Applied and Environmental Microbiology, February 2002, p. 449-455, Vol. 68, No. 2
0099-2240/02/$04.00+0 DOI: 10.1128/AEM.68.2.449-455.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
School of Microbiology and Immunology, University of New South Wales, Sydney 2052, Australia,1 Institute for Biology (Genetics), Humboldt University, Berlin, Germany2
Received 6 July 2001/ Accepted 24 September 2001
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Microcystin is synthesized nonribosomally via a mixed polyketide synthase/nonribosomal peptide synthetase system called microcystin synthetase (2, 12, 23). Recently, the gene cluster encoding the microcystin synthetase complex has been identified and sequenced (25, 34). This 55-kb gene cluster consists of six open reading frames (ORFs) with a mixed nonribosomal peptide synthetase/polyketide synthase nature (mcyA to mcyE and mcyG) and four smaller ORFs with putative precursor and tailoring functions (mcyF and mcyH to mcyJ). Catalytic domains in mcyA to mcyE and mcyG are responsible for incorporation of the precursors phenylacetate, malonyl coenzyme A, S-adenosyl-L-methionine, glutamate, serine, alanine, leucine, D-methyl-isoaspartate, and arginine. The smaller ORFs encode monofunctional proteins which are putatively involved in O-methylation (McyJ), epimerization (McyF), dehydration (McyI), and cellular localization (McyH) (24, 34).
The 10 ORFs are bidirectionally transcribed from a central 737-bp locus between mcyA and mcyD and are arranged in what until now has been classified as two putative operons, mcyABC and mcyDEFGHIJ. It has previously been reported that the mcyB and mcyD transcript levels are similar when they are determined under various light conditions (18). Nevertheless, the operon structure, the transcription start sites for mcyA and mcyD, and the presence and locations of putative promoters for individual genes within the cluster have not been investigated in detail (18, 24). Transcriptional analysis of the mcy cluster not only should increase our understanding of microcystin synthetase regulation and toxin biosynthesis but may also provide useful insights into other nonribosomal systems, some of which are involved in antibiotic production. Knowledge of the structure of the mcy gene cluster may therefore have important implications for further research to produce new antibiotics by combinational biosynthesis.
Transcriptional analysis of gene clusters has traditionally been carried out by Northern blotting, while transcription start sites are commonly mapped by using radioactive primer extension or S1 nuclease mapping (13). However, it has not been possible to detect the mcyABCDEFGHIJ genes on Northern blots, probably because of the very low levels and potential lengths of the transcripts. As a result, reverse transcription (RT)-PCR was used to detect mRNA transcripts in the mcyABCDEFGHIJ cluster. This method has previously been used for transcriptional analysis of cyanobacterial hydrogenase genes in Anabaena sp. (3, 5) and GTPase/ATPase genes in Synechocystis sp. (16).
Transcription initiation points can be mapped by rapid amplification of cDNA ends (RACE), also known as ligation-anchored PCR (30). This method has only recently been modified so that it can be used with prokaryotes (33). It involves production of the desired cDNA by RT, linking of a modified anchor oligonucleotide to the 5' end of cDNA, and successive amplification with a primer complementary to the anchor and primers specific for the cDNA upstream of the reverse transcriptase primer sequence. The addition of the anchor places a known unique sequence at the unmapped 5' end of the cDNA, which can be identified by DNA sequencing of the nested fragment.
Using RT-PCR and RACE, we performed a complete transcriptional analysis of the mcyABCDEFGHIJ cluster, including an analysis of putative transcription initiation points for the mcy genes and alternate transcription start sites for mcyA and mcyD under different light conditions. Our results indicate that complex gene regulation occurs in hybrid nonribosomal peptide-polyketide biosynthesis involving both multiple and alternate messages.
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Sampling, RNA extraction, and DNase treatment.
Both the sampling and RNA extraction procedures used have been described previously (18). After extraction with Trizol (Gibco BRL, Life Technologies, Rockville, Md.), RNA was column purified (SV total-RNA isolation system; Promega, Madison, Wis.). DNA was removed by treatment with DNase (Gibco BRL), followed by phenol-chloroform-isoamyl alcohol (25:24:1) extraction. The amount and purity of the RNA were determined from the optical densities at 260 and 280 nm and by electrophoresis on a 1% formaldehyde gel.
RT.
RT for production of cDNA for RACE or RT-PCR analysis (see below) was carried out by using Superscript II (Gibco BRL). RNA (0.5 to 1 µg) was added to 1x Superscript II buffer containing 10 pmol of reverse primer 2 (Table 1), each deoxynucleoside triphosphate at a concentration of 0.2 mM, 1 mM dithiothreitol, and enough H2O to bring the final volume to 45 µl. The Superscript II enzyme (200 U diluted in enough H2O to bring the final volume to 5 µl) was added only after stepwise primer annealing by a touchdown incubation procedure consisting of 70°C for 2 min, followed by 65°C for 1 min, 60°C for 1 min, 55°C for 1 min, 50°C for 1 min, and 45°C for 1 min, using a thermocycler (Perkin-Elmer). After the enzyme was added, the reaction mixture was incubated at 42°C for 30 min, which was followed by five cycles consisting of 50°C for 1 min, 53°C for 1 min, and 56°C for 1 min. The enzyme was omitted from reaction mixtures that were used as negative controls in the RT-PCR analysis. Untranscribed RNA was removed by alkaline cleavage; 1 µl of 0.5 M EDTA and 12.5 µl of 0.2 M NaOH were added directly to the RT reaction mixture, and then the preparation was incubated at 68°C for 5 min. The reaction was stopped by adding 12.5 µl of 1 M Tris-HCl (pH 7.4). cDNA was precipitated with 60 µl of isopropanol, 5 µl of 3 M sodium acetate, and 20 µg of glycogen. The pellet was dried, resuspended in 20 µl of TE (10 mM Tris-HCl [pH 7.4], 1 mM EDTA [pH 8.0]), and stored at -20°C.
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Table 1. Oligonucleotides used for RT and PCR
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RT-PCR.
The presence of transcripts in selected gene regions was checked by RT-PCR. The reverse primer (R1) (Table 1) used to do this was situated upstream of the original reverse primer used for the RT reaction (R2). PCRs were performed with an initial denaturation step of 95°C for 2 min, followed by 30 cycles of 94°C for 10 s, 50°C for 20 s, and 72°C for 1 min, using 1 µl of cDNA prepared as described above, 10 pmol of reverse primer (R1), and 10 pmol of forward primer (Table 1).
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Fig. 1. RACE products identified for mcyA and mcyD from RNA extracted from cells grown with 31 µmol of photons m-2 s-1 (intermediate light conditions) and exposed prior to sampling to high light conditions (68 µmol of photons m-2 s-1) and low light conditions (16 µmol of photons m-2 s-1). X174 DNA/HaeIII (Promega) was used as a size marker (lanes M). The bands represent 1,353, 1,078, 872, 603, 310, 281, 271, 234, and 194 bp (from top to bottom).
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70 consensus promoter sequences (Fig. 2).
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Fig. 2. Nucleotide sequence of the region separating mcyA and mcyD, including portions of each ORF. The site of transcription initiation for each gene is indicated by +1, and the translation start codon is indicated by boldface type. Putative promoter sequences at -10 and -35 are underlined.
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Fig. 3. RT-PCR analysis showing the presence of transcripts between mcyA and mcyB, between mcyB and mcyC, between mcyD and mcyE, between mcyE and mcyF, between mcyF and mcyG, between mcyG and mcyH, between mcyH and mcyI, and between mcyI and mcyJ. For each gene, negative controls in which RNA was used for the PCR (lanes -) and positive controls in which DNA was used for the PCR (lanes +) were included. X174 DNA/HaeIII (Promega) was used as a size marker (lanes M). The bands represent 1,353, 1,078, 872, 603, 310, 281, 271, 234, and 194 bp (from top to bottom).
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70 promoter motifs (Table 2). A fifth mcyE band below band 2 (Fig. 4) was too small to extend upstream of the translation start site of mcyE. This band was also checked by sequencing and may have indicated that incomplete cDNA synthesis, RNase processing, or transcript degradation occurred. There were no RACE products identified for mcyB and mcyC.
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Fig. 4. RACE products detected for mcy genes in the polycistronic mcyDEFGHIJ transcript (mcyEa, mcyEb, mcyF, mcyG, mcyH, mcyI, and mcyJ). Lanes Ea and Eb show results obtained with two different RNA samples. mcyE RACE products 1, 2, 3, and 4 were purified and sequenced (Table 2). X174 DNA/HaeIII (Promega) was used as a size marker (lanes M). The bands represent 1,353, 1,078, 872, 603, 310, 281, 271, 234, and 194 bp (from top to bottom).
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Fig. 5. Organization of the microcystin synthetase gene cluster, mcyABCDEFGHIJ, showing putative promoters for mcyEFGHIJ (PmcyE to PmcyJ) and the alternate promoters identified for mcyA and mcyD (PmcyA and PmcyD) under high light conditions (AH and DH) and low light conditions (AL and DL).
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Table 2. Putative intercistronic transcription start points, +1 nucleotides, promoter sequences at -10 and -35, and locations of the transcription start points and the translation start sites (ORF) in the mcyABCDEFGHIJ cluster (1 to 55,000 bp)
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Light-dependent transcription start sites were identified for mcyA and mcyD when cells were exposed to 68 µmol of photons m-2 s-1 (high light conditions) and 16 µmol of photons m-2 s-1 (low light conditions) prior to harvesting and RNA extraction. When cells were grown with constant light of 31 µmol of photons m-2 s-1, both transcription start sites were detected (Fig. 1). The use of multiple promoters for expression of the same cyanobacterial gene has previously been reported for glnA (glutamine synthetase) and argD (N-acetylornithine aminotransferase) in Anabaena sp. strain PCC7120 (15, 35), for zwf (glucose-6-phosphate dehydrogenase) in Nostoc punctiforme (32), and for the petH gene encoding ferredoxin:NADP+ reductase in a heterocyst-forming Anabaena sp. (36). In the case of petH, one of the promoters directs constitutive transcription under different nitrogen nutrition conditions, while the other is induced in cells subjected to nitrogen stepdown and in nitrogen-fixing filaments (36). Similarly, Microcystis cells may use different promoters depending on exposure of the cells to different light conditions. Light-dependent transcription has previously been demonstrated for mcyB and mcyD and may indicate that microcystin has a function that is related to irradiance (18).
One of the initial steps in which transcription initiation is regulated is the interaction of the RNA polymerase with conserved promoter sequences situated -10 and -35 bp upstream of the transcription initiation site. Most cyanobacterial -10 promoter sequences are highly conserved with the consensus E. coli
70 promoter motif (TANNNT) (11). The -35 motif, however, shows only weak conservation with the E. coli
70 consensus sequence (TTGACA) in approximately one-half of the promoters mapped for different cyanobacterial genera (11). The transcription initiation sites identified under high light conditions for mcyA and mcyD indicated that there were conserved -10 motifs consisting of TACAAT and TCTATT, respectively (Fig. 2). Conservation was less prevalent in the -10 basal promoter sequences of mcyA (AAAAAT) and mcyD (CTGAAT) transcripts generated under low light conditions. Less conserved promoter motifs generally indicate weaker transcription. However, the -35 regions of the low-light-conditions transcripts of mcyA (TTGTCA) and mcyD (GTGACA) exhibited higher levels of similarity to the E. coli
70 consensus than those identified for the mcyA (TGTGCA) and mcyD (TTCACG) transcripts under high light conditions (Fig. 2).
The less conserved -35 motif in the mcyA and mcyD high-light-conditions transcripts could indicate involvement of cis factors superimposed on the promoter region, as found in regulated E. coli
70 promoters (10). In these types of promoters, the binding sites of activators are close to the -35 region, leading to less conservation of this motif. Thus, it may be speculated that mcyABC and mcyDEFGHIJ are constitutively transcribed from the weak promoters exhibited under low light conditions and that an activator is involved in transcription initiation under high light conditions. Initiation from the alternate promoters under high light conditions may lead to increased transcription under these conditions, as previously determined for mcyB and mcyD (18).
RACE products identified for mcyEFGHIJ indicated that intercistronic promoters were present. Promoter elements at -10 and -35, however, exhibited only weak similarity to the consensus E. coli
70 (Table 2). The absence of typical promoter elements could indicate false predictions of transcription start sites due to incomplete processing of a larger transcript during RT or due to RNA cleavage (6, 14). This may be true especially for the four transcription start sites detected for mcyE. However, weak conservation of the -10 and -35 motifs or the complete absence of -35 regions has previously been documented in genes from various cyanobacterial genera, including the glnA(IV) and psbB(I)(II) genes from Anabaena sp. strain PCC7120, in which the transcription initiation site was verified by in vitro transcription assays (19, 35).
Internal promoters have been identified in the polycistronic operons of several other bacterial gene clusters (9, 22, 38). The his operon in E. coli and Salmonella enterica serovar Typhimurium, for example, consisting of eight polycistronic genes, contains two internal promoters within hisC and hisF, as well as the primary promoter at the 5' end (9). The distal cistrons of the operon are expressed from the two internal promoters, in addition to the primary element. Expression from these alternate promoters appears to depend on various physiological states (17). Similarly, it could be speculated that the intercistronic mcy promoters are functional or more active only under particular growth conditions.
It has also been proposed that internal promoters may have a function, especially in long and generally unstable transcripts, in ensuring adequate expression of the distal genes of the operon or cluster (26). This has been suggested for the 14-kb cap1 gene cluster of Staphylococcus aureus, which is transcribed from one strong primary promoter and five weak internal promoters which exhibit significant activity when the primary promoter is removed (26). The internal promoter of a particular gene, such as ilvEp in E. coli, can contribute as much as 90% of the total expression (21). However, as transcription through a promoter inhibits its activity (promoter occlusion), the internal promoters probably function only when the primary transcript is interrupted, degraded, or otherwise repressed (1). This may also be true for the large 55-kb mcyABCDEFGHIJ gene cluster. RACE products of the mcyEFGHIJ genes were identified in only approximately one-half of the RNA samples tested. Under conditions which favor transcription from the primary promoters at mcyA and mcyD and high transcript stability, the internal promoters may be subject to promoter occlusion. Thus, without knowing the precise conditions which lead to activity of the internal promoters rather than transcription from the primary promoter, we could not consistently reisolate the RACE products which identify the mcy internal promoters.
Alternatively, our results may be explained by the presence of processing (cleavage) sites in the large transcripts. Processing could produce monocistronic mRNAs for translation, as observed in chloroplasts (4, 29). The internal promoters identified for the mcyEFGHIJ genes are somewhat analogous to the chloroplast gene petD. This gene possesses its own promoter for production of a monocistronic transcript. However, it may also utilize the promoter of the upstream gene petA and be transcribed as part of a polycistronic message (29). Here, promoter usage depends on RNA processing events and RNA secondary structures at the 5' end of the gene (4).
Another structural feature of the mcy mRNA was the long untranslated leader regions identified for both mcyA and mcyD (Fig. 2). Transcription initiation sites under high and low light conditions for mcyA were located 206 and 254 bp upstream of the ORF start codon, respectively. This provided a longer mcyABC transcript when cells were cultured under low light conditions. For mcyD, the longer mcyDEFGHJ transcript was identified under high light conditions, under which the transcriptional start site was situated 342 bp upstream of the ORF, compared to 143 bp upstream of the ORF when the organism was grown under low light conditions. Light-stimulated differences in the lengths of transcripts have previously been documented in the pea chloroplast (37). Long untranslated leader regions between the basal promoter motifs and the ORF start codon are also characteristic of light-responsive expression of the psbA and psbD genes in cyanobacteria (7). In these systems, the consensus basal promoter elements are not affected by changes in light intensity, and light-responsive expression is driven by specific cis elements in the untranslated leader regions of the mRNA (8). Light-responsive elements have been identified 11 to 84 bp downstream of the transcription start site for psbDII and 1 to 41 and 39 downstream of the transcription start site for psbAII and psbAIII, respectively (7, 20). Such regions are being investigated further for the mcy cluster by using a reporter vector system. For the psb genes, these regions alone were able to confer a reproducible level of light-responsive expression on a heterologous promoter (8, 20).
In conclusion, we found that the microcystin synthetase gene cluster (mcyABCDEFGHIJ) consists of two polycistronic transcripts, mcyABC and mcyDEFGHIJ, which are transcribed from a central promoter between mcyA and mcyD. Most interestingly, both polycistronic transcripts have alternate transcription start sites which appear to be light dependent. Furthermore, identification of putative intercistronic transcription start sites for individual mcy genes indicated that there is complex gene regulation involving multiple and alternate messages. These findings may prove to be highly significant for our understanding of regulation of the microcystin synthetase gene cluster under particular light conditions and may increase our knowledge concerning a function of microcystin under these growth conditions.
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