Artificially ambiguous genetic code confers growth yield advantage.

A primitive genetic code is thought to have encoded statistical, ambiguous proteins in which more than one amino acid was inserted at a given codon. The relative vitality of organisms bearing ambiguous proteins and the kinds of pressures that forced development of the highly specific modern genetic code are unknown. Previous work demonstrated that, in the absence of selective pressure, enforced ambiguity in cells leads to death or to sequence reversion to eliminate the ambiguous phenotype. Here, we report the creation of a nonreverting strain of bacteria that produced statistical proteins. Ablating the editing activity of isoleucyl-tRNA synthetase resulted in an ambiguous code in which, through supplementation of a limited supply of isoleucine with an alternative amino acid that was noncoding, the mutant generating statistical proteins was favored over the wild-type isogenic strain. Such organisms harboring statistical proteins could have had an enhanced adaptive capacity and could have played an important role in the early development of living systems.

Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway.

Aminoacyl transfer RNA (tRNA) synthetases establish the rules of the genetic code by catalyzing the aminoacylation of tRNAs. For some synthetases, accuracy depends critically on an editing function at a site distinct from the aminoacylation site. Mutants of Escherichia coli that incorrectly charge tRNA(Val) with cysteine were selected after random mutagenesis of the whole chromosome. All mutations obtained were located in the editing site of valyl-tRNA synthetase. More than 20% of the valine in cellular proteins from such an editing mutant organism could be replaced with the noncanonical aminobutyrate, sterically similar to cysteine. Thus, the editing function may have played a central role in restricting the genetic code to 20 amino acids. Disabling this editing function offers a powerful approach for diversifying the chemical composition of proteins and for emulating evolutionary stages of ambiguous translation.

Defining mechanisms of toxicity for linoleic acid monoepoxides and diols in Sf-21 cells.

Linoleic acid monoepoxides have been correlated with many pathological conditions. Studies using insect cells derived from Spodoptera frugiperda (Sf-21 cells) have suggested that conversion of the epoxides to the diols is required for toxicity. However, more recent studies using rabbit renal proximal tubules have suggested that linoleic acid monoepoxides are direct mitochondrial toxins. To better understand these discrepancies, we compared the toxicity of these linoleic acid metabolites in Sf-21 cells using mitochondrial respiration as an end point. Linoleic acid (100 microM) and 12,13-epoxy-9-octadecenoic acid (12,13-EOA, 100 microM) increased the rate of oligomycin-insensitive respiration by approximately 3.5- and 3-fold, respectively, decreased the rate of oligomycin-sensitive respiration by approximately 52 and 68%, respectively, and had no effect on the integrity of the electron transport chain. These effects were concentration-dependent, occurred within 1 min, and recovered to basal levels within 45 min. 12,13-Dihydroxy-9-octadecenoic acid (12,13-DHOA, 100 microM) had no effect on oligomycin-insensitive respiration but decreased the rate of oligomycin-sensitive respiration and uncoupled respiration in a concentration-dependent manner. Approximately 79 and 68% of oligomycin-sensitive respiration and uncoupled respiration was inhibited by 12,13-DHOA (100 microM), respectively. These effects occurred within 1 min and were not reversible in 6 h. Effects similar to those induced by 12,13-DHOA (100 microM) were observed using 12,13-EOA (100 microM) in Sf-21 cells expressing human soluble epoxide hydrolase. These data suggest that in this Sf-21 model linoleic acid and linoleic monoepoxides have transient uncoupling effects, whereas the primary mechanism of toxicity for linoleic acid diols in this model is inhibition of the electron transport chain.

Errors from selective disruption of the editing center in a tRNA synthetase.

Some aminoacyl-tRNA synthetases have two catalytic centers that together achieve fine-structure discrimination of closely similar amino acids. The role of tRNA is to stimulate translocation of a misactivated amino acid from the active site to the editing site where the misactivated substrate is eliminated by hydrolysis. Using isoleucyl-tRNA synthetase as an example, we placed mutations in the catalytic center for editing at residues strongly conserved from bacteria to humans. A particular single substitution and one double substitution resulted in production of mischarged tRNA, by interfering specifically with the chemical step of hydrolytic editing. The substitutions affected neither amino acid activation nor aminoacylation, with the cognate amino acid. Thus, because of the demonstrated functional independence of the two catalytic sites, errors of aminoacylation can be generated by selective mutations in the center for editing.

Transfer RNA-dependent translocation of misactivated amino acids to prevent errors in protein synthesis.

Misactivation of amino acids by aminoacyl-tRNA synthetases can lead to significant errors in protein synthesis that are prevented by editing reactions. As an example, discrete sites in isoleucyl-tRNA synthetase for amino acid activation and editing are about 25 A apart. The details of how misactivated valine is translocated from one site to the other are unknown. Here, we present a kinetic study in which a fluorescent probe is used to monitor translocation of misactivated valine from the active site to the editing site. Isoleucine-specific tRNA, and not other tRNAs, is essential for translocation of misactivated valine. Misactivation and translocation occur on the same enzyme molecule, with translocation being rate limiting for editing. These results illustrate a remarkable capacity for a specific tRNA to enhance amino acid fine structure recognition by triggering a unimolecular translocation event.

Antibody transport in cultured tumor cell layers.

This review summarizes our recent in vitro studies of the factors affecting the tumor penetration of immunoconjugates. The studies were designed to probe the mechanisms of diffusion and convection, using a cultured layer of mouse melanoma cells as a model tumor cell layer and an antibody to the murine transferrin receptor as a model ligand. Transport of the binding antibody was observed to be slower than that of a non-binding control, a result that is consistent with the "binding site barrier" hypothesis (Fujimori et al., J. Nucl. Med., 31: 1191-1198, 1990). Internalization of the antibody/receptor complex was necessary for this effect to be observed, implying that intracellular trafficking is a determinant of net tumor transport rates. Convective fluid flow exhibited a dependence on cell density that is consistent with a Poiseuille flow model, suggesting that convective transport occurs as laminar flow in tortuous channels. Implications for immunoconjugate therapy, limitations of the approach, and future directions of the research program are discussed.

Enzyme structure with two catalytic sites for double-sieve selection of substrate.

High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure of an enzyme with editing activity in translation is presented here at 2.5 angstroms resolution. The enzyme, isoleucyl-transfer RNA synthetase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing" step, the synthetase itself rapidly hydrolyzes only the valylated products. For this two-step substrate selection, a "double-sieve" mechanism has already been proposed. The present crystal structures of the synthetase in complexes with L-isoleucine and L-valine demonstrate that the first sieve is on the aminoacylation domain containing the Rossmann fold, whereas the second, editing sieve exists on a globular beta-barrel domain that protrudes from the aminoacylation domain.

Structural and functional analysis of peptidyl oligosaccharyl transferase inhibitors.

The peptide cyclo(hex-Amb(1)-Cys(2))-Thr(3)-Val(4)-Thr(5)-Nph(6)-NH2 was previously shown to be a slow, tight-binding inhibitor (Ki = 37 nM) of the yeast oligosaccharyl transferase (OT) [Hendrickson et al. (1996) J. Am. Chem. Soc. 118, 7636-7637]. This enzyme catalyzes the transfer of a carbohydrate moiety to an asparagine residue in the consensus sequence Asn-Xaa-Thr/Ser. Herein we present a study of the contribution of the residues in positions 1, 3, 4, and 5 to OT binding. Replacement of the threonine (residue 3) by valine or (S)-2-aminobutyric acid dramatically reduced the potency of the inhibitor while, surprisingly, the incorporation of an additional methylene into the side chain of residue 1 [(S)-2,3-diaminobutyric acid changed to ornithine] had very little effect. Variants with acidic, basic, hydrophilic/polar, and hydrophobic side chains in positions 4 and 5 were also evaluated for both yeast and porcine liver OT inhibition. This aspect of the study reveals that basic (lysine) and acidic (glutamic acid) residues are detrimental to the binding, whereas hydrophobic (valine) and polar/hydrophilic (threonine) residues are both well tolerated. The kinetic behavior of substrate analogs [cyclo(hex-Asn(1)-Cys(2))-Thr(3)-Xaa(4)-Yaa(5)-Nph-NH2] corresponding to inhibitors of weak, medium, and strong potency was also examined in order to provide insight into the nature of these inhibitors.

Development of a cell culture system to study antibody convection in tumors.

The convective transport of fluid and of a binding antibody through a cultured tumor cell layer was investigated with a mouse melanoma cell line (B16F10) grown on a microporous polycarbonate filter (Snapwell inserts). The inserts were precoated with Matrigel or collagen, or were uncoated. The cell layers were exposed to nominal pressure gradients from 5 to 25 cm H2O, and the volume flux was measured by collecting the effluent volume over time. The rate of convective transport of a binding monoclonal antibody that recognizes the murina transferrin receptor (a-TfR) was investigated at a nominal pressure gradient of 15 cm H2O and compared with that of an isotype matched, nonbinding control. The resistance, R, of the cell layer to fluid flow was quantified as the hydraulic conductivity, Lp (= 1/R); the ability of the cell layer to retard antibody transport was quantified as the reflection coefficient, sigma. The resulting Lp values decreased with increasing cell density, in a manner consistent with Poiseuille flow. Collagen or Matrigel precoating also decreased Lp values, with cells grown on Matrigel providing the greatest resistance. The sigma values were 0.67 (+/-0.08) for the a-TfR antibody and 0.51 (+/-0.06) for the control, indicating that the cell layer acts as a semipermeable barrier to convective transport of antibody that is less permeable to the binding antibody.

The physiological responses to walking with and without Power Poles on treadmill exercise.

Power Poles are specially constructed, rubber-tipped ski poles designed for use during walking. Using Power Poles simulates the arm motion of cross-country skiing, thus increasing the muscle mass used during walking. This study investigated the potential increases in exercise intensity and energy cost associated with the use of walking poles. Thirty-two apparently healthy volunteers (16 men and 16 women) between the ages of 19 and 33 years participated. Each completed a treadmill maximal oxygen consumption (VO2max) test and two randomly assigned, submaximal walking trials (one with poles and one without poles) on separate days. Each walking trial was conducted on a level treadmill, for 20 minutes, at an identical self-selected pace. Expired gases, heart rate in beats per minute (bpm), and ratings of perceived exertion (RPE) were recorded each minute. Results between trials were compared using repeated measures analysis of variance and Tukey's post hoc tests. It was found that walking with poles resulted in an average of 23% (4.4 ml.kg-1.min-1) higher VO2, 22% higher caloric expenditure (1.5 kcal.min-1), and 16% (18 bpm) higher heart rate responses compared to walking without poles on a treadmill. RPE values averaged 1.5 units higher with the use of the poles, and the pattern of responses between conditions was similar for men and women. It is concluded that the use of Power Poles can increase the intensity of walking at a given speed and, thus, may provide additional training benefits to walkers.

Metal ion dependence of oligosaccharyl transferase: implications for catalysis.

Oligosaccharyl transferase activity exhibits an absolute requirement for certain divalent metal cations. Studies with reconstituted enzyme suggest a preference for metal ions that can adopt an octahedral coordination geometry. In order to gain insight into the specific role of the metal cation in catalysis, we have investigated the influence of the metal cofactor on catalytic turnover of the tripeptide substrate Bz-Asn-Leu-Thr-NHMe (1) and a closely related sulfur-containing analog, Bz-Asn(gamma S)-Leu-Thr-NHMe (2). The metal ion substitution studies reveal that 1 is effectively turned over in the presence of several metal ions (Mn2+, Fe2+, Mg2+, and Ca2+). In contrast, 2 is only glycosylated in the presence of the thiophilic metal cations manganese and iron. When the enzyme is reconstituted with the oxophilic cations magnesium and calcium, 2 shows minimal substrate behavior. With the amide substrate 1, the distinct preference for manganese over magnesium may argue against direct coordination of the metal to the lipid-linked substrate pyrophosphate moiety. This fact, together with the comparative studies with asparagine- and thioasparagine-containing tripeptides, implicates the metal cofactor in a role that places it proximal to the peptide binding site.

Sulfhydryl modification of the yeast Wbp1p inhibits oligosaccharyl transferase activity.

Chemical labeling of the multimeric Saccharomyces cerevisiae oligosaccharyl transferase indicates that the 48 kDa Wbp1p subunit is an integral component of the catalytically active enzyme. The enzyme was purified following chromatography on concanavalin A agarose, heparin agarose, Q-Sepharose, and hydroxyapatite media. The enzyme activity copurified with a tetrameric complex of polypeptide subunits. Two of the subunits have been identified as the yeast proteins Wbp1p and Swp1p by amino-terminal residue sequencing. A third subunit was identified as a variably glycosylated polypeptide near 64 kDa; preliminary amino acid sequencing showed no identity to known yeast proteins. Modification of a cysteine residue by the reagent methyl methanethiolsulfonate (MMTS) caused time-dependent and concentration-dependent inactivation of the enzyme. To identify the modified subunit of the transferase complex, the labeling reagent S-[(N-biotinoylamino)ethyl] methanethiolsulfonate (BMTS) was synthesized. Like MMTS, BMTS inactivated the oligosaccharyl transferase in a time-dependent manner. Additionally, incubation with the substrate (dolichylpyrophosphoryl)-N,N'-diacetylchitobiose [Dol-PP(GlcNAc)2] protected the enzyme from BMTS inactivation. When the purified enzyme complex was incubated with BMTS, Wbp1p alone was specifically labeled, thereby associating this subunit with catalysis and the binding of the dolichylpyrophosphoryl oligosaccharide substrate in the transferase reaction.

Enhanced immunogenicity of leucine enkephalin following coupling to anti-immunoglobulin and anti-CD3 antibodies.

Leucine enkephalin (Leu-enk) was coupled to both T and B cell antibodies in order to investigate the possibility of enhanced immunogenicity via targeted immunization. The two antibodies used were Hm x Mo CD3 and Gt x Mo Ig, respectively. The data indicate that while both antibody carriers enhanced the immunogenicity of Leu-enk, the use of the Hm x Mo CD3 antibody resulted in a greater number of mice with positive Leu-enk specific serum titers. 12 Leu-enk cell lines were produced and one, LE4H8, was chosen for characterization.

Improved clean-up method for the enkephalins in plasma using immunoaffinity chromatography.

A rapid and selective method of sample clean-up using immunoaffinity chromatography (IAC) was developed to isolate enkephalins from plasma. The enkephalin antibodies were produced utilizing novel protein carriers. Two antibodies, LE4H8 and 33FC6, were selected because of their moderate binding affinity and different epitopes. Enkephalin-spiked plasma was loaded onto the immunoaffinity column and eluted with acidic pH buffer. The eluate was derivatized with naphthalene-2,3-dicarboxaldehyde in the presence of cyanide (NDA-CN), and the enkephalins were separated using reversed-phase liquid chromatography (RPLC). IAC sample clean-up of enkephalin-spiked plasma was compared to the existing solid-phase extraction method. The limit of detection for IAC was 30 pmol. The recovery of the enkephalins from plasma was 90% with a variance ranging from 2 to 9%. The immunoaffinity column was used for approximately 70 samples without any deterioration in performance.