Present address: University of Tuebingen, Institute of Microbiology and Biotechnology, Auf der Morgenstelle 28, 72706 Tuebingen, Germany.
A rare leucine codon in adpA is implicated in the morphological defect of bldA mutants of Streptomyces coelicolor
Article first published online: 22 OCT 2003
Volume 50, Issue 2, pages 475–486, October 2003
How to Cite
Takano, E., Tao, M., Long, F., Bibb, M. J., Wang, L., Li, W., Buttner, M. J., Bibb, M. J., Deng, Z. X. and Chater, K. F. (2003), A rare leucine codon in adpA is implicated in the morphological defect of bldA mutants of Streptomyces coelicolor. Molecular Microbiology, 50: 475–486. doi: 10.1046/j.1365-2958.2003.03728.x
- Issue published online: 22 OCT 2003
- Article first published online: 22 OCT 2003
- Accepted 17 July, 2003.
Streptomycetes are mycelial bacteria that produce sporulating aerial hyphae on solid media. Bald (bld) mutants fail to form aerial mycelium under at least some conditions. bldA encodes the only tRNA species able to read the leucine codon UUA efficiently, implying the involvement of a TTA-containing gene in initiating aerial growth. One candidate for such a gene was bldH, because the bldH109 mutant of Streptomyces coelicolor resembles bldA mutants in some aspects. In the work reported here, adpAc, an S. coelicolor gene similar to the Streptomyces griseus A factor-regulated adpAg, was found to complement the bldH109 mutant partially at both single and multiple copies. The sequence of adpAc from the bldH109 mutant revealed a frameshift. A constructed in frame deletion of adpAc conferred a bald colony phenotype, and the mutant behaved like bldA mutants and bldH109 in its pattern of extracellular signal exchange. Both adpAc and adpAg contain a TTA codon. A TTA-free version of adpAc was engineered by replacing the TTA leucine codon with a cognate TTG leucine codon. The adpA(TTATTG) gene could partially restore aerial mycelium formation to a bldA mutant when it was followed in cis by the gene ornA, as in the natural chromosomal arrangement. This indicated that the UUA codon in adpAc mRNA is the principal target through which bldA influences morphological differentiation. It also implied that translational arrest at the UUA codon in adpAc mRNA caused a polar effect on the downstream ornA, and that the poor translation of both genes contributes extensively to the deficiency of aerial mycelium formation in bldA mutants. Unlike the situation in S. griseus, adpAc transcription does not depend on the host's γ-butyrolactone signalling system, at least in liquid cultures. In addition, sigma factor BldN, which is the homologue of an S. griseus sigma factor AdsA that is absent from adpAg mutants of S. griseus, was present in the constructed adpAc null mutant of S. coelicolor.
In Streptomyces coelicolor, mutation of bldA, which encodes the tRNA for the rare leucine codon UUA, causes pleiotropic deficiencies in both the development of reproductive aerial hyphae and the production of antibiotics on most media (Merrick, 1976; Lawlor et al., 1987). Because most genes containing TTA codons are phenotypically very poorly expressed in bldA mutants, it is assumed that no essential genes contain this codon (Leskiw et al., 1991). (A caveat to this statement arises from the discovery that the UUA-containing mRNA for the pathway-specific regulator of the linked pathways to clavulanic acid and cephamycin C in Streptomyces clavuligerus is translated effectively in a bldA mutant; Trepanier et al., 2002.) Examination of the recently completed genome sequence of S. coelicolor (Bentley et al., 2002) reveals that only 145 of the 7825 genes in the 8.7 Mb genome contain a TTA codon, and none of these is recognizably a housekeeping gene. The TTA-containing genes include pathway-specific regulatory genes for the biosynthesis of at least two of the antibiotics made by S. coelicolor and, in each case, it has been shown that the regulatory gene is the sole and direct means by which bldA exerts its effects on production of the cognate antibiotic (Fernandez-Moreno et al., 1991; Passantino et al., 1991; White and Bibb, 1997; Guthrie et al., 1998). Thus, it appears that there is no globally acting bldA target gene for secondary metabolism and development. It might be supposed that bldA target genes should be found among mutants with developmental defects similar to bldA mutants. The literature describes at least 20 genes with mutations that lead to loss of aerial mycelium formation (the bald phenotype, hence the frequent designation of such genes as bld; for a list of bld genes, see Chater, 2001). DNA complementing most bld mutants has been cloned and characterized, but none of the genes identified contains a TTA codon. Thus, until now, bldA target genes influencing the development of S. coelicolor have remained undiscovered. The purpose of the work described in this paper was to identify such genes.
In extracellular complementation experiments on the rich medium R2YE, Willey et al. (1993) established a hierarchy of extracellular signal exchanges among bld mutants of S. coelicolor. A secreted oligopeptide is taken up via the bldK-specified ABC transporter (Nodwell et al., 1996; Nodwell and Losick, 1998), and its perception leads to the secretion of a second (unknown) extracellular signal, and so on through three further bld gene-dependent steps, until the morphogenetic protein SapB is secreted and allows aerial hyphae to form. Production of the second of the five proposed extracellular signals requires two known genes, bldA and bldH, which fall between bldK and bldG in the cascade. Not only do bldA and bldH have the same extracellular complementation phenotype, they also have a somewhat similar morphological phenotype (although the two previously described bldH mutants make pigmented antibiotics on minimal medium with mannitol as carbon source, unlike bldA mutants; Champness, 1988). In our search for the target gene(s) through which the bldA tRNA exerts its effects on morphological differentiation, we reasoned that bldH was a promising candidate. Our results confirm this prediction.
Complementation of bldH, a potential target of bldA
In order to clone bldH, we attempted to restore aerial mycelium formation to WC109 [the bldH109 mutant used by Willey et al. (1993) in extracellular complementation] with a library of Sau3AI fragments inserted into the positive selection high-copy-number plasmid pIJ699 (Kieser and Melton, 1988). Several colonies (five out of ≈ 9000 transformants) were identified in which aerial growth had been partially restored (Fig. 1). All the clones contained overlapping DNA from the same part of the genome, with a common overlap that included three complete genes (SCO2791–2793 in the genome sequence; Bentley et al., 2002) (Fig. 1A). Further reduction of the DNA in one of the clones localized the bldH-complementing gene(s) to just one open reading frame (ORF), SCO2792, which was indeed one of the 145 TTA-containing S. coelicolor genes (Fig. 1C). Moreover, SCO2792 was a close homologue of adpA, a gene of Streptomyces griseus known to play a key role in development (84.4% identity between the gene products) (Ohnishi et al., 1999). The equivalence with adpA was further supported by local synteny of gene arrangement around the S. coelicolor and S. griseus genes (Fig. 1A). For clarity, in this paper, we use the subscripts c (coelicolor) and g (griseus) to distinguish between the genes of the two organisms. It is relevant to note that mutations in the gene downstream of the two adpA genes, ornA, have been shown previously to give rise to a slow-growing and sparse aerial mycelium formation phenotype, and that some ornAg transcripts emanate from the adpAg promoter region (Ohnishi et al., 2000). It is likely that the oligoribonuclease encoded by ornA is involved in mRNA degradation (Ohnishi et al., 2000).
WC109 was caused to produce aerial mycelium even by a single copy of adpAc (Fig. 1C), reinforcing the possibility that the complementation was true, rather than some kind of suppression effect. We therefore sequenced adpAc from WC109 and found that it contained a frameshift mutation (Fig. 2). The protein resulting from the frameshift was deduced to be terminated at a stop codon only 5 bases downstream from the authentic stop codon, so any potential polar effects on expression of the downstream ornA gene were not expected to be severe; but the weak morphological defect remaining in the complemented mutant could have been attributable to slight polarity. Note that adpAc is separated by about one-third of the genome from the region to which bldH had been mapped genetically (Champness, 1988) [indeed, we had initially failed in attempts to complement bldH109 with a series of 37 overlapping cosmids (p8–1A9; Redenbach et al., 1996) encompassing nearly all the mthB–cysD interval, based on the genetic map location between mthB and cysD suggested by Champness (1988)]. In contrast to WC109, the bald phenotype of WC181, previously believed to be a bldH mutant (Champness, 1988), was not complemented by DNA containing adpAc, and sequencing revealed no mutations in the adpAc region of WC181 DNA, from 500 bp upstream of the start codon to 14 bp downstream of the stop codon (data not shown).
A constructed adpAc mutant shows a bald colony phenotype
An in frame deletion of adpAc was constructed by polymerase chain reaction (PCR) targeting. The resulting mutant, M851, showed a bald phenotype when grown on R2 (Fig. 3), R5 or SMMS media. However, there was no obvious mutant phenotype on MM mannitol or MS (data not shown). Unlike bldA mutants, and like bldH mutants, the colonies produced red pigment on certain media. This pigment might have been either of two known antibiotics made by S. coelicolor. In a simple test to discriminate between them, fuming of the plates with ammonia resulted in a yellow colour characteristic of undecylprodiginines (‘Red’ antibiotic), and not of actinorhodin which would turn blue (data not shown). The constructed mutation was responsible for the phenotype, as a wild-type copy of adpAc introduced on the pSET152 integrating vector fully restored the wild-type phenotype.
If adpAc is a major and direct target for bldA, then the extracellular complementation pattern of M851 should be like that of bldA mutants and WC109, which have been shown to be stimulated to form aerial hyphae by growth close to a bldG mutant, and to be able to stimulate aerial growth of an adjacent bldK culture (Nodwell et al., 1996). Figure 4 shows that this was indeed the case: M851 restored a fringe of aerial mycelium production to a bldK mutant, whereas a bldG mutant restored a fringe of aerial mycelium production to M851.
Transcription of adpAc does not depend on a γ-butyrolactone signalling molecule
In S. griseus, adpAg occupies a crucial position in the signal transduction system by which the γ-butyrolactone signalling molecule A factor activates morphological differentiation and secondary metabolism (Horinouchi, 2002). Expression of adpAg is directly repressed by ArpA, a γ-butyrolactone binding protein, and is induced at transition phase by the production of A factor. S. coelicolor produces a different spectrum of γ-butyrolactones. The S. coelicolor genome contains only one homologue of afsA, the S. griseus gene believed to be responsible for A factor biosynthesis (Horinouchi et al., 1989; Bentley et al., 2002), and disruption of this gene (scbA) eliminated γ-butyrolactone production and had the unexpected effect of increasing pigmented antibiotic production, while having no obvious effects on morphological differentiation (Takano et al., 2001). In addition, a mutant disrupted in scbR (the gene next to scbA), a homologue of arpA, which in S. griseus encodes the A factor-binding protein, produced no γ-butyrolactones, yet showed delayed production of Red (Takano et al., 2001). We analysed adpAc expression by S1 nuclease mapping using RNA isolated from liquid cultures of a wild type and its scbA, scbR disruption derivatives. Three apparent mRNA 5′ ends were detected (Fig. 5A) presumably corresponding to three promoters, and their expression was more or less constant during growth in the wild type (Fig. 5B); the same three mRNA 5′ ends were detected in samples from surface cultures of M145 and M600 (Fig. 5C). There was little difference in the profile of these three mRNAs in any of the strains used, except that, in surface cultures, p1 appeared to be used more abundantly, and the signals were diminished in the latest time samples, possibly approximately coinciding with the onset of sporulation in the aerial mycelium. Gel retardation experiments conducted using ScbR did not show any ScbR binding to the adpAc promoter region (data not shown). These results suggest that, unlike in the case of S. griseus, adpAc is not part of a γ-butyrolactone signal transduction cascade. Consistent with this, there is considerable sequence divergence between the adpA upstream regions of the two species in the region previously shown to bind ArpA in S. griseus, which corresponds to the major promoter of adpAg (Fig. 6; Ohnishi et al., 1999). Interestingly, although none of the three adpAc promoters corresponds in position to the published promoter of adpAg, they all have quite extensive similarity to equivalent regions in the non-coding region upstream of adpAg.
Sigma BldN is present in an adpAc mutant
In S. griseus, AdpA regulates a large number of genes (Horinouchi, 2002). One of these (adsA) encodes a sigma factor needed for development (Yamazaki et al., 2000). In S. coelicolor, the homologous protein, σBldN, is also necessary for aerial growth (Bibb et al., 2000). Levels of σBldN are affected by several different bld mutations. Notably, WC109 (bldH109) lacks σBldN, as detected by Western blotting, and contains no bldN mRNA (Bibb et al., 2000; Bibb and Buttner, 2003). On the simple assumption that bldH and adpAc are the same gene, we expected that the adpAc disruption mutant should also lack bldN expression. We analysed extracts of the mutant by Western blotting with antiσBldN antibodies and unexpectedly found an undiminished signal in the mutant compared with the bldH+ parent (Fig. 7). This result may indicate that either WC109 contains another mutation as well as its adpAc frameshift or the frameshift in adpAc in WC109 affects σBldN levels indirectly through polarity on the downstream oligoribonuclease gene ornA. However, in the adpAc insertion mutant that was constructed first to obtain the in frame mutant, σBldN was also present; so, in the polarity model, we would have to assume that the insertion has a less severe polarity effect than the bldH109 frameshift. Whatever the explanation for the discrepancy between the bldH109 and adpAc phenotypes with respect to bldN, the undiminished expression of bldN in the adpAc mutant again showed that adpA plays a somewhat different role in S. coelicolor from that previously found in S. griseus.
The TTA codon in adpAc contributes markedly to the bldA dependence of normal development
Our discovery that a TTA-containing gene, adpAc, is needed for normal aerial mycelium development, and is involved in the same step in the extracellular signalling cascade for sporulation as bldA, led to the possibility that it might be the sole bldA target gene essential for differentiation. To test this, we generated a mutant copy of adpAc in which the TTA codon had been changed to the alternative leucine codon TTG. This mutant adpAc was inserted into pSET152, both with and without the downstream ornA gene, to give pHL72 and pHZ2528 respectively. The constructs were then introduced into a bldA mutant (J1700). The TTA-free adpAc restored aerial mycelium formation, but only when coupled in cis to ornA (Fig. 8), suggesting that bldA affects the translation of both adpAc and the downstream TTA-free ornA, and showing that the TTA codon in adpAc is a major contributor to the morphological deficiency of bldA mutants. Consistent with the idea of a cis-acting effect of the TTA codon in adpAc on ornA, some of the J1700/pHZ2528 adpAc(TTA)/adpAc(TTG) heterogenote colonies displayed sporulating sectors (which remained unpigmented), suggesting that recombinational interaction of the two adpAc copies had inserted the TTG codon into the adpAc copy located in its natural chromosomal position, where bldA-independent expression could bypass possible polarity on ornA.
Several pieces of evidence indicate that the principal cause of the bldH109 phenotype is a mutation in adpAc. Thus, adpAc at least partially complements bldH109; bldH109 contains a frameshift mutation in adpAc; an adpAc knockout mutant is defective in aerial growth but retains pigmented antibiotic production; and the adpAc mutant has the same extracellular complementation phenotype as the bldH109 mutant. The only other previously known candidate bldH mutant (WC181) proved not to be allelic with WC109. bldH (= adpAc) is the first S. coelicolor bld gene shown to contain a TTA codon, raising the possibility that it could provide (part of) the explanation for the morphological deficiency of bldA mutants. This hypothesis was strongly supported by the finding that the morphological defect of a bldA deletion mutant was largely suppressed by a TTA-free copy of adpAc when the mutation was in cis with a copy of the downstream gene ornA. Further work will be needed to establish whether this requirement for ornA is indeed a reflection of co-transcription of the two genes, especially in view of the 341 bp interval between them – in S. griseus the equivalent interval is 9 bp (Ohnishi et al., 2000).
We can now account for most of the main aspects of the bldA phenotype: failure to make actinorhodin is because of the presence of a TTA codon in actIIorf4, the essential pathway-specific activator gene for actinorhodin biosynthesis (Fernandez-Moreno et al., 1991; Passantino et al., 1991); failure to make undecylprodigiosin pigments is because of a TTA-containing gene, redZ, that is the first of two pathway-specific activators in the mini-cascade leading to undecylprodigiosin biosynthesis (White and Bibb, 1997; Guthrie et al., 1998); failure to make methylenomycin results from TTA codons in regulatory elements in the gene cluster for methylenomycin biosynthesis (S. O’Rourke, C. J. Bruton, N. Hartley and K. F. Chater, manuscript in preparation); and failure to make aerial hyphae is largely attributable to a TTA codon in a regulatory gene, adpAc. It was interesting to find that adpAc is not needed for undecylprodigiosin synthesis, in view of the fact that its apparent orthologue in S. griseus is needed for streptomycin biosynthesis, aerial growth and yellow pigment formation. In addition, the regulation of adpAc and adpAg seems to differ, notably in their dependence on γ-butyrolactones; and the promoter regions of adpA in the two species have only punctuated similarity to each other and show different transcriptional start points (Fig. 6). The S. coelicolor genome contains some seven adpA-like genes, of which adpAc is the most similar and the only one to show local synteny with adpAg. While it is clear that adpAc is not important for the production of at least one of the pigmented antibiotics of S. coelicolor (undecylprodigiosin), we cannot rule out the possibility of such a role for other adpA-like genes – indeed, if any of those genes do carry out such a role, then it is possible that adpAc does interact with secondary metabolism pathways, with this activity being masked by the presence of one or more other genes with overlapping function. A similar explanation is possible for the observation that, in S. coelicolor, adpAc is not needed for the expression of bldN, whereas in S. griseus, the equivalent sigma factor gene (adsA) is adpAg dependent (Yamazaki et al., 2000). We did not observe any obvious actinorhodin production in the constructed adpAc mutant, for reasons that remain to be determined. However, we note that actinorhodin production can be activated in a bldA mutant by changing the TTA codon in the actII-orf4 pathway-specific regulatory gene (Fernandez-Moreno et al., 1991). As the bldA mutation would have effectively inactivated adpAc expression in this strain, actinorhodin production is evidently not strongly dependent on adpAc. AdpA proteins are members of the AraC family of regulators, and AdpAg has been shown to bind DNA (Ohnishi et al., 1999), reinforcing the growing evidence that most bld genes are regulatory. Thus, the subsequent steps in the bld gene-mediated extracellular signalling cascade are defined by mutations in bldG (encoding a homologue of such antiantisigma proteins as SpoIIAA in Bacillus subtilis; Bignell et al., 2000), bldC and bldD (encoding DNA-binding proteins; A. Hunt, personal communication; Elliot et al., 1998; 2001). It follows that the bld genes that define the extracellular complementation cascade are not likely to be directly involved in the synthesis of a diffusible extracellular factor. We therefore assume that each of these regulatory genes directly or indirectly activates a pathway for production of the relevant factor. In addition, the pattern of extracellular complementation among the bld mutants used to define the cascade implies, for any one mutant, that none of the bld genes defining other steps is inactive in that mutant by any mechanism other than signal deficiency. In other words, we suggest that none of these bld genes is dependent for expression in a gene-to-gene manner on any of the bld genes governing other steps in the cascade. This in turn implies that the bld genes represent at least four distinct intracellular regulatory systems that must be activated to permit morphological differentiation on the rich R2YE medium, and which intercommunicate via the extracellular signals. In the simplest case, the extracellular signals would bind directly to the product of the bld gene involved in the next step in the cascade to activate production of the next signal. Signal production is presumed to be associated with different aspects of physiology, also under bld gene control, that are characteristic of the region of the colony from which aerial hyphae emerge. These aspects might include starvation, secondary metabolism, storage metabolism, cell–cell contact or controlled cell death. Only when all the bld gene-dependent processes have been activated, we suggest, will it be appropriate for aerial hyphae to emerge. This model has also been discussed in some detail by Chater and Horinouchi (2003).
Bacterial strains, plasmids, growth conditions
Streptomyces coelicolor A3(2) strains (Table 1) were manipulated as described previously (Kieser et al., 2000). For routine subcloning, Escherichia coli K-12 strains JM101, DH5α (Sambrook et al., 1989) and ET12567 (dam dcm hsdS; MacNeil et al., 1992) were grown and transformed according to Sambrook et al. (1989). ET12567 was used to propagate unmethylated cosmid DNA for introduction of DNA into S. coelicolor by transformation or conjugation. pIJ699, a high-copy-number positive selection vector (Kieser and Melton, 1988), was used for shotgun cloning in Streptomyces. pIJ2925 was a high-copy-number pUC-type plasmid used for routine subcloning (Kieser et al., 2000). pSET152 (Bierman et al., 1992), which integrates into the S. coelicolor chromosome by site-specific recombination at the bacteriophage φC31 attachment site, attB (Kuhstoss and Rao, 1991), was used to introduce single copies of genes into the S. coelicolor chromosome. SCC13 and SCC105 (Redenbach et al., 1996) were two cosmids carrying adpAc. E. coli BW25113/pIJ790 was the host for λRED-mediated PCR-targeted mutagenesis (Gust et al., 2003), and E. coli DH5α/BT340 was the host for FLP recombinase-mediated deletion of disruption cassettes to leave non-polar, phenotypically unmarked deletion mutations (Datsenko and Wanner, 2000). pIJ773 (Gust et al., 2003) was used as the template for amplification of a disruption cassette containing aac(3)IV (conferring apramycin resistance) and the RK2 origin of transfer (oriT), flanked by recognition sites for FLP recombinase.
|Strain||Relevant genotype||Source or reference|
|M145||Prototroph||Kieser et al. (2000)|
|M600||Prototroph||Chakraburtty and Bibb (1997)|
|NS17||bldK::aadA||Nodwell et al. (1996)|
|WC103||hisA1 uraA1 strA1 bldG103||Champness (1988)|
|WC109||hisA1 uraA1 strA1 bldH109||Champness (1988)|
|WC181||hisA1 uraA1 strA1′ bldH181′||Champness (1988)|
|J1700||hisA1 uraA1 strA1 bldA39||Lawlor et al. (1987)|
|M751||M145 ΔscbA||Takano et al. (2001)|
|M752||M145 ΔscbR||Takano et al. (2001)|
|M757||M145 adpAc::aadC(3)IV||This study|
|M851||M145 ΔadpAc||This study|
|J1501||hisA1 uraA1strA1||Kieser et al. (2000)|
Several different Streptomyces media were used. SMMS medium was as reported by Takano et al. (2001). MS agar (Kieser et al., 2000) was used to make spore suspensions and for plating out conjugations with E. coli ET12567 containing the RP4 derivative pUZ8002 (Flett et al., 1997). R2, R2YE or R5 media and minimal medium (MM mannitol) (Kieser et al., 2000) were used for scoring sporulation. All Streptomyces cultivation was at 30°C.
Shotgun cloning of bldH
pIJ699 was digested with BamHI and BglII, then the 4.8 kb BglII fragment was gel purified. Self-religation of this vector fragment forms a long uninterrupted perfect palindrome, rendering the plasmid non-viable in host bacteria (Kieser and Melton, 1988). After partial digestion of M145 genomic DNA with Sau3AI, 4–8 kb fragments were agarose gel purified and ligated with the purified 4.8 kb pIJ699 BglII fragment. The ligation mixture was introduced into WC109 (bldH109) protoplasts, and transformants were selected by flooding the regeneration plates with thiostrepton (25 µg ml−1). Five individual colonies were found to form aerial mycelium at day 5 among ≈ 9000 transformants. The plasmids isolated from these colonies were named pSPH1, pSPH2, pSPH3, pSPH4 and pSPH5. For subcloning to localize the complementing DNA (Fig. 1), first the insert of pSPH2 was excised as a 3.2 kb HindIII fragment and inserted into pIJ2925 to give pHZ2511. The 2.4 kb BglII fragment of pHZ2511 was then ligated with BglII-digested pIJ699 to give pHZ2512, and the 0.9 kb SacII fragment was ligated with SacII-digested pSET152 to give pHZ2513. The 2.4 kb BglII fragment was also cloned in pSET152 to give pHZ2517.
Identification of the insert boundaries of the bldH complementing clones
The pSPH1 to pSPH5 plasmid insert boundaries were amplified by ligation-mediated PCR (LM-PCR) and sequenced. The oligonucleotides used were: UNIV5-AD1 (5′-GACTCGC GAATTCCGACAGTTGA), AGA1-AD2 (5′-GGCCTCAACT GTCG) and UNI699 (5′-CTAACGTCTGGAAAGACGAC). UNIV5-AD1 and AGA1-AD2 were annealed to give an adaptor with a 5′-GGCC overhang, which is cohesive with EagI digestion ends. UNI699 was complementary to a sequence near the cloning site of pIJ699. The plasmids to be sequenced were digested with EagI and then ligated with the adaptor. With the ligation mixture as template, UNIV5-AD1 and UNI699 were used to prime amplification of the two vector-insert junctions of each clone. The PCR product was gel purified and sequenced with UNI699 as primer. The sequences of the plasmid-insert boundaries were compared with the S. coelicolor genome sequence (http://www.sanger.ac.uk/Projects/S_coelicolor/) to reveal the inserts.
PCR sequencing of bldH
The adpAc alleles of WC109 and WC181 were sequenced as follows. First, the entire adpAc segments were PCR amplified from both strains using Pfu, a high-fidelity DNA polymerase. The primers were adp1 (5′-CCGAATTCCACCTGCACGGA CAGG) and adp2 (5′-AGGGATCCGTCTGCTCACCTCACG), which were complementary to sequences upstream and downstream of the adpAc ORF but with an EcoRI and a BamHI site respectively. The amplification included the region from 303 bp upstream of the translation start codon GTG to 14 bp downstream of the stop codon. The purified 1525 bp PCR products of the two strains were digested with BamHI and EcoRI and cloned into pIJ2925 to give pHZ2516 and pHZ2519 respectively. pHZ2516 and pHZ2519 were then sent to TaKaRa Biotechnology (Dalian) for sequencing. The resulting sequences were compared with the EMBL database to identify any mutations. The DNA region around the mutated point found in WC109 was further confirmed by sequencing the PCR products using genomic DNA of both strains as templates. The primers for PCR and sequencing were adp19 (5′-CCATGTCGACAATGTCCCAAG) and adp4 (5′-GGGTCGACGTGCACCGACGG). The promoter regions of both strains, from 500 bp upstream to 111 bp downstream of the GTG start codon, extending 125 bp into the upstream divergent gene, were PCR amplified and sequenced. The primers used were adp2 (5′-GTCTGCTGCTGCGGCGT TCCG) and adp11 (5′-GAACTCTCGAAGATGGGGCCG).
S1 nuclease mapping
RNA was isolated as described by Strauch et al. (1991). For each S1 nuclease reaction, 30 or 40 µg of RNA was hybridized in NaTCA buffer [Murray, 1986; solid NaTCA (Aldrich) dissolved to 3 M in 50 mM PIPES, 5 mM EDTA, pH 7.0] to about 0.002 pmol (≈ 104 Cerenkov counts min−1) of the following probes. For adpAc, the oligonucleotide 5′-CACCCT TCGGGTCTGTCGCTC, which anneals within the adpAc coding region, was uniquely labelled at its 5′ end with [32P]-ATP using T4 polynucleotide kinase and used in the PCR with the unlabelled oligonucleotide 5′-GTCTGCTGCTGCGGCG TTCCG, which anneals upstream of the adpAc promoter, to generate a 463 bp probe. The cosmid SCC13 (Redenbach et al., 1996) was used as the PCR template. For hrdB, the probe was made as described previously (Aigle et al., 2000). Subsequent steps were as described by Strauch et al. (1991). The sequence ladder was generated using a Sequenase 7-deaza-GTP sequencing kit (USB) with the same labelled primer as was used for the probe.
Construction and complementation of in frame deletion mutants of adpAc
A mutant adpAc allele, in which most of the adpAc coding region (amino acids 57–378 out of 398) was deleted, was constructed by PCR targeting using oligonucleotide primers (5′-C A T C T TCGAGAGTTCCATACCGCTGCGGTGTTCGGG ATCATTCCGGGGATCCGTCGACC and 5′-G C G G C G G GTCTGG A ACGGGACCGCGTTCTCCGGGGCGAGGTGTAGGCTGGAGCTGCTT) with 5′ ends overlapping the 5′ and 3′ ends of the adpA coding sequence, and 3′ (priming) ends designed to amplify the apramycin resistance disruption cassette of pIJ773. The PCR product was introduced into E. coli BW25113/pIJ790 containing cosmid SCC13, preinduced for λRED functions by the addition of arabinose, to obtain an adpAc-disrupted version of SCC13. The disrupted cosmid was isolated and transferred via E. coli strain ET12567/pUZ8002 to S. coelicolor M145 by conjugation. Single cross-over exconjugants were selected on MS agar containing apramycin. Three such colonies were taken through two rounds of non-selective growth on MS agar, and spores were then plated for single colonies, which were scored for kanamycin sensitivity. Deletions within adpAc were confirmed by Southern hybridization (Kieser et al., 2000) using a PCR-generated probe (labelled with 32P by random oligopriming; Pharmacia). One such strain was designated M757. To construct a phenotypically unmarked in frame deletion, the adpAc-disrupted cosmid SCC13 adpAc::aac(3)IV was introduced into E. coli DH5α/BT340 to excise the disruption cassette from the cosmid by FLP recombinase. The resulting cosmid SCC13 ΔadpAc was then transferred to S. coelicolor M757 by conjugation via ET12567. Single cross-over exconjugants were selected on MS agar containing kanamycin and apramycin. Three such colonies were then taken through one round of non-selective growth on MS agar, and spores were plated for single colonies, which were scored for kanamycin and apramycin sensitivity. All the colonies tested were kanamycin and apramycin sensitive and were deleted for adpAc. Deletion within adpAc was confirmed by Southern hybridization using the same probe described above, and one such strain was designated M851. To complement the mutants, pHZ2517 (see above), which was a pSET152 derivative containing adpAc and its promoter, was transferred into S. coelicolor by conjugation via ET12567. Exconjugants were purified by single-colony isolation on medium containing apramycin, and plasmid integration was confirmed by Southern hybridization.
Site-directed mutation of the TTA codon of adpAc and construction of relevant integrative plasmids
There is a TTA codon 674–676 nucleotides downstream of the start codon of adpAc. In order to change the TTA leucine codon to a TTG leucine codon, the insert of pSPH2 was cloned into pIJ2925 at the HindIII site to give pHZ2511. Then, pHZ2511 was digested, and the 2.4 kb BglII fragment, which carries the entire adpAc, was cloned into the BamHI site of pIJ2925 to give pHZ2514, which was used as the PCR template for site-directed mutagenesis. Two synthetic oligonucleotides were designed: ADPA-TTGL (5′-CAGGTCTTT GCCGGAGGAGATCGG) and ADPA-TTGR (5′-CTCCTCCG GCAAAGACCTGTCGAGG). ADPA-TTGL and ADPA-TTGR were complementary to opposite strands of the TTA codon region of adpAc and contained the desired mutation as shown in bold/underline . The site-directed mutation procedure was modified from the Stratagene Quickchange kit instructions. The PCR was carried out with Pfu DNA polymerase. DMSO was added to the reaction mixture to a final concentration of 5%. The cycling conditions were 95°C for 30 s, 55°C for 1 min, 68°C for 10 min and 50 s (12 cycles). After temperature cycling, the PCR product was treated with DpnI to digest the methylated parental DNA template and to select for mutation-containing synthesized DNA. The mixture was then used to transform E. coli DH5α. Plasmid DNA from two transformants was sequenced to show that the inserted DNA fragment of both plasmids contained the designed TTATTG mutation and there was no other mutation. Then the 2.4 kb BglII fragment was excised from the mutated plasmid, gel purified and inserted into the BamHI site of pSET152 to give pHZ2528. Thus, pHZ2528 carried the intact adpAc with a TTATTG mutation and the phage φC31 attachment function for integrating into the chromosomal attB site. In order to get an integrative construct carrying the TTA-free adpAc together with the downstream gene ornA, pHL72 was constructed by replacing the 0.7 kb BclI–EcoRI fragment of pHZ2528 with a 1547 bp BclI–EcoRI fragment from a PCR amplification primed with adpa3 (5′-TGTCGGTGTTCGGGA TCG-3′) and ornA-C-EI (5′-CCGGAATTCAAGTGTACAGGG TCCGAAGG-3′), with M145 DNA as template. adpa3 was complementary to the adpAc sequence. ornA-C-EI was complementary to a sequence downstream of ornA, but contained an engineered EcoRI site. pHL71 was the same as pHL72 but still carried the TTA codon.
Western blotting was done exactly as described by Bibb and Buttner (2003).
Much of this work was supported by a Joint Project grant from the National Natural Science Foundation of China and The Royal Society to Zixing Deng and Keith Chater. Eriko Takano was supported by a grant from the Human Frontiers Science Program to Mervyn Bibb. Meifeng Tao was supported by a grant from National Natural Science Foundation of China (no. 39970012). Maureen Bibb, Mark Buttner, Mervyn Bibb and Keith Chater were supported by a Competitive Strategic Grant from the BBSRC to the John Innes Centre. We thank Bertolt Gust for advice on targeted mutagenesis, Helen Kieser for providing cosmids, and Kay Fowler for providing oligonucleotides UNIV5-AD1, AGA1-AD2 and UNI699. Some of the initial attempts to use cosmids to complement bldH were done by Eunja Kim.
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