Expression in Escherichia coli of a synthetic gene coding for horse heart myoglobin

A gene for expression of horse heart myoglobin in Escherichiacoli has been constructed in one step from long synthetic oligonucleotides.The synthetic gene contains an efficient translation initiationsignal and used codons that are commonly found in E.coli. Uniquerestriction sites are placed throughout the gene. It has beeninserted in a phagemid vector and is expressed from the lacpromoter in E.coli at high efficiency, the soluble heme proteinrepresenting 10% of soluble protein. Two versions of horse heartmyoglobin were produced with aspartic acid or asparagine atresidue 122. Comparison of chromatographic mobilities of thesetwo proteins with authentic horse heart myoglobin identifiedaspartic acid as the correct residue 122. The availability ofthis gene, which is designed to facilitate oligonucleotide mutagenesisor cassette mutagenesis, will allow systematic structure—functionanalysis of horse heart myoglobin.     

High level expression of a synthetic gene coding for IgG-binding domain B of Staphylococcal protein A

A gene coding for one of the IgG-binding domains of Staphylococcalprotein A, designated domain B, was chemically synthesized.This gene was tandemly repeated to give dimeric and tetramericdomain B genes by the use of two restriction enzymes which gaveblunt ends. The genes were highly expressed in Escherichia colito afford a large amount of dimeric and tetrameric domain Bproteins. The single domain B protein was efficiently producedas a fusion protein with a salmon growth hormone fragment. Thefusion protein was converted to monomeric domain B by cyanogenbromide cleavage. The CD spectra of the monomeric, dimeric andtetrameric domain B proteins were essentially the same as thatof native form protein A, showing that their secondary structureswere very similar. The dimeric and tetrameric domain B proteinsformed precipitates with IgG as protein A. This system permitsthe efficient production of mutated single and multiple IgG-bindingdomains which can be used to study structural changes and proteinA–immunoglobulin interactions.     

Geometry of interaction of metal ions with histidine residues in protein structures

An analysis of the geometry and the orientation of metal ionsbound to histidine residues in proteins is presented. Cationsare found to lie in the imidazole plane along the lone pairon the nitrogen atom. Out of the two tautomeric forms of theimidazole ring, the NE2-protonated form is normally preferred.However, when bound to a metal ion the ND1-protonated form ispredominant and NE2 is the ligand atom. When the metal coordinationis through ND1, steric interactions shift the side chain torsionalangle, X₂ from its preferred value of 90 or 270. The orientationof histidine residues is usually stabilized through hydrogenbonding; ND1-protonated form of a helical residue can form ahydrogen bond with the carbonyl oxygen atom in the precedingturn of the helix. A considerable number of ligands are foundin helices and ß-sheets. A helical residue hound toa heme group is usually found near the C-terminus of the helix.Two ligand groups four residues apart in a helix, or two residuesapart in a ß-strand are used in many proteins to bindmetal ions.     

Internalization and translocation of a new chimeric protein composed of Pseudomonas aeruginosa exotoxin A and mouse dihydrofolate reductase as a model system

In an attempt to introduce a large peptide that is not normallytranslocated across membranes into the cytosol of eukaryoticcells, we created a new chimeric protein termed CEDH betweenPseudomonas aeruginosa exotoxin A (ETA) and a variant enzymeof Mus musculus dihydrofolate reductase (DHFR) with reducedaffinity for antifolates, ETA^1–413.DHFR^1–187.ETA^609–613.We have defined, genetically constructed and expressed the chimericprotein in Escherichia coli. We showed that the CEDH chimericprotein, purified to homogeneity on an immunoaffinity resin,confers a methotrexate-resistant phenotype to Chinese hamsterovary cells. Furthermore, the chimeric protein allowed the growthof dihydrofolate reductase-deficient Chinese hamster ovary cellsin the absence of hypoxanthine and thymidine. These resultsdemonstrated that the chimeric protein exhibited enzyme activityand possessed the tightly folded native structure, and thatthe DHFR protein can be selectively internalized and translocatedvia domains of exotoxin A. These data show that the ETA systemis an efficient system for the delivery of a variety of largepolypeptides into the cytosol without stress to the target cells,and extends the use of this delivery system to proteins thatare not normally translocated across membranes.     

Protein secretion controlled by a synthetic gene in Escherichia coli

The inability of Escherichia coli to secrete proteins in growthmedium is one of the major drawbacks in its use in genetic engineering.A synthetic gene, homologous to the one coding for the kil peptideof pColE1, was made and cloned under the control of the lacpromoter, in order to obtain the inducible secretion of homologousor heterologous proteins by E.coli. The efficiency of this syntheticgene to promote secretion was assayed by analysing the productionand secretion of two proteins, the R-TEM1 ß-lactamase,and the -amylase from Bacillus licheniformis. This latter proteinwas expressed in E.coli from its gene either on the same plasmidas the kil gene or on a different plasmid. The primary effectof the induction of the kil gene is the overproduction of thesecreted proteins. When expressed at a high level, the kil genepromotes the overproduction of all periplasmic proteins andthe total secretion in the culture medium of both the ß-lactamaseor the -amylase. This secretion is semi-selective for most periplasmkproteins are not secreted. The kil peptide induces the secretionof homologous or heterologous proteins in two steps, first actingon the cytoplasmic membrane, then permeabilizing the outer membrane.This system, which is now being assayed at the fermentor scale,is the first example of using a synthetic gene to engineer anew property into a bacterial strain.     

Recombinant pro-regions from papain and papaya proteinase IV are selective high affinity inhibitors of the mature papaya enzymes

Proteolytic enzymes require the presence of their proregionsfor correct folding. Of the four proteolytic enzymes from Caricapapaya, papain and papaya proteinase IV (PPIV) have 68% sequenceidentity. We find that their proregions are even more similar,exhibiting 73.6% identity. cDNAs encoding the pro-regions ofthese two proteinases have been expressed in Escherichia coliindependently from their mature enzymes. The recombinant pro-regionsof papain and PPIV have been shown to be high affinity inhibitorsof all four of the mature native papaya cysteine proteinases.Their inhibition constants are in the range 10^–6–;10^–;9M. PPIV was inhibited two to three orders of magnitude lesseffectively than papain, chymopapain and caricain. The pro-regionof PPIV, however, inhibited its own mature enzyme more effectivelythan did the proregion of papain. Alignment of the sequencesof the four papaya enzymes shows that there is a highly variablesection towards the C-terminal of the pro-region. This regionmay therefore confer selectivity to the pro-regions for theindividual proteolytic enzymes.     

Ligand-induced conformational changes in wild-type and mutant yeast pyruvate kinase

A mutant form of pyruvate kinase in which serine 384 has beenmutated to proline has been engineered in the yeast Saccharomycescerevisiae. Residue 384 is located in a helix in a subunit interfaceof the tetrameric enzyme, and the mutation was anticipated toalter the conformation of the helix and hence destabilize theinterface. Previous results indicate that the mutant favoursthe T quarternary conformation over the R conformation, andthis is confirmed by the results presented here. Addition ofphosphoenol-pyruvate (PEP), ADP and fructose-1,6-bisphosphate(Fru 1,6-P₂) singly to the wild-type and mutant enzymes resultsin a significant quenching of tryptophan fluorescence (12–44%),and for Fru-1,6-P₂, a red shift of 15 nm in the emission maximum.Fluorescence titration experiments showed that PEP, ADP andFru-1,6-P₂ induce conformations which have similar ligand-bindingproperties in the wild-type and mutant enzymes. However, theFru-1,6-P₂ induced conformation is demonstrably different fromthose induced by either ADP or PEP. The enzymes differ in theirsusceptibility to trypsin digestion and N-ethylmaleimide inhibition.The thermal stability of the enzyme is unaltered by the mutantion.Far-UV CD spectra show that both enzymes adopt a similar overallsencondary structure in solution. Taken together, the resultssuggest that the Ser384-Pro mutaion causes the enzyme to adopta diffenrent tertiary and/or quaternary structure from the wild-typeenzyme and affects the type and extent of the conformationalchanges induced in the enzyme upon ligand binding. A simplifiedminimal reaction mechanism is proposed in which the R and Tstates differ in both affinity and K_cat. Thus, in terms of themodels of cooperativity and allsoteric interaction, pyruvatekinase is both a K and a V system.     

Lipid modification of proteins and their membrane transport

An effective method for artificial attachment of lipid anchorsto water-soluble proteins has been developed. To this end, aprotein molecule is modified in a system of reversed micellesby a water-insoluble reagent, e.g. fatty acid chloride. Fattyacylated proteins acquire an ability to translocate across lipidmembranes and penetrate intact cells. This principle of impartingtransmembrane properties to water-soluble proteins makes itpossible to realize in vivo a direct transport of antibodiesacross the hemato-encephalic barrier into the brain and to developa method for virus suppression by fatty acylated anti-viralantibodies capable of penetrating infected cells. The effectof a drastic increase in the biological activity of exogenousprotein factors, e.g. Staphylococcus aureus enterotoxin A, asa result of their artificial fatty acylation has been discovered.The above-mentioned phenomena are discussed in relation to thein vivo data, indicating that post-translational modificationof proteins by fatty acids and phospholipids is very widespreadin nature and evidently plays an important role in protein transportand sorting. In this connection, lipid modification of proteinsis regarded as a possible general step of protein transportin vivo.     

Selection of a thermostable variant of chloramphenicol acetyltransferase (Cat-86)

The moderate thermophile Bacillus stearothermophilus was usedas a host in which to detect more thermostable variants of theB.pumilus chloramphenicol acetyltransferase (Cat-86) protein.Seventeen mutants were isolated and detected by their abilityto grow in the presence of chloramphenicol at a previously restrictivetemperature (58°C). The genes encoding these proteins weresequenced; all 17 mutants carried the same C to T transitionthat conferred an amino acid substitution of alanine by valineat position 203 of the protein sequence. The wild-type and onemutant Cat-86 protein were purified to homogeneity using affinitychromatography, and kinetic and thermal stability studies wereundertaken. Both enzymes had similar sp. act. in the regionof 215 U/mg, with K_m values for chloramphenicol in the range13.8–15.4 µM and for acetyl CoA in the range 13.6–15.5µM. The A203V mutant shows greater stability than thewild-type Cat-86 protein at temperatures above 50°C andappears to pass through a transition state between 48 and 50°C.     

Site-directed mutagenesis to fine-tune enzyme specificity

We have used a combination of a genetic selection and oligonucleotide-directedmutagenesis to introduce a series of amino add replacementsfor a single residue into Escherichia coliglutaminyl-tRNA synthetase.The mutant enzymes mischarge supFtRNA^Tyr, with glutamine, tovarying degrees depending on the polarity of the side chainintroduced but apparently not depending on the size or shapeof the side chain. These results indicate that repulsive charge-chargeinteractions may be important for specific recognition of nucleicacids by proteins and illustrate how a mutant, derived fromgenetic selection, may be further modified in activity by oligonucleotide-directedmutagenesis.     

Analysis of the invariant Phe82 residue of yeast iso-1-cytochrome c by site-directed mutagenesis using a phagemid yeast shuttle vector

A phagemid (pING4) carrying the yeast iso-1-cytochrome c genewas constructed which bears all the elements necessary for replicationin yeast and bacteria and may be converted into a single-strandedform of DNA for site-directed mutagenesis and nucleotide sequencing.The recombinant vector was used to create a complete set of19 amino acid changes at position 82, a phylogenetically conservedphenylalanine residue in mitochondrial cytochrome c. All thedifferent forms of cytochrome c were functional in vivo, basedupon their ability to support respiration when the mutant proteinswere expressed in a yeast strain (otherwise devoid of cytochromec) grown on non-fermentable carbon sources, with only the straincontaining the Cys82 variant having a substantially decreasedgrowth rate. These results are interpreted in terms of the availablestructural and functional information previously reported ona subset of cytochrome c proteins with mutations at position82.     

The consequences of engineering an extra disulfide bond in the Penicillium camembertii mono-and diglyceride specific lipase

The extracellular lipase from Penicillium camembertii has uniquesubstrate specificity restricted to mono- and diglycerides.The enzyme is a member of a homologous family of lipases fromfilamentous fungi. Four of these proteins, from the fungi Rhizomucormiehei, Humicola lanuginosa, Rhizopus delemar and P.camembertii,have had their structures elucidated by X-ray crystallography.In spite of pronounced sequence similarities the enzymes exhibitsignificant differences. For example, the thermo-stability ofthe P.camembertii lipase is considerably lower than that ofthe H.lanuginosa enzyme. Since only the P.camembertii enzymelacks the characteristic long disulfide bridge, correspondingto Cys22–Cys268 in the H.lanuginosa lipase, we have engineeredthis disulfide into the former enzyme in the hope of obtaininga significantly more stable fold. The properties of the doublemutant (Y22C and G269C) were assessed by a variety of biophysicaltechniques. The extra disulfide link was found to increase themelting temperature of the protein from 51 to 63°C. However,no difference is observed under reducing conditions, indicatingan intrinsic instability of the new disulfide. The optimal temperaturefor catalytic activity decreased by 10°C and the optimumpH was shifted by 0.7 units to more acidic.     

Overproduction and purification of the regulatory subunit of Escherichia coli aspartate transcarbamoylase

An Escherichia coli strain/plasmid system has been developedfor the overexpression of the regulatory subunit of E.coli aspartatetranscarbamoylase (ATCase). Production of large quantities ofregulatory subunit, by the method described here, should facilitatefuture experiments, such as X-ray crystallography, NMR and hybridizationexperiments, aimed at understanding the heterotropic mechanismthat regulates the activity of ATCase. The plasmid used forthe over-expression carries the gene for the regulatory subunit,pyrI, downstream from the strong pyrB promoter. The host strain,EK1104 [Nowlan, S.F. and Kantrowitz, E.R. (1985) J. Biol. Chem.,260, 14712–14716] carries a deletion in the pyrBI regionof the chromosome, as well as a leaky pyrF allele. When thisstrain/plasmid system is grown under limiting pyrimidine levels,large quantities of the regulatory subunit of ATCase are producedwithout any trace of catalytic subunit or holo-enzyme. A procedurefor the purification of the regulatory subunit from cell extractshas also been developed yielding {small tilde}50 mg of purifiedregulatory subunit per liter of initial culture. The regulatorysubunit produced in this fashion is fully competent in reassociationexperiments with the native catalytic subunit. Furthermore,the reassociated holoenzyme exhibits kinetic properties identicalto those of the wild type enzyme. In addition, we report theconstruction of a pUC119 based plasmid which carries a uniqueNdeI site at the fMet of the pyrB gene of ATCase. This plasmid,which was used in the construction of the system for the overexpressionof the regulatory subunit of ATCase, has been shown to be ofgeneral use for the expression of foreign proteins in E.coli.     

Effects of signal peptide changes on the secretion of bovine somatotropin (bST) from Escherichia coli

Bovine somatotropin (bST) was secreted from Escherichia coliat moderate levels of 1–2 µg/ml/OD using expressionvectors in which the bST gene was fused to the lamB secretionsignal. To study the secretion properties of bST in E.coli further,two approaches for modifying the secretion signal were employed.In the first case, fusion proteins were constructed with sixalternative bacterial secretion signals: three from E.coli proteins(HisJ, MalE and OmpA), two from bacteriophage proteins (M13coat protein and PA-2 Lc) and one from the chitinase A proteinof Serratia marcescens. The results, as monitored by Westernblot analysis of both total cell protein and the periplasmicfraction, showed that these changes in the secretion signaldid not significantly affect the secretion properties of bST.In the second approach, a library of random mutations was createdin the lamB secretion signal and 200 independent clones werescreened. The level of secreted bST was determined by growingindividual clones in duplicate in microtiter wells, inducingprotein expression and measuring the bST released by osmoticshock using a particle concentration fluorescent immunoassay.The secretion properties of several novel variants in the LamBsignal peptide are presented.     

Development of an optimized expression system for the screening of antibody libraries displayed on the Escherichia coli surface

Polypeptide library screening technologies are critically dependentupon the characteristics of the expression system employed.A comparative analysis of the lpp–lac, tet and araBAD promoterswas performed to determine the importance of tight regulationand expression level in library screening applications. Thesurface display of single-chain antibody (scFv) in Escherichiacoli as an Lpp–OmpA' fusion was monitored using a fluorescentlytagged antigen in conjunction with flow cytometry. In contrastto the lpp–lac promoter, both tet and araBAD promoterscould be tightly repressed. Tight regulation was found to beessential for preventing rapid depletion of library clones expressingfunctional scFv and thus for maintaining the initial librarydiversity. Induction with subsaturating inducer concentrationsyielded mixed populations of uninduced and fully induced cellsfor both the tet and araBAD expression systems. In contrast,homogeneous expression levels were obtained throughout the populationusing saturating inducer concentrations and could be adjustedby varying the induction time and plasmid copy number. Underoptimal induction conditions for the araBAD system, proteinexpression did not compromise either cell viability or librarydiversity. This expression system was used to screen a libraryof random scFv mutants specific for digoxigenin for clones exhibitingimproved hapten dissociation kinetics. Thus, an expression systemhas been developed which allows library diversity to be preservedand is generally applicable to the screening of E.coli surfacedisplayed libraries.     

Alteration of the amino acid substrate specificity of clostridial glutamate dehydrogenase by site-directed mutagenesis of an active-site lysine residue

Two residues, K89 and S380, thought to interact with the -carboxylgroup of the substrate L-glutamate, have been altered by site-directedmutagenesis of clostridial glutamate dehydrogenase (GDH). Thesingle mutants K89L and S380V and the combined double mutantK89L/S380V were constructed. All three mutants were satisfactorilyoverproduced in soluble form. However, only the K89L mutantwas retained by the dye column normally used in purifying thewild-type enzyme. All three mutant enzymes were purified tohomogeneity and tested for substrate specificity with 24 aminoacids. The single mutant S380V showed no detectable activity.The alternative single mutant K89L showed an activity towardsL-glutamate that was decreased nearly 2000-fold compared withwild-type enzyme, whereas the activities towards the monocarboxylicsubstrates -aminobutyrate and norvaline were increased 2- to3-fold. A similar level of activity was obtained with methionine(0.005 U/mg) and norleucine (0.012 U/mg), neither of which giveany activity with the wild-type enzyme under the same conditions.The double mutant showed decreased activity with all substratescompared with the wild-type GDH. In view of its novel activities,the K89L mutant was investigated in greater detail. A strictlylinear relationship between reaction velocity and substrateconcentration was observed up to 80 mM L-methionine and 200mM L-norleucine, implying very high K_m values. Values of k_cat/K_m,for L-methionine and L-norleucine were 6.7x10^–2 and 0.15s^–1M^–1, respectively. Measurements with dithiobisnitrobenzoicacid showed that the mutant enzymes all reacted with a stoichiometryof one -SH group per subunit and all showed protection by coenzyme,indicating essentially unimpaired coenzyme binding. With glutamateor 2-oxoglutarate as substrate the K_m values for the vestigialactivity in the mutant enzyme preparations were strikingly closeto the wild-type K_m values. Both for wild-type GDH and K89L,L-glutamate gave competitive product inhibition of 2-oxoglutaratereduction but did not inhibit the reduction of 2-oxocaproatecatalysed by K89L enzyme. This suggests that the low levelsof glutamate/2-oxoglutarate activity shown by the mutant enzymeare due to trace contamination. Since stringent precautionswere taken, it appears possible that this reflects the levelof reading error during overexpression of the mutant proteins.CD measurements indicate that the S380V mutant has an alteredconformation, whereas the K89L enzyme gave an identical CD spectrumto that of wild-type GDH; the spectrum of the double mutantwas similar, although somewhat altered in intensity. The resultsconfirm the key role of K89 in dicarboxylate recognition byGDH.     

Mutagenesis of conserved residues within the active site of Escherichia coli alkaline phosphatase yields enzymes with increased kcat

The likelihood for improvement in the catalytic properties ofEscherichia coli alkaline phosphatase was examined using site-directedmutagenesis. Mutants were constructed by introducing sequencechanges into nine preselected amino acid sites within 10 A ofthe catalytic residue serine 102. When highly conserved residuesin the family of alkaline phosphatases were mutated, many ofthe resulting enzymes not only maintained activity, but alsoexhibited greatly improved tra,. Of –170 mutant enzymesscreened, 5% (eight mutants) exhibited significant increasesin specific activity. In particular, a substitution by serineof a totally invariant AsplOl resulted in a 35-fold increaseof specific activity over wild-type at pH 10.0. Up to 6-foldincreases the k_cat/k_m ratio were observed.     

Potential of genetic algorithms in protein folding and protein engineering simulations

Genetic algorithms are very efficient search mechanisms whichmutate, recombine and select amongst tentative solutions toa problem until a near optimal one is achieved. We introducethem as a new tool to study proteins. The identification andmotivation for different fitness functions is discussed. Theevolution of the zinc finger sequence motif from a random startis modelled. User specified changes of the repressor structurewere simulated and critical sites and exchanges for mutagenesisidentified. Vast conformational spaces are efficiently searchedas illustrated by the ab initio folding of a model protein ofa four ß strand bundle. The genetic algorithm simulationwhich mimicked important folding constraints as overall hydrophobicpackaging and a propensity of the betaphilic residues for transpositions achieved a unique fold. Cooperativity in the ßstrand regions and a length of 3–5 for the interconnectingloops was critical. Specific interaction sites were considerablyless effective in driving the fold.     

Monte Carlo docking of protein-DNA complexes: incorporation of DNA flexibility and experimental data

A Monte Carlo simulation program (MONTY) has been developedto dock proteins onto DNA. Protein and DNA interact via square-wellpotentials for hydrogen bond and van der Waals interactions.The effect of the inclusion of DNA flexibility and experimentallyderived restraints has been tested on members of the helix-turn-helixfamily of DNA binding proteins. Unwinding and bending the DNAdouble helix improves the number of correctly retrieved hydrogenbonds in simulations starting from the 434 cro protein monomercomplexed with a standard B-DNA O_Rl half-site. Agreement withphosphate ethylation interference and mutagenesis data is rewardedwith energy bonuses. This protocol was tested on protein-DNAcomplexes of 434 cro, lac headpiece and a mutant lac headpieceresembling the gal repressor headpiece with the recognitionhelices in correct and reversed orientations in the DNA majorgroove. The inclusion of experimental data gives an improvedconvergence of the correctly oriented structures and allowsfor an easier discrimination between correctly and incorrectlydocked complexes     

Enzyme-catalyzed dehalogenation of pentachloroethane: why F87W-cytochrome P450cam is faster than wild type

Under anaerobic conditions, cytochromes P450 can reductivelydehalogenate heavily halogenated hydrocarbons, such as one-and two-carbon organic solvents. This catalytic capacity hasdrawn attention to the potential use of engineered forms ofP450s in the remediation of contaminated deep subsurface ecosystems.Loida (1994, PhD Thesis, University of Illinois at Urbana-Champaign,IL) and S.G.Sligar (personal communication) have observedrecentlythat an active-site variant of cytochrome P450cam (F87W) dechlorinatespentachloroethane approximately three times faster than thewild-type enzyme. Molecular dynamics simulations have revealedthat the mutant enzyme binding pocket remains smaller, and thatpentachloroethane assumes configurations closer to the heme-Fein the F87W mutant twice as often as in the wild-type enzyme.This result is consistent with a collisional model of dehalogenation,which agrees with experimental observations [Li and Wackett(1993) Biochemistry, 32, 9355–9361] that solutions containingwild-type P450cam dehalogenate pentachloroethane 100 times fasterthan those containing free heme. The simulations suggest thatit is unlikely that Trp87 significantly stabilizes the developingnegative charge on the substrate during carbon-halogen bondreduction. The design of improved microbiai enzymes that incorporateboth steric and electronic effects continues for use in remediatinghalogenated contaminants in situ