Rapid construction and characterization of synthetic antibody libraries without DNA amplification

We report on a simple method to rapidly generate very large libraries of genes encoding mutant proteins without the use of DNA amplification, and the application of this methodology in the construction of synthetic immunoglobulin variable heavy (V_H) and light (V_κ) libraries. Four high quality, chemically synthesized polynucleotides (90–140 bases) were annealed and extended using T4 DNA polymerase. Following electroporation, >10⁹ transformants could be synthesized within 1 day. Fusion to β‐lactamase and selection on ampicillin resulted in 3.7 × 10⁸ V_H and 6.9 × 10⁸ V_κ clones highly enriched for full‐length, in‐frame genes. High‐throughput 454 DNA sequencing of >250,000 V_H and V_κ genes from the pre‐ and post‐selection libraries revealed that, in addition to the expected reduction in reading‐frame shifts and stop codons, selection for functional expression also resulted in a statistical decrease in the cysteine content. Apart from these differences, there was a good agreement between the expected and actual diversity, indicating that neither oligonucleotide synthesis nor biological constrains due to protein synthesis of V_H/V_κ‐β‐lactamase fusions introduce biases in the amino acid composition of the randomized regions. This methodology can be employed for the rapid construction of highly diverse libraries with the near elimination of PCR errors in invariant regions. Biotechnol. Bioeng. 2010; 106: 347–357. © 2010 Wiley Periodicals, Inc.     

Superoxide radical is involved in the sclerotial differentiation of filamentous phytopathogenic fungi: identification of a fungal xanthine oxidase

This study shows that the direct indicator of oxidative stress superoxide radical (O·??) is involved in the sclerotial differentiation of the phytopathogenic filamentous fungi Rhizoctonia solani, Sclerotinia sclerotiorum, Sclerotium rolfsii, and Sclerotinia minor. The production rate of O·?? and the antioxidant enzyme superoxide dismutase (SOD) levels in the sclerotiogenic fungi were significantly higher and lower, respectively, than those of their non-differentiating counterpart strains, which strongly suggests that the oxidative stress of the sclerotium differentiating fungi is higher than that of the non-differentiating ones. Xanthine oxidase (XO), which was detected for the first time in fungi in general, was localized in the cytoplasmic membrane. The contribution of XO in the overall O·??production was very significant, reaching 30-70% among the strains, especially in the transition developmental stage between the undifferentiated and the differentiated state, suggesting a sclerotium triggering and a phytopathogenic role of XO during plant infection. The additional finding that these fungi secrete extracellular SOD can be related to their protection from the response of plants to produce O·?? at infection sites.     

Global profiling of surface plasma membrane proteome of oviductal epithelial cells

In mammalian reproduction, many important events occur within the female reproductive tract, especially within the oviduct. These include transport and final maturation of the female and male gametes, fertilization, embryonic development, and transport of the embryo to the uterus. The plasma membrane molecules of oviductal epithelia that are in direct contact with gametes and embryo(s) and potentially mediate these processes are poorly characterized, and their function is poorly understood. Defining the oviductal cell surface proteome could provide a better understanding of the basis of reproductive processes taking place within the oviduct. We aimed to provide a detailed profile of the surface plasma membrane proteome of the oviductal epithelium by biotinylation of proteins at the cell surface, followed by highly specific purification of these proteins using avidin. This approach for enrichment of oviductal cell surface proteome was validated by immunohistochemistry, gel electrophoresis, and western blot analysis experiments. The enriched molecules were identified using two different technologies: (i) the combination of 2D gel electrophoresis with mass spectrometry and (ii) 1D gel electrophoresis with mass spectrometry (a modified multidimensional protein identification technology (MudPIT) technique). The number of proteins identified using the MudPIT approach was approximately 7 times the number of proteins identified by 2D gel electrophoresis using the same samples (40 versus 276, respectively). Some of the proteins found at the surface of oviductal cells had previously been reported as present in the oviduct and to have known functions in relation to reproductive processes. The other category of proteins that were highly represented in the oviductal surface proteome were various members of the family of heat-shock proteins. To the best of our knowledge, this is the first comprehensive study to identify and characterize proteins at the surface of the epithelium of the mammalian oviduct.     

Amphiphilic model conetworks based on cross-linked star copolymers of benzyl methacrylate and 2-(dimethylamino)ethyl methacrylate: synthesis, characterization, and DNA adsorption studies

Six amphiphilic model conetworks of a new structure, that of cross-linked "in-out" star copolymers, were synthesized by the group transfer polymerization (GTP) of the hydrophobic monomer benzyl methacrylate (BzMA) and the ionizable hydrophilic monomer 2-(dimethylamino)ethyl methacrylate (DMAEMA) in a one-pot preparation. The synthesis took place in tetrahydrofuran (THF) using tetrabutylammonium bibenzoate (TBABB) as the catalyst, 1-methoxy-1-(trimethylsiloxy)-2-methyl-propene (MTS) as the initiator, and ethylene glycol dimethacrylate (EGDMA) as the cross-linker. Three heteroarm star-, two star block-, one statistical copolymer star-, and one homopolymer star-based networks were prepared. The synthesis of these star-based networks involved four to six steps, including the preparation of the linear (co)polymers, the "arm-first" and the "in-out" star copolymers, and finally the network. The precursors and the extractables were characterized using gel permeation chromatography (GPC) and proton nuclear magnetic resonance (1H NMR) spectroscopy. The degrees of swelling (DSs) of all the networks were measured in THF, while the aqueous DSs were measured as a function of pH. The DSs at low pH were higher than those at neutral or high pH because of the protonation of the DMAEMA units and were found to be dependent on the structure of the network. The DSs in THF were higher than those in neutral water and were independent of the structure. Finally, DNA adsorption studies onto the networks indicated that the DNA binding was governed by electrostatics.     

Site-protected fixation and immobilization of Escherichia coli cells displaying surface-anchored beta-lactamase

Bacteria displaying heterologous receptors or enzymes on their surface hold great potential as whole-cell adsorbents and biocatalysts, respectively. For industrial applications, such surface-engineered cells need to be killed and chemically fixed to prevent disintegration and leakage of the displayed proteins under process conditions. It is also highly desirable to couple the chemically stabilized cells onto a solid support matrix for additional mechanical stability, flexibility in reactor choice, and easy separation from processed medium. Recently, we described the development of a readily scalable methodology for cell killing, fixation, and outer membrane stabilization via glutaraldehyde fixation followed by secondary crosslinking (Freeman, A., Abramov, S. and Georgiou, G. 1996. Biotechnol. Bioeng. 52: 625-630). Glutaraldehyde treatment was also found, however, to reduce the specific activity of a model enzyme, beta-lactamase displayed on the surface of E. coli. Here, we show that crosslinking carried out in the presence of beta-lactamase inhibitors, namely phenyl boronic acid or sodium borate, protects the active site from chemical modification resulting in up to threefold higher specific activities without affecting the cell-stabilizing effect of the glutaraldehyde treatment. To prepare an immobilized whole cell biocatalyst, residual unreacted surface aldehyde groups were employed to immobilize covalently the fixed bacteria onto chitosan-coated cellulose powder. The binding of the bacteria onto chitosan-coated cellulose was quantitative up to cell loading of 83 mg dry cell weight/g of support. Cell immobilization did not introduce mass transfer limitations and created only a modest reduction in Vmax. Thus, chemical crosslinking, affected in presence of reversible active-site inhibitors and coupled with cell immobilization on chitosan-coated cellulose represents a widely useful methodology for the process application of recombinant bacteria displaying surface-anchored heterologous proteins.     

Parity and age composition for Anopheles darlingi root (Diptera: Culicidae) and Anopheles albitarsis Lynch-Arribálzaga (Diptera: Culicidae) of the northern Amazon Basin, Brazil.

Parity and age composition for Anopheles darlingi and Anopheles albitarsis in the northern Amazon Basin, Brazil, were investigated. Anopheline ovaries and ovarioles were examined in order to determine whether hourly and seasonal parity status for the vectors An. albitarsis and An. darlingi would vary in two different landscapes (forest and savanna/forest) where malaria is endemic in the northern Amazon Basin. A total of 1,199 anophelines (535 An. darlingi and 664 An. albitarsis) was dissected for parity status, ovariole dilatations, and follicular stages. The total number of nulliparous and parous females for both species varied by time of collection, locality, and season. During the rainy season for the first two h of collection, more nulliparous An. albitarsis and An. darlingi females were collected in the first hour (18:00-19:00), but during the second hour (19:00-20:00) more parous females of both species were captured. During the dry season in Copaíbas, more parous females of An. albitarsis were observed in the first hour while more nulliparous females were observed in the second hour. Nulliparous and parous females of both species for both hours were not significantly different at Road 19 in the dry season. This location was characterized by a forest malaria pattern of transmission with higher numbers of parous females and population stability in the dry season. In Copaíbas, the density and parity of An. darlingi increased during the rainy season, and it could be classified as an alluvial malaria pattern of transmission. For Copaíbas, control measures would be more successful if adopted at the transition from dry to rainy season. Further investigation on longitudinal spatio-temporal change in longevity and survival rates would help us to clarify differences in vector competence for An. darlingi and An. albitarsis and add to the understanding of differences regarding prevailing landscapes in malaria epidemiology in the northern Amazon Basin.     

Phage shock protein PspA of Escherichia coli relieves saturation of protein export via the Tat pathway

Overexpression of either heterologous or homologous proteins that are routed to the periplasm via the twin-arginine translocation (Tat) pathway results in a block of export and concomitant accumulation of the respective protein precursor in the cytoplasm. Screening of a plasmid-encoded genomic library for mutants that confer enhanced export of a TorA signal sequence (ssTorA)-GFP-SsrA fusion protein, and thus result in higher cell fluorescence, yielded the pspA gene encoding phage shock protein A. Coexpression of pspA relieved the secretion block observed with ssTorA-GFP-SsrA or upon overexpression of the native Tat proteins SufI and CueO. A similar effect was observed with the Synechocystis sp. strain PCC6803 PspA homologue, VIPP1, indicating that the role of PspA in Tat export may be phylogenetically conserved. Mutations in Tat components that completely abolish export result in a marked induction of PspA protein synthesis, consistent with its proposed role in enhancing protein translocation via Tat.     

The fluorescence detection of superoxide radical using hydroethidine could be complicated by the presence of heme proteins

This study shows that hydroethidine (HE) used for the qualitative detection of superoxide anion can also be oxidized by heme proteins such as the mitochondrial cytochromes, hemoglobin, and myoglobin, forming spectrally nonhomogenous mixtures of HE-derived products of various oxidation states. All oxidation products show excitation/emission peaks (490-495/580-600 nm) near the excitation/emission peaks (475/570 nm) of the HE-superoxide oxidation product, and this may pose serious interference problems to the fluorescent detection of the superoxide radical. This paper discusses possible precautionary steps that should be taken to minimize the interfering problems in the HE-superoxide assay and suggests its use mainly for reactive oxygen species detection.     

The X-ray structure of Escherichia coli RraA (MenG), A protein inhibitor of RNA processing

The Escherichia coli protein regulator of RNase E activity A (RraA) has recently been shown to act as a trans-acting modulator of RNA turnover in bacteria; it binds to the essential endonuclease RNase E and inhibits RNA processing in vivo and in vitro. Here, we report the 2.0A X-ray structure of RraA. The structure reveals a ring-like trimer with a central cavity of approximately 12A in diameter. Based on earlier sequence analysis, RraA had been identified as a putative S-adenosylmethionine:2-demethylmenaquinone and was annotated as MenG. However, an analysis of the RraA structure shows that the protein lacks the structural motifs usually required for methylases. Comparison of the observed fold with that of other proteins (and domains) suggests that the RraA fold is an ancient platform that has been adapted for a wide range of functions. An analysis of the amino acid sequence shows that the E.coli RraA exhibits an ancient relationship to a family of aldolases.