Design and Chemoenzymatic Synthesis of A Tissue Plasminogen Activator Gene with Unique Restriction Sites: A Model for Studying Protein Domain Function

Abstract

We have designed and constructed a cassette tPA gene with unique restriction sites in the interdomain regions. Each domain was chemoenzymatically assembled, cloned and sequenced. We have constructed and expressed the full-length molecule and some deletion mutants.     

Structure-function analysis of tissue-type plasminogen activator by linker-insertion, point and deletion mutagenesis

We undertook a structure--function analysis of human tissue plasminogen activator (tPA) using linker-scanning and deletion mutagenesis. Synthetic oligonucleotide linkers were introduced into the tPA cDNA at pre-existing restriction enzyme sites. This generated a series of tPA variants which contained small primary sequence alterations consisting of point mutations, deletions or insertions. The majority of the linker-insertion variants demonstrate a significant reduction in amidolytic and fibrinolytic activity in comparison to wild-type tPA. The exceptions are the variants with linker-inserts placed at the BglII(115) and StyI(277) sites of the tPA cDNA (4SLEG5 and 57LEA58 respectively), which encode insertions at the boundaries of the finger domain. The variants with linker-inserts in the light chain (protease domain) of tPA are the lowest in enzymatic activity. Particularly sensitive to mutation are highly conserved amino acids. Heavy chain deletion variants were constructed from point mutants at the domain boundaries of tPA. Deletion of the kringle domains lowers the fibrinolytic activity to a greater extent than deletion of the finger or growth factor domains. We conclude that alterations in any domain of the tPA molecule, and particularly in the highly conserved residues within these domains, can affect fibrinolytic activity.     

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

A gene for expression of horse heart myoglobin in Escherichia coli has been constructed in one step from long synthetic oligonucleotides. The synthetic gene contains an efficient translation initiation signal and used codons that are commonly found in E. coli. Unique restriction sites are placed throughout the gene. It has been inserted in a phagemid vector and is expressed from the lac promoter in E. coli at high efficiency, the soluble heme protein representing approximately 10% of soluble protein. Two versions of horse heart myoglobin were produced with aspartic acid or asparagine at residue 122. Comparison of chromatographic mobilities of these two proteins with authentic horse heart myoglobin identified aspartic acid as the correct residue 122. The availability of this gene, which is designed to facilitate oligonucleotide mutagenesis or cassette mutagenesis, will allow systematic structure-function analysis of horse heart myoglobin.     

含有分裂型内含肽DnaE基因的表达盒设计、合成及高效表达载体的构建

目的:建立一种简便、快捷的基因从头设计、优化与合成策略,进行含有分裂型内含肽DnaE基因的表达盒全合成并构建高效表达载体。方法:以免费软件GeneDesign 3.0为主要平台,同时结合Tandem Repeats Finder、UNAFold等不同生物信息学软件,对含有DnaE基因、合适酶切位点的表达盒进行设计与分段合成;合成寡核苷酸片段通过重叠PCR进行组装与克隆。结果:利用建立的设计流程,合成了大小为44～64 nt的14段寡核苷酸片段,通过重叠PCR,实现了14段寡核苷酸片段的一次性组装,经过克隆、酶切鉴定、序列分析得到了序列完全正确的表达载体。结论:建立了一套有效的、基于免费软件的基因从头设计与合成的策略,构建了可以用于环肽小分子文库表达与筛选的表达载体。     

A synthetic IgG-binding domain based on staphylococcal protein A

A synthetic IgG-binding domain based on staphylococcal protein A was designed with the aid of sequence comparisons and computer graphic analysis. A strategy, utilizing non-palindromic restriction sites, was used to overcome the difficulties of introducing site-specific changes into the repetitive gene. A single mutagenized gene fragment was polymerized to different multiplicities, and the different gene products were expressed in Escherichia coli. Using this scheme, protein A-like proteins composed of different numbers of IgG-binding domains were produced. These domains were changed to lack asparagine--glycine dipeptide sequences as well as methionine residues and are thus, in contrast to native protein A, resistant to treatment with hydroxylamine and cyanogen bromide.     

Construction and expression of a synthetic wheat storage protein gene

A synthetic wheat high-molecular-weight (HMW) glutenin storage protein gene analog was constructed for expression in E. coli. This first synthetic HMW-glutenin gene and future modifications are intended to allow systematic dissection of the molecular basis of HMW-glutenin role in the visco-elastic properties critical for wheat product processing and utilization. The design of the gene included four features: different construction strategies for the separate assembly of major polypeptide domains, the inclusion of convenient restriction sites for modifications, use of a codon selection similar to E. coli highly expressed genes, and the ability to produce repetitive sequence domains of exact numbers of defined repeats. The complete synthetic HMW-glutenin construct was 1908 bp, and contained 32 identical copies of one of the HMW-glutenin repetitive domain motifs. The gene expressed the novel HMW-glutenin protein to relatively high levels in bacterial cultures and the protein exhibited the known anomalous behavior of HMW-glutenins in SDS-PAGE.     

Directional cloning of cDNA using a selectable SfiI cassette

To increase the efficiency of directionally cloning cDNA, we have constructed a pair of vectors and devised a cDNA cloning strategy that improves upon previously published methods. The vectors, pLIB: AZ and pLIB: ZA, have two unique (distinct religation specificities; GGCCN/NNNNGGCC) SfiI sites (SfiI.A and SfiI.B) flanking a stuffer fragment which contains the tetracycline-resistance element. These vectors permit the directional cloning of cDNA in both sense (pLIB: AZ) and antisense (pLIB: ZA) orientations relative to the promoter for phage T3 RNA polymerase. cDNA that was synthesized using a primer with a 5' sequence of a SfiI.B site followed by an oligo(dT)16 3' tail was then ligated to an adaptor with the sequence of a SfiI.A site produced directional molecules that could be cloned into the pLIB vectors. Complex libraries with 10(7) members were produced from as few as 6 x 10(5) cells. The SfiI sites and stuffer can be subcloned as a cassette to permit directional cloning in other vectors, as there are several restriction enzyme sites flanking this region to the 5' and 3'.     

人组织性纤溶酶原激活物衍生物在大肠杆菌硫氧化还原蛋白融合表达系统中的表达

目的:克隆含tPA中355个氨基酸密码子(1-3和176-527氨基酸)的cDNA序列(tPA355),将其在大肠杆菌融合蛋白表达系统中表达,并在体外复性使其具有激活纤溶酶原的生物活性。方法:采用RT-PCR技术从人黑色素瘤细胞Bowes中克隆出tPA355cDNA,然后在pET32a(+)BL21(DE3)大肠杆菌表达系统中表达,将表达出的融合蛋白Trx-tPA355(Thioredoxin,Trx)包涵体在体外进行变性、复性和纯化以使其具有激活纤溶酶原的生物活性。结果:测序结果表明本研究克隆的编码tPA中355个氨基酸密码子的cDNA序列与美国专利(公开号:5,587,159)中对应的序列完全一致,将其在pET32a(+)/BL21(DE3)大肠杆菌表达系统中表达可获得稳定表达的融合蛋白Trx-tPA355包涵体,该包涵体占菌体总蛋白的30%左右,此融合蛋白经变性、复性后具有激活纤溶酶原的生物活性。结论:含tPA中355个氨基酸密码子(1-3和176-527氨基酸)的cDNA在大肠杆菌Trx融合蛋白表达系统中可获得稳定表达,表达的融合蛋白产物在体外经变性、复性后具有激活纤溶酶原的生物活性。     

Synthesis and expression in Escherichia coli of a gene for kappa-bungarotoxin

A gene which codes for the 66-residue polypeptide of kappa-bungarotoxin has been chemically synthesized by linking together 3 synthetic double-stranded oligonucleotides in a bacterial plasmid. The synthesis incorporated six unique silent restriction sites spaced throughout the gene for use in cassette mutagenesis. Direct expression of the kappa-bungarotoxin polypeptide by itself in Escherichia coli failed to result in a stable product. The toxin polypeptide was stabilized and expressed in E. coli as part of a fusion protein with rat intestinal fatty acid binding protein under control of the nalidixic acid inducible recA promoter. Two fusion protein constructs were prepared that differed only in the cleavage site between the fatty acid binding protein and the toxin polypeptide. One contained a factor Xa cleavage site, and the other, since the toxin itself is devoid of methionine, contained a methionyl residue that served as a cyanogen bromide cleavage site. The fusion proteins were isolated by ion-exchange chromatography and reverse-phase HPLC. The construct containing the factor Xa cleavage site could not be cleaved under nondenaturing conditions. On the other hand, kappa-bungarotoxin was efficiently cleaved from the methionyl fusion protein with CNBr. The toxin polypeptide was isolated by reverse-phase HPLC and ion-exchange chromatography and produced a complete and specific blockade of neuronal nicotinic acetylcholine receptors in chick ciliary ganglia which was indistinguishable from that produced by a comparable amount of venom-purified kappa-bungarotoxin.     

Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites

A method is described for the efficient insertion of mutagenic oligodeoxynucleotide cassettes which allow saturation of a target amino acid codon with multiple mutations. Restriction sites are introduced by oligonucleotide-directed mutagenesis procedures to flank closely the target codon in the plasmid containing the gene. The restriction sites to be introduced are chosen based on their uniqueness to the plasmid, proximity to the target codon and conservation of the final amino acid coding sequence. The flanking restriction sites in the plasmid are digested with the cognate restriction enzymes, and short synthetic duplex DNA cassettes (10-25 bp) are inserted. The mutagenic cassette is designed to restore fully the wild-type coding sequence, except over the target codon, and to eliminate one or both restriction sites. Elimination of a restriction site facilitates selection of clones containing the mutagenic oligodeoxynucleotide cassette. To make the cassettes, single-stranded oligodeoxynucleotides and their complements are synthesized in separate pools containing different codons over the target. This method has been successfully applied to generate 19 amino acid substitutions at position 222 in the subtilisin protein sequence.     

High resolution analysis of functional determinants on human tissue-type plasminogen activator

Sixty-four variants of human tissue-type plasminogen activator (tPA) were produced using recombinant DNA techniques. Charged residues were converted to alanine in clusters of from one to four changes per variant; these clusters spanned all the domains of the molecule. The variants were expressed by mammalian cells and were analyzed for a variety of properties. Variants of tPA were found that had reduced activity with respect to each tested property; in a few cases increased activity was observed. Analysis of these effects prompted the following conclusions: 1) charged residues in the nonprotease domains are less involved in fibrin stimulation of tPA activity than those in the protease domain, and it is possible to increase the fibrin specificity (i.e. the stimulation of tPA activity by fibrin compared to fibrinogen) by mutations at several sites in the protease domain; 2) the difference in enzymatic activity between the one- and two-chain forms of tPA can be increased by mutations at several sites on the protease domain; 3) binding of tPA to lysine-Sepharose was affected only by mutations to kringle-2, whereas binding to fibrin was affected most by mutations in the other domains; 4) clot lysis was influenced by mutations in all domains except kringle-2; 5) sensitivity to plasminogen activator inhibitor-1 seems to reside exclusively in the region surrounding residue 300. A model of the tPA protease domain has been used to map some of the critical residues and regions.     

An intein-cassette integration approach used for the generation of a split TEV protease activated by conditional protein splicing

Ligand-induced conditional protein splicing (CPS) using a split intein allows the covalent reconstitution of a protein from two polypeptide fragments. The small molecule rapamycin binds to the fused FKBP and FRB dimerizer domains and thereby induces folding of the split intein, which then removes itself in the trans-splicing reaction. CPS has great potential for the experimental control of protein activity in living cells, however, only one such example was reported yet. This discrepancy is due to the challenging reconstitution of a protein from two inactive fragments because of folding, stability, and solubility issues. Moreover, in CPS the split intein must be active in the specific sequence context. We here report the novel concept, design, and application of a CPS cassette for facile target gene modification to identify active split intein insertion sites. The CPS cassette encodes the split intein and dimerizer domain gene fragments as well as a selectable genetic marker for yeast. The addition of short sequences in the PCR-amplification of the CPS cassette allowed its site-specific insertion into the target gene by homologous recombination. Our approach thus avoids the extensive DNA cloning steps typically required. By this strategy, we identified two CPS variants of the tobacco etch virus (TEV) protease that are conditionally activated by rapamycin in yeast and we show their potential for the manipulation of intracellular proteins through proteolysis events. Our results suggest that more proteins will be amenable to CPS control and that intein cassette integration is a powerful tool for the development of such conditional variants as well as for other application of cis- and trans-splicing inteins.     

Cloning and expression of truncated form of tissue plasminogen activator in Leishmania tarentolae

An expression cassette containing kringle 2 and serine protease domains (K2S), tissue plasminogen activator (tPA), together with a signal sequence derived from Leishmania tarentolae and two fragments of the small subunit ribosomal RNA locus, was introduced into L. tarentolae. The transfected cells produced recombinant K2S (rK2S) protein extracellularly with serine protease activity. Expression and enzyme activity of rK2S in the supernatant was 930 i.u./ml. The specific activity of purified rK2S was 7.4 U/mg of protein. Replacement of the human signal sequence tPA with the signal sequence derived from Leishmania increased the secretion of recombinant protein up to 30 times.     

Total chemical synthesis of a gene for hepatitis B virus core protein and its functional characterization

We have chemically synthesized a DNA duplex of 560 nucleotides that codes for the hepatitis B virus (HBV) core protein. The synthetic gene contains 27 unique internal restriction sites. Thereby, it can easily be mutagenized by replacement of rather short restriction fragments. A number of restriction recognition sequences are in common between the synthetic and the authentic gene, thus allowing for the transfer of synthetic segments into the cloned viral genome. Several unexpected mutations in the synthetic gene were readily corrected utilizing the multiple unique restriction sites. In Escherichia coli, the expression level of the synthetic gene product amounts to about 4% of the total soluble protein. It forms particles closely resembling native HBV cores. After transfer of the synthetic gene into the viral genome, transient expression in a hepatoma cell line yields proteins indistinguishable from the native gene products. The synthetic gene thus provides a useful tool for studies on the structure and function of the isolated HBV core protein as well as the gene and its various products in the viral life-cycle.     

Tissue-type plasminogen activator variants with domain duplications and rearrangements

The interactions between tPA domains that are important for catalysis are poorly understood. We have probed the function of interdomain interactions by generating tPA variants in which domains are duplicated or rearranged. The proteins were expressed in a transient mammalian expression system and tested in vitro for their ability to activate plasminogen, induce fibrinolysis and bind to a forming fibrin clot. Duplication of the heavy chain domains of tPA produced enzymatically active tPA variants, many of which demonstrated similar in vitro amidolytic and fibrinolytic activity and similar fibrin affinity to the parent molecule. Zymographic analysis of the domain duplication tPA variants showed one major active species for each variant. Selection of the residues duplicated and the interdomain spacing were found to be critical considerations in the design of tPA variants with duplicated domains. We also rearranged the domains of tPA such that kringle 1 replaced the second kringle domain and vice versa. An analysis of these variants indicates that the first kringle domain can confer fibrin affinity to a tPA variant and function in place of kringle 2. Therefore, in wild-type tPA, the functions of kringle 1 and kringle 2 must be dependent partially on their orientation within the heavy chain of the protein. The functional autonomy of the heavy and light chains of tPA is demonstrated by the activity of a tPA variant in which the order of the heavy and light chains was reversed.     

Molecular identification and sequence analysis of Hillarin, a novel protein localized at the axon hillock.

The monoclonal antibody Lan3-15 identifies a novel protein, Hillarin, that is localized to the axon hillock of leech neurons. Using this antibody we have identified a full length cDNA coding for leech Hillarin and determined its sequence. The gene encodes a 1274 residue protein with a predicted molecular mass of 144013 Da. Data base searches revealed that leech Hillarin has potential orthologues in fly and nematode and that these proteins share two novel protein domains. The W180 domain is characterized by five conserved tryptophans whereas the H domains share 21 invariant residues. In contrast to the arrangement in fly and nematode the cassette containing the W180 and H domains is repeated twice in leech Hillarin. This suggests that the leech Hillarin sequence originated from a duplication event of an ancestral protein with single cassette structure.     

tPA突变体在哺乳动物细胞中的表达

利用携带有二氢叶酸还原酶(dhfr)基因的pCI载体,实现tPA突变体(FrGGI)在CHO-dhfr^-细胞中的高效表达,获得高表达细胞株。采用分子克隆常规技术,将去除3’端非蛋白编码区的tPA突变体cDNA与pCI载体连接,构建真核表达载体pCI—tPA;采用阳离子脂质体转染法转染CHO-dhfr^-胞。经酶切及测序鉴定,证明所构建的质粒正确,转染CHO—dhfr细胞后,经过MTX加压筛选,得到了10株表达水平较高的细胞株,其活性可达每106细胞4000U／24h。以上结果为进行tPA突变体工程细胞株的筛选奠定了基础。     

Phage lambda cDNA cloning vectors for subtractive hybridization, fusion-protein synthesis and Cre-loxP automatic plasmid subcloning

We describe the construction and use of two classes of cDNA cloning vectors. The first class comprises the lambda EXLX(+) and lambda EXLX(-) vectors that can be used for the expression in Escherichia coli of proteins encoded by cDNA inserts. This is achieved by the fusion of cDNA open reading frames to the T7 gene 10 promoter and protein-coding sequences. The second class, the lambda SHLX vectors, allows the generation of large amounts of single-stranded DNA or synthetic cRNA that can be used in subtractive hybridization procedures. Both classes of vectors are designed to allow directional cDNA cloning with non-enzymatic protection of internal restriction sites. In addition, they are designed to facilitate conversion from phage lambda to plasmid clones using a genetic method based on the bacteriophage P1 site-specific recombination system; we refer to this as automatic Cre-loxP plasmid subcloning. The phage lambda arms, lambda LOX, used in the construction of these vectors have unique restriction sites positioned between the two loxP sites. Insertion of a specialized plasmid between these sites will convert it into a phage lambda cDNA cloning vector with automatic plasmid subcloning capability.