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Applied and Environmental Microbiology, May 2002, p. 2397-2403, Vol. 68, No. 5
0099-2240/02/$04.00+0 DOI: 10.1128/AEM.68.5.2397-2403.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Section of Molecular Microbiology, BioCentrum, Technical University of Denmark, DK-2800 Lyngby, Denmark
Received 1 November 2001/ Accepted 11 February 2002
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Genetic tools for modulating enzyme activities by changing gene expression have long been available and have been employed for fundamental studies of cell physiology, e.g., with inducible systems like the lac-type promoters (31, 15, 26) or the nisin promoter (6). These methods, however, are less well suited for modulating gene expression on an industrial scale. In addition, according to metabolic control analysis (11, 19), truly rate-limiting steps will rarely be found in a metabolic pathway, and it will therefore frequently be necessary to increase the levels of many enzymes to achieve an increased flux.
We recently reported a new approach for obtaining promoter libraries (17, 18), which is based on randomization of the DNA sequences (spacers) that separate the individual consensus sequences of promoters. The method takes advantage of the fact that actual sequences of bases in these spacer areas are less important for the strength of a particular promoter than the resulting DNA structure. By randomizing many base pairs simultaneously in the vicinity of the consensus sequences, it is possible to change the DNA structure and the binding of transcription factors to the promoter sequences, and the promoter libraries obtained by this approach contain promoters with virtually any activity. The individual promoters in such libraries then allow for accurate, simultaneous, and individual modulation of several enzyme activities in a cell, and this method is therefore well suited for both metabolic optimization and metabolic control analysis (1, 2).
A disadvantage of the above-mentioned method is the time-consuming cloning work that is needed when bringing several individual promoters to express a target gene. In addition, the strength of promoters is often context dependent, so that the ranking of individual promoters may change when they are moved into a new context, which may further increase the number of genetic constructions to be made. The method also has the disadvantage that the 5' end of the mRNA of the modulated gene is likely to be altered, which may affect gene expression and cause problems, particularly in cases where the expression of several genes in an operon should be modulated proportionally (2).
We report here a modification to the Jensen-Hammer method (17, 18) which is far less laborious and at the same time removes the above-mentioned limitations. The method is illustrated for modulating chromosomal gene expression in Lactococcus lactis, but it should in principle be universally applicable.
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M15 Tn10(Tetr)]} or KW1 [metB strA purB(aad-uid-man) hsr hsm+ gusA-] (32) was used. The plasmid pRC1 (20), an E. coli vector derived from pBluescript containing genes for erythromycin resistance, was used for the purpose of integrating synthetic promoters upstream of the las operon. The plasmid pG+host8 (21), a replication-thermosensitive derivative of pWV01, was used to replace the native las promoter with a synthetic promoter on the chromosome. The plasmid pLB85 (3), a pMOSBlue derivative (Ampr Ermr) harboring attP of TP901-1 and a promoterless gusA gene encoding ß-glucuronidase, was used to introduce an extra copy of pfk, transcribed from synthetic promoters, into the TP901-1 attP locus on the chromosome of MG1363.
Growth media and growth conditions.
E. coli strains were grown aerobically at 37°C in Luria-Bertani broth (27). L. lactis strains were grown in batch cultures (100-ml flasks) without aeration but with slow stirring in M17 broth (30) or defined SA medium (14). The cultures were supplemented with 1% glucose and incubated at 30°C.
Antibiotics.
Erythromycin was used at 5 µg/ml for L. lactis and 200 µg/ml for E. coli. Tetracycline was used at 5 µg/ml for L. lactis and 8 µg/ml for E. coli.
Enzymes.
All enzymes used in connection with the measurements of lactate dehydrogenase (LDH), pyruvate kinase (PK), and phosphofructokinase (PFK) activities were purchased from Boehringer Mannheim, Kvistgård, Denmark.
DNA techniques.
All manipulations were performed as described by Sambrook et al. (27). Taq polymerase was applied for analytical purposes, while PCR products intended for cloning were generated using Elongase enzyme mix (Life Technologies A/S, Tåstrup, Denmark). Chromosomal DNA from L. lactis was isolated using the method described for E. coli with the modification that cells were treated with 20 µg of lysozyme per ml for 2 h before lysis. Cells of L. lactis were made competent by growth in GM17 medium containing 1% glycine and transformed by electroporation as previously described by Holo and Nes (12). After electroporation, cells were plated on GM17. E. coli cells were transformed using electroporation.
RNA isolation, primer labeling, and primer extension.
RNA from L. lactis was isolated from 10 ml of M17 culture (1% glucose) at an optical density (600 nm) of approximately 0.8. The cells were harvested by centrifugation and resuspended in 500 µl of ice-cold TE buffer (Tris [10 mM] and EDTA [1 mM], pH 7.5). The following were mixed in a 2-ml centrifuge tube: 0.6 g of glass beads (100-µm diameter), 0.17 ml of 2% Macaloid (clay), 0.5 ml of phenol-chloroform (1:1), 0.05 ml of 10% sodium dodecyl sulfate, and the resuspended cells. The suspension was vortex mixed for 5 min at maximum speed and then centrifuged for 15 min at 12,000 x g. The aqueous phase was transferred to a new centrifuge tube and extracted once with an equal volume of phenol-chloroform (1:1). The RNA was precipitated by adding 1/10 volume of 3 M sodium acetate and 3 volumes of 96% ethanol. The pellet was washed with 70% ethanol and dissolved in an appropriate volume of TE buffer.
The primer 5'-CCTCCGAAATTGAGATACACAGC-3' was labeled using T4 polynucleotide kinase (Life Technologies A/S) and [
-33P]ATP. Primer extension was performed using SuperScript reverse transcriptase (Life Technologies A/S) with 40 µg of RNA in a 20-µl reaction volume.
Enzyme measurements.
The activities of PFK, PK, and LDH were measured in cell extracts obtained by sonication. Cells were grown in SA medium and harvested at an optical density of approximately 0.7 (450 nm). The cells were washed twice with ice-cold 0.2% KCl and then resuspended in ice-cold sonication buffer. The sonication buffer for LDH and PK activity measurements was 50 mM triethanolamine-10 mM KH2PO4-10 mM EDTA-50% glycerol (pH 4.7); that for PFK activity measurements was 50 mM Tris-HCl-0.1 mM EDTA-50% glycerol-1 mM dithiothreitol (pH 7.5). The cell suspension was sonicated three times for 45 s with an interval of 30 s. The preparation was kept on ice during the sonication. Following sonication, the cell debris and intact cells were removed by centrifugation (10 min at 20,000 x g) in a 4°C centrifuge. As a measure of the degree of cell disruption, the optical density at 280 nm was used. The enzyme activities were determined from the consumption of NADH by using a Zeiss M500 spectrophotometer. PFK was assayed as described by Fordyce et al. (7), except that the final concentrations in the assay mixture were 1 mM ATP, 1 mM fructose 6-phosphate, 0.2 mM NADH, 10 mM MgCl2, 10 mM NH4Cl, 0.3 U of triose phosphate isomerase per ml, 1 U of glycerol 3-phosphate dehydrogenase per ml, and 0.3 U of aldolase. PK was assayed as described by Crow and Pritchard (5), with final concentrations in the assay mixture of 1 mM GDP, 1 mM phosphoenolpyruvate, 1 mM fructose 1,6-bisphosphate, 10 mM MgCl2, 0.2 mM NADH, and 6.3 U of LDH per ml. LDH was measured as described by Crow and Pritchard (4), with final concentrations in the assay mixture of 10 mM pyruvate, 0.2 mM NADH, and 1 mM fructose 1,6-bisphosphate. All measured enzyme activities were related to the optical density at 280 nm of the extract for the purpose of determining relative activities.
ß-Glucuronidase activities were determined by the procedure described by Miller (23) and modified by Israelsen et al. (13), except that para-nitro-ß-glucuronic acid (Biosynth AG) was used as the substrate (25). The activity is given in Miller units and calculated as described by Miller (23).
Construction of strains with elevated PFK activity.
A PCR fragment was generated using the forward primer 5'-ACGACTAGTGGATCCATNNNNNAGTTTATTCTTGACANNNNNNNNNNNNNNTGRTATAATANNCTAGACAACAAATGAACATGG-3', which carries SpeI and BamHI sites and has homology to the 5' end of the mRNA of the las operon, and the reverse primer 5'-GAACTGCAGCTCTGCCCTAATTATGCG-3', which carries a PstI site and has homology to the intergenic region between the pfk gene and the pyk gene. The resulting PCR product, containing synthetic promoters followed by a full-length pfk gene, was digested with SpeI and PstI and cloned in the vector pLB85 digested with XbaI and PstI. Following ligation, the plasmids were transformed directly into L. lactis LB436, a derivative of strain MG1363 containing plasmid pLB65, which encodes the TP901-1 integrase, and the cells were plated on GM17 plates with selection for erythromycin resistance and with 200 µg of X-Gluc (5-bromo-4-chloro-3-indolyl-ß-D-glucuronic acid) per ml of medium. In this strain, pLB85 and other plasmids containing the attB site from TP901-1 will integrate with high frequency into the corresponding attachment site for phage TP901-1 on the L. lactis chromosome (3).
Construction of strains with synthetic promoters in front of the las operon.
A PCR fragment was generated using the promoter primer shown above as the forward primer and the reverse primer 5'-CGGGGTACCGGTCTCCTTTATAACCAGC-3', which carries a KpnI site and has homology to the 3' end of the pfk gene. The PCR product was digested with BamHI and KpnI, cloned in the vector pRC1 digested with the same enzymes, and transformed into the E. coli host strain ABLE-C. A plasmid library consisting of approximately 5,000 clones was obtained and used for transformation of L. lactis MG1363 with selection for erythromycin resistance. One hundred twenty colonies appeared after incubation, and subsequently chromosomal DNA was prepared from these strains and used to confirm the integration by PCR with the primers 5'-GTAATACGACTCACTATAGGGC-3' (homologous to the pRC1 vector) and 5'-TCCCCGCGGTCACGAAGCAATTCAACG-3' (homologous to the C-terminal part of pfk).
Replacement of the native las promoter with a synthetic promoter from CS8.
A PCR fragment containing the las upstream region was generated using the forward primer 5'-GGTACTCGAGGTGGAATTTTCTTTGAAGGTC-3' (carrying an XhoI site) and the reverse primer 5'-GGAAGGATCCCTTTACAAACTGTATGAAACG-3' (carrying a BamHI site). The PCR product was digested with XhoI and BamHI and cloned in the vector pG+host8 digested with the same enzymes, using KW1 as the host strain. Next, a PCR fragment was generated with chromosomal DNA from CS8 as the template and the primers 5'-GTAATACGACTCACTATAGGGC-3' (homologous to the pRC1 vector) and 5'-CTAGTCTAGAGGTCTCCTTTATAACCTTC-3' (carrying an XbaI site and homologous to the C-terminal region of the pfk gene). The resulting PCR fragment was digested with BamHI (restriction site originating from promoter primer [see above]) and XbaI and cloned in the vector with the upstream region digested with the same restriction enzymes, again using KW1 as the host. The resulting plasmid was used to replace the wild-type las promoter as further described in Results.
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The method requires two PCR primers (Fig. 1). The first primer carries a restriction site, a promoter with randomized spacers, and a sequence with homology to the 5' end of the mRNA of the target gene. In Fig. 1, N indicates 25% each of A, C, G, and T, while R indicates 50% each of A and G. The second primer also carries a suitable restriction site and a sequence with homology either within the gene in question or downstream of it, allowing for the generation of either a truncated version (strategy I) or a full-length version (strategy II) of the gene behind synthetic promoters. Due to the use of the degenerate promoter primer, a modified PCR protocol is applied. First, a standard PCR is performed. The resulting PCR product is then diluted fourfold and used as a template for a single PCR cycle containing a denaturation step and an annealing step and ending with an elongation step. This last cycle removes annealing between heterologous strands of promoter sequences. The resulting fragment can be cloned after suitable digestion with restriction enzymes into a vector, thereby generating a plasmid library.
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FIG. 1. Overview of the approach used for modulating enzyme activities. (A) Chromosome with an arbitrary gene (geneX) and its upstream region (upsX). The promoter primer (N can be any of the four bases, while R is 50% A and 50% G) and two reverse primers are shown. (B) Two possible PCR products, the first of which contains a truncated geneX and the second of which contains a full-length geneX. (C) The resulting plasmids obtained after cloning of the PCR fragments. If a chromosomal promoter is to be replaced by a synthetic one, then strategy I is used. If the resulting plasmid is to be used in a simple integration event, then strategy Ib is used. If the resulting plasmid is to take part in a double-crossover event, then strategy Ia is used. If the plan is to introduce an additional gene copy into the chromosome, then strategy II is used.
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FIG. 2. Correlation between ß-glucuronidase activity and relative PFK activity in strains containing an additional gene copy of pfk transcribed from synthetic promoters.
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FIG. 3. Relative LDH activity measured in strains with synthetic promoters in front of the las operon. Overnight cultures were used for these measurements, and these activities are generally somewhat higher than those measured in extracts from exponentially grown cells.
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FIG. 4. Relative activities of PFK, PK, and LDH measured in extracts from strains with synthetic promoters in front of the las operon during exponential-phase growth. The selected strains cover the entire activity range. MG1363 is the wild-type strain.
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FIG. 5. Strategy used for replacement of the native las promoter with the synthetic promoter obtained from CS8. The plasmid has two regions homologous to the las locus and allowed for the construction of a strain, CS1006, in which the vector has been excised (see text for further details).
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FIG. 6. Primer extension using RNAs from the wild-type strain MG1363 and from strain CS1006, in which a synthetic promoter has replaced the las promoter. Arrows indicate the transcript start. Note the alternative transcript start that was observed in both strains, also indicated by arrows.
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We used an extended PCR protocol for introducing the synthetic promoters with randomized DNA stretches in front of the relevant genes. The protocol entailed diluting the PCR product from the standard PCR; adding new primers, buffer, deoxynucleoside triphosphates, and polymerase; and running an extra PCR cycle. This was done in order to avoid possible annealing of heterologous DNA strands in the final rounds of the standard PCR when primers and substrate may be depleted or when the polymerase may no longer be active. However, even with this modified protocol, half of the DNA fragments obtained from the final PCR cycle will still have extensive mismatches in the promoter area, namely, the half of the DNA fragments in which the newly synthesized DNA strand started from a promoter primer. This could in principle also be avoided if a primer with only the constant 5' DNA sequence of the promoter primer was used in the final PCR cycle (in the present study this primer should be 5'-ACGACTAGTGGATCCAT).
After performing metabolic optimization with the method presented here, it is often desirable to remove plasmids integrated in the chromosome. This can be done in order to improve genetic stability, to allow the reuse of a selectable marker in subsequent steps of optimization, or simply to end up with a strain without antibiotic markers. We have here illustrated how this can be achieved in two steps: first, a promoter of proper strength is identified by integrating a promoter library in front of a target gene and screening for optimal activity of the encoded enzyme, and second, this specific synthetic promoter is amplified along with (part of) the target gene by PCR and cloned together with an upstream DNA fragment in a vector for subsequent gene replacement. The advantage of this approach is that in the first step of the procedure the integration takes place at a high frequency in the correct position, which facilitates the subsequent screening work. However, in some cases it may be an advantage to combine these two steps (which amounts to strategy Ia in Fig. 1), as follows. A library of PCR products with degenerate promoters and target genes is cloned directly into a gene replacement vector which already harbors the relevant upstream DNA region. The resulting plasmid library is then used for consecutive integration and excision events to generate strains with optimized expression levels of the target gene. The screening procedure involved here is somewhat more laborious, but fewer cloning steps are involved.
The method presented in this paper should be applicable to the construction of strains for numerous specific purposes in prokaryotic as well as eukaryotic systems. With respect to metabolic optimization, the method has several advantages over existing inducible expression systems. One advantage is that after the optimal promoter activity has been determined, the strain is in principle ready for use in the industrial fermentation process. Another important feature is the option to simultaneously modulate, to different extents, the expression of many genes or operons located at different positions of the genome in the same strain. With the existing systems now available, one would then quickly run out of expression systems to use.
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