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Applied and Environmental Microbiology, March 2003, p. 1647-1654, Vol. 69, No. 3
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.3.1647-1654.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Department of Microbiology, The Ohio State University, Columbus, Ohio 43210,1 Natural Products Microbiology, Merck Research Laboratories, Rahway, New Jersey 070652
Received 8 May 2002/ Accepted 15 December 2002
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(Life Technologies, Inc., Gaithersburg, Md.) and E. coli Top10 (Invitrogen, San Diego, Calif.) were used for propagation of E. coli plasmids. The plasmids used and generated in this study are shown in Table 1. |
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TABLE 1. Plasmids used and generated in this study
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DNA and RNA preparation.
Plasmid DNA was routinely prepared from 5-ml cultures of E. coli or Streptomyces by the method of Carter and Milton (6). Streptomycete RNA was prepared with Trizol (Life Technologies, Inc.) after lysozyme pretreatment of the mycelia for 20 min at 37°C. An additional phenol-chloroform extraction with one volume of buffered phenol, pH 8.0 (Life Technologies), was performed on the RNA preparations if further enzymatic manipulation was planned.
DNA sequencing and analysis.
DNA sequence determination was performed by using the dideoxynucleoside termination procedure of Sanger et al. (24) or an ABI 377 automated sequencing system (Perkin Elmer Applied Biosystems, Foster City, Calif.).
DNA sequence files were managed by using Clone Manager 5 (Scientific & Educational Software, Inc., State Line, Pa.) and BioEdit 4.74 (12), analyzed with software from Genetics Computer Group, University of Wisconsin, Madison, Wis. (8), as well as with the suite of analysis tools available from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) and the Pôle Bio-Informatique Lyonnais Network Protein Sequence Analysis server (http://pbil.ibcp.fr/NPSA; Lyon, France).
Cloning procedures and plasmid construction.
E. coli and Streptomyces cultures were transformed as described by Sambrook et al. (23) and Hopwood (14), respectively. Enzymes were purchased from Life Technologies, Inc., or from New England Biolabs, Inc. (Beverly, Mass.), and were used per the manufacturer's instructions. General cloning methods were conducted as described by Sambrook et al. (23). Double-stranded DNA (dsDNA) linkers for use in plasmid construction were prepared from complementary oligonucleotides (Life Technologies, Inc.) designed to yield dsDNA fragments with the desired 5' or 3' overhangs. Equimolar quantities of the separate oligonucleotides were mixed in a buffer containing 10 mM Tris chloride (pH 8.0) and 10 mM MgCl2 that was heated to 99°C for 10 min, allowed to cool, and used for ligations. The oligonucleotides used in this fashion are shown in Table 2.
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TABLE 2. Oligonucleotides used for dsDNA linker preparation
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Primer extension analyses.
Reverse transcription reactions were conducted with the fluoresceinylated primers 5'FGACGACCGGCGCGCCCTCAGCG3' (snpA) or 5'FGTGTTCGATGCGCCGCAGCTGCGTG3' (snpR); RNA was prepared from 48-h TSBP-S cultures of S. lividans TK24(pANT842) and rTth reverse transcriptase (Perkin Elmer, Foster City, Calif.) yielding 5' fluorescein-labeled single-stranded DNA fragments with 3' termini corresponding to the 5' termini of the snpA or snpR mRNAs. Both extension reaction mixtures contained 1.0 µg of RNA and were held at 60°C for 70 min and were separated on an ABI 377 along with dideoxy-terminator sequencing reactions generated with the same primer and plasmid template, and the subsequent gel was image cropped and adjusted for contrast by using Adobe Photoshop 5.0 (Adobe Systems Inc., San Jose, Calif.).
Protein electrophoresis, blotting, and immunodetection.
Culture broth samples were clarified by centrifugation at 14,000 x g for 20 min. Equal volumes of cleared broth were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis in a Mini-Protean II apparatus (Bio-Rad) and were transferred to polyvinylidene difluoride membranes with a Mini Trans-Blot cell (Bio-Rad). The blotting procedure was performed as described by Ausubel et al. (1), with polyclonal rabbit anti-human endostatin (1:20,000; Judy Boice at Merck & Co., Inc.) and alkaline phosphatase-conjugated goat anti-rabbit immunoglobulin G (1:6,000; Bio-Rad) as the primary and secondary antibodies, respectively. Immun-Star substrate (Bio-Rad) was used to indicate bound secondary antibody, and the results were visualized by using X-ray film by standard methods (1). Insoluble recombinant human endostatin produced in E. coli (Judy Boice at Merck & Co., Inc.) was used as a standard.
Nucleotide sequence accession numbers.
The complete Streptomyces sp. strain C5 snpR gene DNA sequence has been deposited in GenBank under the accession number AY072041. Additionally, the DNA sequences for plasmids pANT849, pANT1200, pANT1201, and pANT1202 have been deposited under the accession numbers AY072037, AY072038, AY072039, and AY072040, respectively.
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Analysis of the SnpR, SlpR, and MprR primary sequences by the method of Dodd and Egan (10) indicated that all three were probably strong DNA binding proteins, with helix-turn-helix scores of 5.09, 4.59, and 4.51, respectively. For all three sequences the putative DNA binding region begins at residue 18 (glycine) and continues to residue 39 (arginine/threonine). The strongest conservation between the three proteins was found in the amino-terminal region of the sequences, which contains the helix-turn-helix motif implicated in DNA binding. This is consistent with the observations of Henikoff et al. (13), who found that the original members of the LysR family shared their strongest identity in a region aligning with LysR residues 21 to 40.
Reporter gene constructs.
To study the effect of SnpR on snpA transcription, four reporter gene plasmids were constructed. The reporter gene aphII, encoding neomycin phosphotransferase (NptII), was placed under the control of the snpA promoter with an intact snpR gene in plasmid pANT852. Deletion of the snpR DNA gave pANT853, identical to pANT852 except for the lesion in snpR. To compare snpA promoter activity with another well-characterized streptomycete promoter, the aphII gene was also placed under the transcriptional control of the melC1 promoter in pANT856. In both the snpA and melC1 promoter plasmids the SphI site was used as the 5' end of the non-snp or non-melC DNA contains an ATG codon encoding the amino-terminal methionine of SnpA or MelC1; thus, the aphII reporter gene was positioned similarly downstream of the two promoters. Additionally, the aphII fragment used in these cloning steps contained its native ribosome binding site.
Comparison of different reporter constructs.
To evaluate the effect of snpR in snpA expression and to compare the snpA and melC1 promoters, MSEM-grown cultures of S. lividans HLP-6, harboring pANT849, pANT852, pANT853, pANT855, or pANT856, were harvested after 48 h of growth, disrupted, and measured for NptII production by enzyme-linked immunosorbent assay (Table 3). Cultures containing pANT849 and pANT855, reporter-negative vector controls, produced only background levels of NptII. The snpR-minus construct and the melC1 promoter construct each produced around 30 pg of NptII per µg of soluble protein, and the snpR-positive construct produced around 1,800 pg of NptII per µg of soluble protein. Thus, the presence of an intact snpR gene conferred a ca. 60-fold increase of NptII production over transcription in its absence or transcription from the melC1 promoter.
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TABLE 3. NptII reporter production by recombinant Streptomyces cultures
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TABLE 4. Comparison of NptII production by the snpA and ermE* promoters
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FIG. 1. Profile of SnpR-activated snpAp-driven reporter gene expression and culture growth. Samples from triplicate 0.5-liter cultures of S. lividans TK24(pANT852) grown in TSBP-S medium were processed for NptII determination as described in the text. With the mean total cellular protein curve indicating the growth phase of the fermentation (filled circles), NptII accumulation increased with culture age (open circles). This suggests that the snpA promoter is active in stationary phase. Values shown represent means ± standard errors; the two data points without error bars represent the averages of two samples. Streptomycetes growth curves generated from optical density readings and total protein levels were comparable (data not shown).
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FIG. 2. Transcriptional mapping, nucleotide sequence, and features of the Streptomyces sp. strain C5 snpA-snpR intergenic region. Primer extension reactions with either an snpA-specific primer (A) or an snpR-specific primer (B) were conducted in the absence and presence of reverse transcriptase (-RT and +RT, respectively) and were run next to dideoxy-terminator sequencing reactions prepared with the same primer. Panel C shows the snpA-snpR intergenic region with the transcriptional start points (TSPs) and optimal -10 and -35 regions for each. Spacing between these putative RNA polymerase binding sites is 19 nucleotides for the snpR TSP and 18 nucleotides for the snpA TSP. The likely SnpR binding site is indicated, with the T-N11-A thymidine and adenine in boldface and the inverted repeat indicated within arrows. The snpA and snpR start codons are also indicated in boldface.
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To provide for the use of multiple, compatible, and selectable plasmids, the aphII neomycin phosphotransferase gene and the acc(3)-IV apramycin resistance gene were incorporated, along with an improved MCS, in into new vectors. Because it has been observed that high-copy-number plasmids exceeding approximately 10 kbp in size exhibit instability in both E. coli and Streptomyces (2, 29), the plasmids were reduced in size and unnecessary restriction sites were eliminated. Plasmids pANT894 and pANT895 are neomycin- and apramycin-selectable snp-based expression vectors, respectively, and together with pANT857 they represent the second generation of snp-based expression vectors. These plasmids were further improved with the addition of an enhanced MCS containing additional unique restriction enzyme sites, stop codons in all three frames (for expression of gene fragments lacking their native stop codon), and the strong S. coelicolor mmr transcriptional terminator (18). This third generation of snp-based expression vectors is comprised of three plasmids: pANT1200, which is selectable in E. coli with ampicillin and in Streptomyces with thiostrepton; pANT1201, selectable in both hosts with neomycin; and pANT1202, selectable in both hosts with apramycin. The MCS and unique restriction enzyme sites of these three plasmids are shown in Fig. 3. In support of streptomycete antibiotic biosynthesis studies, snp-based vector systems have been used to express numerous genes from the Streptomyces sp. strain C5 daunomycin biosynthesis gene cluster. The doxA monooxygenase (9), several components of the dps polyketide synthase (20), and the dnm glycosyltransferase (A. J. Woo and W. R. Strohl, unpublished data) all have been successfully expressed by using the snpR-activated snpA promoter.
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FIG. 3. The pANT1200 series MCS. (A) The MCS of the pANT1200 series of vectors contains 11 restriction endonuclease sites, followed by stop codons in three frames (in boldface) and a bidirectional transcriptional terminator. (B) Of the 11 restriction enzyme sites in the MCS, most are unique, with the exceptions shown. The NcoI site downstream of the terminator is not unique in any of the plasmids, while the DraI site is unique in pANT1201 and pANT1202.
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-amylase (VAA) was inserted into pANT1201 such that the resulting plasmid, pANT3022, contained unique BamHI and HindIII sites. The BamHI site was engineered so that two codons, GGA and TCC, which encode glycine and serine residues, were positioned three codons downstream of the putative signal peptide recognition sites of the VAA signal sequence. A human endostatin cDNA clone modified to contain a 5' BamHI site encoding an amino-terminal glycine-serine extension was inserted into pANT3022 to generate pANT3032, and the snp-VAA-endostatin cassette was transferred to a pIJ101-based streptomycete vector to make pANT3052. The vector insert joint of the snp-VAA-endostatin cassette is shown in Fig. 4A.
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FIG. 4. Nucleotide sequence of pANT3052 signal peptide-endostatin junction and recombinant endostatin production profile for S. lividans TK24(pANT3052). (A) The important features of the signal peptide-endostatin junction in the VAA-endostatin construct include the ClaI site positioned over the snpA transcription-translation start site; the putative VAA signal peptidase cleavage site, which is indicated by the arrow head; and the BamHI site, which encodes glycine and serine residues. The BamHI site is the point of fusion between the vector DNA and the human endostatin cDNA. The amino acid sequence of the translated product is shown, with the native human endostatin residues capitalized. (B) An anti-human endostatin Western blot of clarified broth samples from an S. lividans TK24(pANT3052) culture showing the accumulation of recombinant endostatin, predominantly after logarithmic growth phase. The lanes are labeled with the time point of the sample in hours. Lane S represents 2.1 ng of recombinant endostatin standard, while the remaining lanes represent 5-µl aliquots of clarified culture broth.
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Manual and computer-assisted evaluation of the snpA-snpR intergenic sequence for recognizable DNA motifs suggested a number of potentially important features. The most pronounced was an inverted repeat, centered on a T-N11-A sequence, within 100 nucleotides of the snpA start codon (see Fig. 2C). This motif, originally described by Henikoff et al. (13), is typical of many LysR-like protein binding sites. Thus, this snp intergenic feature is likely to be the SnpR binding site. Searches for sequences resembling promoters, however, were unsuccessful. Neither computer-assisted (21) nor manual screening for sequences resembling consensus streptomycete promoters (4, 26) revealed any candidate sequences.
Primer extension mapping of the snpR transcriptional start point to a position 138 nucleotides upstream of the predicted snpR start codon positions the -35 element within the likely SnpR binding site of the snpA-snpR intergenic region. The overlapped orientation of snpRp and the likely SnpR binding site suggests a potential negative autoregulatory role for the snpR gene product in snpR transcription. Such negative autoregulation is a feature of many LysR-like systems (25). In contrast, the transcriptional start site of snpA mapped to the adenine of the snpA ATG start codon, indicating the proteinase transcript is a leaderless mRNA species. Thus, the AGGA sequence immediately upstream of the snpA ATG, although optimally positioned and originally speculated to function as a Shine-Dalgarno sequence (16), is not involved in translation initiation.
This promoter structure has significant functional implications for the various expression plasmids based on the snpA promoter. Since the snp locus has been successfully used for expression of both streptomycete and non-streptomycete genes, several observations can be made about the translational events possibly occurring. When the DNA inserted into the expression system contains both the gene of interest and its native Shine-Dalgarno sequence, such as with the aphII reporter gene or doxA gene (9), conventional translation initiation may occur. These situations may include the synthesis of a short polypeptide from the 5' AUG of the chimeric transcript, however. Inspection of the mRNA encoded by the aphII reporter constructs shows that a 21-amino-acid polypeptide would be synthesized by translation of the open reading frame starting with the 5' AUG before terminating with a UGA codon just 5' of the aphII AUG. Similarly, the doxA expression cassette of pANT195 encodes an RNA transcript containing an open reading frame with eight codons, starting with the 5' AUG and terminating at a UGA codon overlapping the doxA AUG (27).
For expression and secretion of endostatin by the snp system, however, the ATG start codon of the new open reading frame (within the ClaI site) is superimposed on the transcriptional start point of the chimeric transcript. Although this translational context is similar to that of wild-type snpA in replacing the native coding sequence with the chimeric open reading frame, any native translational signals downstream of the ATG are lost and are not suitably replaced, as with the aphII and doxA fusions. Thus, the observed production of recombinant endostatin by this construct indicates that the leaderless endostatin expression cassette is recognized by the host ribosomes and is translated properly.
The fact that many leaderless mRNAs are translated with high efficiency despite the absence of Shine-Dalgarno sequences (15) indicates that an alternative method of translation initiation is occurring in these cases. Tedin et al. showed that in E. coli translation initiation factor 3 (IF3) antagonizes translation initiation from leaderless transcripts, and in vivo IF3 levels are inversely proportional to efficiency of leaderless mRNA translation (28). The model proposed suggests that a subpopulation of IF3-deficient 30S ribosomes form ternary complexes on leaderless transcripts during exponential growth, while 70S ribosomes are responsible for these initiation events in stationary phase (28). Notably, 70S ribosomes, which show a high preference for terminal AUG codons, accumulate after logarithmic growth has ceased (28). This may explain the productivity of the snpA promoter during stationary phase observed with both aphII expression (Fig. 1) and endostatin secretion (Fig. 4B).
The production and secretion of soluble endostatin by using the snp system was significant because this human protein has been difficult to produce adequately by other systems. Endostatin is a novel angiogenesis inhibitor of clinical interest (19, 22). It is notable that the endostatin produced in these fermentations was stable in the culture broth and continued to accumulate without noticeable degradation after 120 h of culture incubation. Most likely this results from a combination of vector stability, properly folded protein, and low water activity in the culture medium (at inoculation, the sucrose concentration was 15% [wt/vol]). By semiquantitative Western blot densitometry the level of endostatin produced by S. lividans(pANT3052) was estimated to be 2 mg per liter of fermentation broth at the 65-h time point, well into stationary phase. Even without the extensive optimization that is often applied in such projects (for examples see reference 11), this level of production is similar to those of several other systems designed to produce and secrete mammalian proteins with Streptomyces (3).
Present address: Department of Biologics Research, Merck Research Laboratories, Rahway, NJ 07065. ![]()
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