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1 Department of Biology, Ursinus College, PO Box 1000, Collegeville, PA 19426, USA
2 Biology Department, Hanover College, PO Box 890, Hanover, IN 47243, USA
Correspondence
Jeffrey A. Hughes
hughes{at}hanover.edu
| ABSTRACT |
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Present address: Little Britain Veterinary Services, 281 Sleepy Hollow Road, Nottingham, PA 19362, USA.
| INTRODUCTION |
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Though well supported by genetic and biochemical data, the role of SAM has not been directly tested in vivo. This is due to three problems inherent in studies involving SAM in bacteria: SAM typically cannot cross bacterial cell membranes (including those of Escherichia coli), SAM synthetase inhibitors (e.g. methionine analogues such as ethionine) induce side effects unrelated to SAM deprivation (Alix, 1982
; Pine, 1978
), and known viable SAM synthetase mutants are leaky even under restrictive conditions (Hafner et al., 1977
; Mulligan et al., 1982
). We circumvented these difficulties by transforming cells with plasmid expression vectors containing the cloned coliphage T3 SAM hydrolase (SAMase) gene, resulting in in vivo SAMase activity not otherwise found in E. coli. This enzyme cleaves SAM into homoserine and 5'-methylthioadenosine, removes SAM from the cell, and inhibits a variety of SAM-related activities (Hughes et al., 1987
; Posnick & Samson, 1999
; Val & Cronan, 1998
). Introducing SAMase activity should specifically remove the co-repressor without affecting the MetJ aporepressor and demonstrate the effect of reduced SAM concentrations on the expression of elements of the met regulon. Results from our assays of met gene expression in cells containing in vivo SAMase activity firmly support the role of SAM as the co-repressor. They also indicate that other factors including and possibly in addition to MetR play roles in influencing SAM-related met gene regulation.
| METHODS |
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gt2 constructs containing Salmonella typhimurium met gene promoter : : lacZ fusions were assayed for metB (
Blac; Urbanowski & Stauffer, 1986
Elac; Plamann et al., 1988
Flac; Stauffer & Stauffer, 1988
Hlac; Urbanowski & Stauffer, 1989b
Jlac; Urbanowski & Stauffer, 1986
Rlac; Urbanowski & Stauffer, 1987
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Enzyme assays.
Cystathionine synthetase (MetB) activity was determined in toluenized cells by the O-succinylhomoserine-dependent oxidation of reduced nicotinamide adenine dinucleotide, measured as A340 (Holloway et al., 1970
; Kaplan & Flavin, 1966
). Cystathionase (MetC) activity was assayed by the cystathionine-dependent reduction of Ellman's reagent, measured as A410 (Flavin, 1962
; Holloway et al., 1970
).
-Galactosidase expression of met : : lacZ fusion genes was monitored by the rate of ONPG hydrolysis (Miller, 1972
). SAMase was assayed by passing reaction mixes inoculated with 14COOH-SAM (Amersham Biosciences) over Affi-gel 601 (Bio-Rad) cis-diol affinity columns and determining the net percentage of total counts that failed to bind the column and were assumed to be in 14COOH-L-homoserine (Hughes et al., 1987
). SAM synthetase activity was measured as the percentage of [35S]methionine (Amersham Biosciences) converted to labelled cis-diol (Affi-gel 601)-binding compounds (e.g. SAM and its metabolites S-adenosylhomocysteine, 5'-methylthioadenosine and 5'-methylthioribose) after incubation with toluenized cells under conditions for the SAM synthetase assay (Hafner et al., 1977
; Hughes et al., 1987
). Protein concentrations were determined by the Lowry method. In all cases, assays were conducted on at least five cultures from independently transformed cells, grown to stationary phase, performed according to minor modifications of published procedures, and quantified spectrophotometrically (with a Spectronic 21 or Beckman DU-64) or by liquid scintillation (Beckman LS5000TD) using Beckman ReadySafe scintillation cocktail. Statistical comparisons employed Student's t test, with P<0·05 indicating significant differences between paired samples.
| RESULTS |
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Effect of in vivo SAMase expression in met wild-type cells in a complete medium
Three systems were used initially to survey the consequence on met gene expression of the in vivo expression of SAMase in E. coli K-12 BW545. The results of these assays are presented in Table 2
.
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Secondly, we expressed SAMase in the BW545-derived GW strains that carry the lacZ gene fused behind the host's promoters for metA, metE and metF. The use of these metlac fusion strains simplified the assays and expanded our survey to include another three genes. Introduction of SAMase activity into GW2517 (metA : : lacZ), GW2521 (metF : : lacZ) and GW2522 (metE : : lacZ) also greatly enhanced expression of these genes.
We then lysogenized BW545 with recombinant
gt2 phage carrying metB, E, F, H, J or R gene promoters from S. typhimurium fused to lacZ, constructs that have been used extensively to assay met gene expression in E. coli (see Methods for appropriate references). metB, E, F and R showed dramatic induction of activity while metJ and metH showed much smaller but still significant increases. Both the E. coli and S. typhimurium promoters for metE and metF responded similarly to the introduction of in vivo SAMase activity, although the S. typhimurium promoters directed a somewhat higher basal level of gene expression. While results from the cystathionine synthetase (MetB) assays showed less enhanced enzyme expression than those revealed by assays of MetB activity gauged through the S. typhimurium promoter metlac fusions, in both cases the assays indicated substantial SAMase-mediated enzyme induction.
Because of the similarity of results seen using E. coli and S. typhimurium promoters, the simplicity of the reporter assays, and the fact that BW545
lysogens are met wild-type strains while GW strains are methionine auxotrophs, we used these lysogens for all subsequent experiments. We deemed the use of met wild-type cells to be especially important. For example, defects in homocysteine biosynthesis in MetA strains or in its use in MetE or MetF strains would likely alter MetR-mediated gene activation (Byerly et al., 1990
; Cowen et al., 1993
; Mares et al., 1992
; Urbanowski et al., 1987
) and introduce complex and unpredictable effects beyond those provoked by SAMase expression.
Effect of in vivo SAMase expression in met wild-type cells in a methionine-limited medium
Because cells transformed with pHBBR2 grow poorly in defined media (data not shown), we routinely cultured cells in antibiotic-supplemented YT complete medium. On the other hand, it was necessary to grow cells in a methionine-deficient medium to determine the impact of methionine on met gene expression. To ensure reliable growth, cells were first cultured overnight in YT medium, washed and diluted 10-fold into YT medium, M9 minimal medium or M9 medium supplemented with L-methionine, and then cultured once again overnight. This regimen allowed growth in defined media and showed a reliable pattern of methionine-influenced gene expression (Table 3
). With the exception of metH and metJ, the tested genes were significantly induced in cells grown without methionine in the absence of SAMase, while in vivo SAMase activity provoked a significant induction of expression for every gene tested under all conditions. The metA, B, E, F and R genes were most dramatically affected by either the absence of methionine from the culture medium or the presence of the SAMase expression vector. metC expression showed less dramatic results, although it is possible the different and possibly less sensitive method used to assay metC activity accounted in part for its apparently lower degree of sensitivity to either condition.
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| DISCUSSION |
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The current model explains the trends in expression of genes shown to be sensitive to SAM levels and/or the absence of the MetJ aporepressor, but understanding the low but significant SAMase-mediated induction of metJ requires more thought. metJ is autoregulated, as shown by the repressive effect of excess levels of the aporepressor on metJ expression with or without added SAM (Shoeman et al., 1985
; Urbanowski & Stauffer, 1986
). SAM enhances this autoregulatory activity, so the removal of SAM by SAMase may simply decrease the effectiveness of this regulation, requiring higher concentrations of MetJ to regulate its own gene. This concept is further supported by both the higher level of metJ expression in MetJ-deficient cells and the lack of further metJ induction in cells lacking the aporepressor (Table 5
).
It is more difficult to explain the enhanced induction of all met genes in response to SAMase activity in metJ : : Tn5 and metK : : Tn5 backgrounds through the activity of the MetJSAM repressor alone. MetJ cells lack the MetJ aporepressor and, consequently, should fully and constitutively express genes regulated solely by the MetJSAM complex. However, cells bearing these Tn5-inactivated metJ and metK alleles as well as other metJ and metK alleles that allow constitutive expression of met genes (data not shown) consistently show enhanced expression of all tested met genes in the presence of in vivo SAMase activity with the single exception of metJ in MetJ-deficient cells noted above. Some or all of the enhanced met expression in cells with this particular metK : : Tn5 insertion may be due to residual SAM synthesis that occurs in these cells (e.g. DNA from these cells is fully Dam methylated and SAM is detectable at <5 % of wild-type levels; personal observations), and it would be interesting to test the expression of these genes under SAM-limiting conditions known to be lethal (Newman et al., 1998
). At the same time the hyperinduction of met genes by SAMase suggests a need to dissect the impact of other factors known to regulate met gene expression under these conditions and to search for other sources of regulation.
The impact that SAMase-enhanced levels of MetR and/or homocysteine might have on met gene expression warrants the most careful consideration. MetR by itself activates metH expression (Urbanowski & Stauffer, 1989a
; Urbanowski et al., 1987
), and a MetRhomocysteine complex in the absence of the MetJSAM repressor is needed for efficient expression of metE (Plamann et al., 1988
; Urbanowski et al., 1987
). In addition, MetR cells are impaired to some degree in expression of metA and metF, each of which is downregulated when homocysteine levels increase, a result presumably of increased levels of the MetRhomocysteine complex and a concomitant decrease of the free MetR activator protein in the cell (Cowen et al., 1993
; Mares et al., 1992
). It is also possible that MetR, free or bound to homocysteine, is needed in some way for efficient expression of other met genes. Consequently, assuming that levels of MetR are normally sufficient only to induce submaximal expression of its target genes, the induction of metR directed by SAMase activity could boost expression of MetR-activated genes.
The above logic is contradicted by the observation that metR expression is also induced in metJ : : Tn5 and metK : : Tn5 cells lacking SAMase. These cells should therefore also exhibit enhanced met gene expression comparable to cells with high levels of SAMase if increased levels of MetR synthesis are responsible for the extra level of expression of these genes. SAMase also presumably enhances synthesis of homocysteine through induction of metA, B and C, and this could also play a role in enhancing met gene expression. Depending on the fate of any extra homocysteine produced as a consequence of SAMase expression, this should lead to a higher level of the MetRhomocysteine activator complex (and less free MetR). Increased levels both of MetR and homocysteine would presumably also occur in both MetJ- and MetK-deficient cells, both of which are induced for metA, B and C with or without in vivo SAMase activity. These and other conflicting and unresolved possibilities surrounding SAMase-mediated induced met gene induction can only be resolved by further investigation of the role of MetR activity and/or homocysteine levels, or by searching for other unidentified regulatory elements that influence met gene activity such as revealed by the role of SAM in the S-box system of Bacillus subtilis (Murphy McDaniel et al., 2003
).
Explanations for this effect might also be found outside of the met regulon. One possible explanation for the increased expression of met genes in metJ- and metK-deficient cells would include any positive effect on gene transcription resulting from SAMase-mediated hypomethylation of chromosomal DNA. Methylation of promoter sequences, particularly in studies with -GATC- sequence methylation mediated by the Dam methylase, results in reduced transcription for some genes in E. coli (e.g. Stauffer & Stauffer, 1988
; reviewed by Palmer & Marinus, 1995
; Plumbridge, 1987
). Reduction of SAM pools to levels below those needed for Dam- or Dcm-mediated DNA methylation has been achieved with the in vivo expression of recombinant SAMase (Hughes et al., 1987
; Macintyre et al., 2001
; Posnick & Samson, 1999
). Should met gene promoters or those of genes whose activity impacts met gene expression be hypomethylated, or should any other consequence of hypomethylation affect DNA packing or structure, an increase in the transcription of their corresponding genes could result. Answers to these possibilities await studies with Dam- or Dcm-deficient strains.
| ACKNOWLEDGEMENTS |
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gt2 met gene reporter phage constructs were gratefully received from George Stauffer, University of Iowa. | REFERENCES |
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Received 4 September 2005;
revised 25 January 2006;
accepted 27 January 2006.
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