Mutant Escherichia coli penicillin acylase with enhanced stability at alkaline pH

Increased stability at alkaline pH should be a valuable attribute for the utilization of penicillin acylase in bioreactors employed to convert penicillins into 6-aminopenicillanic acid, a precursor of semisynthetic penicillins. In these systems, base is added for pH control, which results in local alkaline conditions that promote enzyme inactivation. Hydrolysis and synthesis reactions are also pH dependent. Here, we report work in which the gene coding for Escherichia coli penicillin acylase was subjected to oligonucleotide-directed random mutagenesis at regions coding for amino acids predicted to be at the surface of the enzyme. The resulting mutant library, cloned in E. coli, was screened by a filter paper assay of the colonies for the presence of penicillin acylase activity with enhanced stability at alkaline pH. Characterization of one of the selected clones revealed the presence of a mutation, Trp431-Arg, which would presumably alter the surface charge of the protein. In vitro experiments demonstrated a near twofold increase in the half-life of the mutant enzyme when stored at pH 8.5 as compared with the wild-type enzyme, with a comparable specific activity at several pH values. In general, the mutant displayed increased stability toward the basic side in the pH-stability profile. (c) 1995 John Wiley & Sons, Inc.

Improving random mutagenesis by purification of the oligonucleotide variants

An oligonucleotide-based mutagenesis method is presented where, contrary to most classical mutagenic approaches, preselection of the variants is performed at the oligonucleotide level to avoid cloning of non-desired sequences. The method relies on the generation of differentially phosphate-protected oligonucleotides. Protection of the phosphates is accomplished by substoichiometric incorporation of an Fmoc-protected and n-propyl-protected trinucleotide phosphoramidite during ordinary oligonucleotide assembly. Instead of the alkali-labile beta-cyanoethyl group introduced in ordinary assembly, the trinucleotide introduces the alkali-stable n-propyl group. As a result, single mutants carry three ionic phosphates less than the wild-type sequence, double mutants carry six ionic phosphates less and so on. This difference in ionic ratio enables separation of the variants by conventional polyacrilamide gel electrophoresis. In the exemplified library described herein, two sub-populations containing mainly triple and quadruple mutants were selected out of five possible sub-populations.

Different strategies to recover the activity of monomeric triosephosphate isomerase by directed evolution

A monomeric version of triosephosphate isomerase from Trypanosoma brucei, MonoTIM, has very low activity, and the same is true for all of the additional monomeric variants so far constructed. Here, we subjected MonoTIM to directed evolution schemes to achieve an activity improvement. The construction of a suitable strain for genetic selection provided an effective way to obtain active catalysts from a diverse population of protein variants. We used this tool to identify active mutants from two different strategies of mutagenesis: random mutagenesis of the whole gene and randomization of loop 2. Both strategies converged in the isolation of mutations Ala43 to Pro and Thr44 to either Ala or Ser, when randomizing the entire gene or to Arg in the case of randomization of loop 2. The kinetic characterization of the two more active mutants showed an increase of 11-fold in k(cat) and a reduction of 4-fold in K(m) for both of them, demonstrating the sensitivity of the selection method. A small difference in growth rate is observed when both mutant genes are compared, which seems to be attributable to a difference in solubility of the expressed proteins.

Orthogonal combinatorial mutagenesis: a codon-level combinatorial mutagenesis method useful for low multiplicity and amino acid-scanning protocols

We describe here a method to generate combinatorial libraries of oligonucleotides mutated at the codon-level, with control of the mutagenesis rate so as to create predictable binomial distributions of mutants. The method allows enrichment of the libraries with single, double or larger multiplicity of amino acid replacements by appropriate choice of the mutagenesis rate, depending on the concentration of synthetic precursors. The method makes use of two sets of deoxynucleoside-phosphoramidites bearing orthogonal protecting groups [4,4'-dimethoxytrityl (DMT) and 9-fluorenylmethoxycarbonyl (Fmoc)] in the 5' hydroxyl. These phosphoramidites are divergently combined during automated synthesis in such a way that wild-type codons are assembled with commercial DMT-deoxynucleoside-methyl-phosphoramidites while mutant codons are assembled with Fmoc-deoxynucleoside-methyl-phosphoramidites in an NNG/C fashion in a single synthesis column. This method is easily automated and suitable for low mutagenesis rates and large windows, such as those required for directed evolution and alanine scanning. Through the assembly of three oligonucleotide libraries at different mutagenesis rates, followed by cloning at the polylinker region of plasmid pUC18 and sequencing of 129 clones, we concluded that the method performs essentially as intended.

Introducing transglycosylation activity in a liquefying alpha-amylase

By mutating Ala-289 by Phe or Tyr in the Bacillus stearothermophilus alpha-amylase, we induced this enzyme to perform alcoholytic reactions, a function not present in the wild-type enzyme. This residue was selected from homology analysis with neopullulanase, where the residue has been implicated in the control of transglycosylation [Kuriki et al. (1996) J. Biol. Chem. 271, 17321-173291. We made some inferences about the importance of electrostatic and geometrical modifications in the active site environment of the amylase to explain the behavior of the modified enzyme.

Alcoholysis reactions from starch with alpha-amylases

The ability of alpha-amylases from different sources to carry out reactions of alcoholysis was studied using methanol as substrate. It was found that while the enzymes from Aspergillus niger and Aspergillus oryzae, two well-studied saccharifying amylases, are capable of alcoholysis reactions, the classical bacterial liquefying alpha-amylases from Bacillus licheniformis and Bacillus stearothermophilus are not. The effect of starch and methanol concentration, temperature and pH on the synthesis of glucosides with alpha-amylase from A. niger was studied. Although methanol may inactivate alpha-amylase, a 90% substrate relative conversion can be obtained in 20% methanol at a high starch concentration (15% w/v) due to a stabilizing effect of starch on the enzyme. As the products of alcoholysis are a series of methyl-oligosaccharides, from methyl-glucoside to methyl-hexomaltoside, alcoholysis was indirectly quantified by high performance liquid chromatography analysis of the total methyl-glucoside produced after the addition of glucoamylase to the alpha-amylase reaction products. More alcoholysis was obtained from intact soluble starch than with maltodextrins or pre-hydrolyzed starch. The biotechnological implications of using starch as substrate for the production of alkyl-glucosides is analyzed in the context of these results.

Combination of DMT-mononucleotide and Fmoc-trinucleotide phosphoramidites in oligonucleotide synthesis affords an automatable codon-level mutagenesis method

BACKGROUND

Synthetic DNA has been used to introduce variability into protein-coding regions. In protocols that produce a few mutations per gene, the sampling of amino-acid sequence space is limited by the bias imposed by the genetic code. It has long been apparent that the incorporation of trinucleotides in the synthetic regime would circumvent this problem and significantly enhance the usefulness of the technique.

RESULTS

A new method is described for the creation of codon-level degenerate oligodeoxyribonucleotides that combines conventional dimethoxytrityl (DMT) mononucleoside phosphoramidite chemistry with 9-fluorenylmethoxycarbonyl (Fmoc) trinucleotide phosphoramidites (whose synthesis is reported in the paper). The substoichiometric use of these Fmoc-trinucleotides in an automatable, solid-phase synthesis procedure afforded DNA fragments comprising the wild-type sequence and a controllable distribution of mutants within two- and three-codon stretches of DNA, within the multiple cloning site of the conventional cloning vector pUC19.

CONCLUSIONS

DMT and Fmoc are compatible protecting groups in conventional oligonucleotide synthesis methods, resulting in controllable levels of codon-based mutagenesis.

Microbial sensor for new-generation cephalosporins based in a protein-engineered beta-lactamase

A protein-engineered beta-lactamase, constructed by site-directed mutagenesis in Escherichia coli (E104M/G238S), and having broadened specificity, was able to degrade cephalosporins of first, second, and third generations. Manipulations of culture conditions allowed an increase in beta-lactamase specific activity by up to twofold. The resultant bacteria were used to construct an immersable whole-cell biosensor for the detection of new-generation cephalosporins. Cells were immobilized on agar membranes, which in turn were attached to the surface of a flat pH electrode, thus constituting a biosensor based on the detection of pH changes. The sensor was able to detect second- and third-generation cephalosporins: cefamandole (0.4-4 mM), cefotaxime (0.4-3.5 mM), and cefoperazone (0.3-1.85 mM). Response times were between 3.5 and 11 min, depending on the kind of cephalosporin tested. The biosensor was stable for at least 7 d, time during which up to 100 tests were performed.

In vivo studies on the positive control function of NifA: a conserved hydrophobic amino acid patch at the central domain involved in transcriptional activation

The eubacterial enhancer-binding proteins activate transcription by binding to distant sites and, simultaneously, contacting the RNA polymerase r54 promoter complex (Esigma54). The positive control function is located at the central domain of these proteins, but it is not know which specific region has the determinants for the interaction with Esigma54. Here, we present genetic evidence that a small region of hydrophobic amino acids, previously denominated C3, at the central domain of Bradyrhizobium japonicum NifA is involved in positive control. We obtained 26 missense mutants along this conserved region. Among these, only strains expressing the NifA(F307-->Y) and NifA(A310-->S) mutant proteins retained some of the transcriptional activity (<20%), whereas those carrying NifA(E298-->D) and NifA(T308-->S) had very low but detectable activity (< 1.0%). The rest of the NifA mutants did not induce any measurable transcriptional activity. When expressed in the presence of wild-type NifA, the great majority of the mutants displayed a dominant phenotype, suggesting that their oligomerization determinants were not altered. In vivo dimethyl-sulphate footprinting experiments for a subset of the NifA mutants showed that they were still able to bind specifically to DNA. Analysis of intragenic supressors highlight the functional role of a hydroxyl group at position 308 to activate transcription.

Isolated domain II and III from the Bacillus thuringiensis Cry1Ab delta-endotoxin binds to lepidopteran midgut membranes

The DNA fragment encoding Cry1Ab domain II-III (45.3 kDa) was cloned and expressed. Domain II-III is expressed in low yields. In vitro binding analysis to Manduca sexta and Trichoplusia ni larval midgut tissue sections demonstrated that domain II-III fragment bound along the microvilli of the midgut epithelium, indicating that this fragment retains binding functionality in the absence of domain I. Binding of domain II-III to the midgut brush border membrane proteins from T. ni larvae indicated that Cry1Ab toxin and domain II-III bind to the same 150 kDa protein. In contrast, in M. sexta membranes, Cry1Ab toxin binds to 200 and 120 kDa proteins, and domain II-III only binds to the 200 kDa protein. Finally, binding assays with isolated brush border membrane vesicles showed that the interaction of domain II-III with the membrane vesicles is highly reversible, supporting the proposition that the integration of domain I into the membrane could participate in the irreversible binding of the toxin. These studies confirm that this part of the toxin is involved in binding interactions and could be separated as a discrete fragment that conserves at least part of its functionality.

A proposed architecture for the central domain of the bacterial enhancer-binding proteins based on secondary structure prediction and fold recognition

The expression of genes transcribed by the RNA polymerase with the alternative sigma factor sigma 54 (E sigma 54) is absolutely dependent on activator proteins that bind to enhancer-like sites, located far upstream from the promoter. These unique prokaryotic proteins, known as enhancer-binding proteins (EBP), mediate open promoter complex formation in a reaction dependent on NTP hydrolysis. The best characterized proteins of this family of regulators are NtrC and NifA, which activate genes required for ammonia assimilation and nitrogen fixation, respectively. In a recent IRBM course (@ontiers of protein structure prediction," IRBM, Pomezia, Italy, 1995; see web site http://www.mrc-cpe.cam.uk/irbm-course95/), one of us (J.O.) participated in the elaboration of the proposal that the Central domain of the EBPs might adopt the classical mononucleotide-binding fold. This suggestion was based on the results of a new protein fold recognition algorithm (Map) and in the mapping of correlated mutations calculated for the sequence family on the same mononucleotide-binding fold topology. In this work, we present new data that support the previous conclusion. The results from a number of different secondary structure prediction programs suggest that the Central domain could adopt an alpha/beta topology. The fold recognition programs ProFIT 0.9, 3D PROFILE combined with secondary structure prediction, and 123D suggest a mononucleotide-binding fold topology for the Central domain amino acid sequence. Finally, and most importantly, three of five reported residue alterations that impair the Central domain. ATPase activity of the E sigma 54 activators are mapped to polypeptide regions that might be playing equivalent roles as those involved in nucleotide-binding in the mononucleotide-binding proteins. Furthermore, the known residue substitution that alter the function of the E sigma 54 activators, leaving intact the Central domain ATPase activity, are mapped on region proposed to play an equivalent role as the effector region of the GTPase superfamily.

Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants

EcoRI recognizes and cleaves DNA at GAATTC sites and is one of the best characterized sequence-specific restriction endonucleases (ENases). In previous studies, an EcoRI mutant, which exhibited relaxed substrate specificity and cleaved both canonical and EcoRI star sites, was isolated. This mutant enzyme has Tyr instead of His114. Here, we subjected residue 114 of the EcoRI ENase to saturation mutagenesis. The resulting mutant enzymes were characterized both in vivo and in vitro, resulting in the identification of mutants with canonical (H114K, Q, D, I) or relaxed (H114Y, F, S, T) specificity, as well as one mutant with severely impaired activity (H114P). In the X-ray structure of an EcoRI-substrate complex, His114 is located between the catalytic and recognition regions of EcoRI and may directly contact the DNA phosphate backbone. Based on our genetic and biochemical findings and the X-ray structure, we propose that His114 participates in substrate recognition and catalysis, either directly, via protein-DNA interactions, or indirectly, by mediating conformational changes that trigger DNA cleavage in response to substrate recognition.

A new TEM beta-lactamase double mutant with broadened specificity reveals substrate-dependent functional interactions

Using a random combinatorial mutagenesis of TEM beta-lactamase, directed against residues potentially involved in substrate discrimination, followed by selection on third generation cephalosporins, we obtained the double mutant E104M/G238S. Additionally, by using cloning strategies and site-directed mutagenesis we constructed the individual single mutants and also the single modification E104K and the double mutant E104K/G238S, which broaden the specificity of clinically isolated TEM beta-lactamase variants. The kinetic characterization of the purified double mutant E104M/G238S and its single counterparts E104M and G238S was carried out. The single mutant E104M exhibited increased kcat values against all substrates tested. Km values remained similar to the values shown by the wild-type enzyme. The mutation at E104M was responsible for the increased hydrolysis rate against cefuroxime shown by the double mutant E104/G238S. The effect of mutation G238S varied more pronouncedly, depending on the substrate. In general, a lower Km was observed, but also a decreased kcat. The double mutant E104M/G238S exhibited a higher hydrolytic rate against cefotaxime compared with the corresponding single mutations. We observed nearly a 1000-fold greater kcat/Km for the double mutant than for the wild type. This improvement in catalysis was the consequence of increased kcat and decreased Km values. Computed contact interactions from modeling substrate complexes show reliable results only for benzylpenicillin. The modeling results with this substrate confirmed the observed enzyme activities for the different single and double mutants. Analysis of the apparent coupling energies, as calculated from the kinetic parameters of the single and double mutants, showed that the quantitative effect of a second mutation on a single mutant was either absent, additive, partially additive, or synergistic with respect to the first mutation, depending on the substrate analyzed.

Substitution of Asp for Asn at position 132 in the active site of TEM beta-lactamase. Activity toward different substrates and effects of neighboring residues

Using a random, combinatorial scheme of mutagenesis directed against the conserved SDN region of TEM beta-lactamase, and selective screening in ampicillin-plates, we obtained the N132D mutant enzyme. The kinetic characterization of this mutant indicated relatively small effects compared to the wild-type. Both pK1 and pK2 for catalysis were decreased about 1 unit relative to the pK's for the wild type. This effect was predominantly due to changes in Km. In contrast to the wild-type, the pH-rate profiles of the mutant showed that Km for several side chain-containing penicillin substrates increases when the pH is above 5.5. 6-Aminopenicillanic acid, which lacks a side chain, did not show this effect. With benzylpenicillin, ampicillin, and carbenicillin, kcat for the mutant showed a similar pH dependence as the wild type. With 6-aminopenicillanic acid, kcat for the mutant was greater than that for the wild type. The nature of the 104 side chain may affect the environment of Asp132; double mutants N132D/E104X (where X can be Q or N) are unable to confer antibiotic resistance to bacterial cells. The computed contact interactions from modeling substrate complexes between benzylpenicillin or 6-aminopenicillanic acid with the N132D mutant confirmed the importance of the protonation state of residue Asp132 for the complex stability with side chain-containing substrates. The data indicate that the contact between the side chain of residue 132 and the substrate is relevant for the ground state recognition, but because of close contact with several important groups in its neighborhood, residue 132 is also indirectly involved in the catalytic step of the wild-type enzyme.

Combinatorial libraries of proteins: analysis of efficiency of mutagenesis techniques

A number of considerations are made on the efficiency of mutagenesis techniques used in protein engineering, particularly those that include a random component. The expected outcome of different protocols is analyzed using computer programs. Special emphasis is made on the effect that the degeneracy of the genetic code has on the bias of the representation of amino acid replacements. The consequences of using alternative methods is analyzed in terms of the likelihood of obtaining underrepresented amino acid substitutions in mutant libraries. A consideration is also made of the outcome of combinatorial mutagenesis experiments with regard to the size of the amino acid window and the multiplicity of replacements that could be sampled with different methods. Optimal mutagenesis rates for specific conditions could be derived from the presented data and the computer program made available with this paper.

Microbial systems and directed evolution of protein activities

Recent advances in recombinant DNA methodology have had an important impact on the capacity to manipulate protein-coding sequences. The appearance of new, powerful screening systems completes a scenario for conducting directed evolution experiments. We review here some of the latest developments in experimental approaches to directed evolution, utilizing microbial systems. These include phage display, surface display, operator-repressor systems, and novel mutagenesis approaches. We also highlight the achievements and limitations of current methodologies. We present strategies used by our own group that permitted isolation of specificity mutants of beta-lactamase. Possible improvements for the future of the variation-selection approach to the study and manipulation of proteins are presented.

The delta-endotoxin protein family displays a hydrophobic motif that might be implicated in toxicity

A computer-based analysis of hydropathy and surface probability of representative members of each class of the Cry family of proteins was performed. A highly conserved hydrophobic motif within the previously described block, D2, is present not only in lepidopteran toxin genes but also in toxins active against diptera and coleoptera. An interesting feature of this hydrophobic motif is the presence of an aspartic residue (highly hydrophilic) in its middle part. Comparison with the amino acid sequence from diphtheria toxin showed that it also contains a hydrophobic motif similar to the one present in the Bacillus thuringiensis toxins. It also contains an aspartic residue in the middle part and some speculations are presented on the function of this specific region with regard to the toxic mechanism of action.

Combinatorial mutagenesis of three major groove-contacting residues of EcoRI: single and double amino acid replacements retaining methyltransferase-sensitive activities

A library of mutant ecoRIR genes encoding EcoRI restriction endonuclease was generated using trinucleotide blocks and a combination of recombinant DNA procedures, including primer extension and the polymerase chain reaction. Codons corresponding to three amino acids (E144, R145 and R200), previously implicated in the specific recognition of the DNA substrate, were combinatorially mutated so as to generate a library that potentially contains all 20(3) possible single, double and triple aa replacements, in a balanced distribution. Inspection of the phenotypes of Escherichia coli colonies bearing the mutant genes showed that several of them retained activities that were deleterious to the cells but were still protected by the EcoRI methyltransferase. These included new enzyme variants, including non-conservative single (Thr or Val for Glu144) and double (Val for Glu144 and Thr for Arg145) replacements.

Rotavirus YM gene 4: analysis of its deduced amino acid sequence and prediction of the secondary structure of the VP4 protein

We have determined the complete nucleotide sequence of the VP4 gene of porcine rotavirus YM. It is 2,362 nucleotides long, with a single open reading frame coding for a protein of 776 amino acids. A phylogenetic tree was derived from the deduced YM VP4 amino acid sequence and 18 other available VP4 sequences of rotavirus strains belonging to different serotypes and isolated from different animal species. In this tree, VP4 proteins were grouped by the hosts that the corresponding viruses infect rather than by the serotypes they belong to, suggesting that this protein is involved in the host specificity of the viruses. In an attempt to predict the secondary structure of the VP4 protein, we selected the more divergent VP4 sequences and made a secondary structure analysis of each protein. In spite of variations within the individual structures predicted, there was a general structural pattern which suggested the existence of at least two different domains. One, comprising the amino-terminal 63% of the protein, is predicted to be a possible globular domain rich in beta-strands alternated with turns and coils. The second domain, represented by the remaining, carboxy-terminal part of VP4, is rich in long stretches of alpha-helix, one of which, 63 amino acids long, has heptad repeats resembling those found in proteins known to form alpha-helical coiled-coils. The predicted secondary structure correlates well with the available data on the protein accessibility delineated by immunological and biochemical findings and with the spike structure of the protein, which has been determined by cryoelectron microscopy.

Molecular evolution of class A beta-lactamases: phylogeny and patterns of sequence conservation

We present a multiple alignment of the amino acid sequences of eight class A beta-lactamases and utilized it to propose a phylogeny, based on the nucleotide sequences of their corresponding genes. We have also used the alignment, together with the alpha-carbon co-ordinates of the Staphylococcus aureus protein, to search systematically for neighbouring residues that share the same pattern of conservation among the different members of the protein family. The distribution of invariant residues and of groups of residues with co-ordinate changes map, predominantly, at the region of the active site and at interfaces between structural elements, respectively. We have also contrasted the distribution of conserved residues with the positions which are known to differ in mutants and variants of class A beta-lactamases.

Plasmid vector pBR322 and its special-purpose derivatives--a review

The plasmid pBR322 was one of the first EK2 multipurpose cloning vectors to be designed and constructed (ten years ago) for the efficient cloning and selection of recombinant DNA molecules in Escherichia coli. This 4363-bp DNA molecule has been extensively used as a cloning vehicle because of its simplicity and the availability of its nucleotide sequence. The widespread use of pBR322 has prompted numerous studies into its molecular structure and function. These studies revealed two features that detract from the plasmid's effectiveness as a cloning vector: plasmid instability in the absence of selection and, the lack of a direct selection scheme for recombinant DNA molecules. Several vectors based on pBR322 have been constructed to overcome these limitations and to extend the vector's versatility to accommodate special cloning purposes. The objective of this review is to provide a survey of these derivative vectors and to summarize information currently available on pBR322.

Construction and characterization of new cloning vehicles. VII. Construction of plasmid pBR327par, a completely sequenced, stable derivative of pBR327 containing the par locus of pSC101

In vitro recombinant DNA experiments, using plasmid pBR327 and a DNA fragment derived from plasmid pSC101 containing the par region, resulted in the construction of plasmid pBR327par. This new cloning vehicle has all the cloning properties of the parental plasmid, and is more stable than pBR327. Since the nucleotide sequence of the par region has been determined, this new vector is completely characterized. Some features of the sequence with possible functional significance are discussed.

The use of synthetic oligodeoxyribonucleotides to produce specific deletions in the araBAD promoter of Escherichia coli B/r

Two oligodeoxyribonucleotides were chemically synthesized and used to specifically mutate the regulatory region of the araBAD operon in Escherichia coli B/r. One oligodeoxyribonucleotide introduced a 3-bp deletion in the araC activator binding site, the other a 3-bp deletion in the CRP-cAMP binding site. The mutations were introduced onto an ara insert cloned in an M13 vector using the synthetic oligodeoxyribonucleotides as primers and the (+) strand of an M13 mp2::ara hybrid phage as a template in an in vitro polymerization reaction. Hybridizations using the original synthetic oligodeoxyribonucleotide as a radioactive probe identified phage containing the desired deletion. The mutant ara inserts were subcloned into a stable plasmid for functional analysis. Transcription studies performed on strains containing the mutant ara plasmids demonstrated that both mutations reduced the amount of araBA mRNA synthesized in the presence of L-arabinose.

Construction and characterization of new cloning vehicles. V. Mobilization and coding properties of pBR322 and several deletion derivatives including pBR327 and pBR328

A DNA sequence essential for the R64drd11 + ColK-mediated conjugal transfer of pBR322 has been located in a 540 bp HaeIII fragment (HaeIII-2) between the vegetative origin of replication and the tetracycline resistance (Tcr) gene of this vector. The pBR322 derivatives pBR327 and pBR328 lack this DNA sequence and are not mobilized by conjugation. Two derivatives of pBR328 were constructed by re-inserting the HaeIII-2 fragment in both orientations into the chloramphenicol-resistance gene of the same vector. One orientation of the HaeIII-2 fragment permitted mobilization by conjugation while the opposite orientation prevented mobilization. Further examination of pBR322 and derivatives revealed that the region between the origin of replication and Tcr gene also plays a role in regulating plasmid copy number.