three carboxy terminal fragments contain mostly β-strands and loops, a minor helix content increasing with the size of the fragment, showing that the 93–131 region previously called a hinge is structured. Fourier transformed infrared spectra also showed that fragment 93–236 contains α-helices, β-sheets and turns but fragment 132–236 contains no detectable α-helix, only β-sheets and turns. Papain is known to cleave the γ repressor, but it is shown here that it cannot cleave the operator-bound repressor dimer. For the 132–236 fragment, both the wt and the SN228 mutant previously shown to be dimerization defective in the intact, gave similar dimerization properties as investigated by HPLC at 2 to 100 µM protein concentration, with a KD of 13.2 µM and 19.1 µM respectively. The papain cleavage for wt and SN228 proceed at equal rates for the first cleavage at 92–93; however, the subsequent cleavages are faster for SN228. The three Cys residues in the 132–236 fragment were found to be unreactive upon incubation with DTNB, indicating the thiol sulfur atoms are buried in the repressor carboxy terminal domain. Denaturation of the 132–236 fragment studied by tryptophan fluorescence shows two transitions centered at 1.5 M and 4.5 M of urea.