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Journal of Bacteriology, October 2002, p. 5495-5501, Vol. 184, No. 19
0021-9193/02/$04.00+0 DOI: 10.1128/JB.184.19.5495-5501.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Departments of Microbiology,1 Biochemistry, University of Illinois, Urbana, Illinois 618012
Received 6 May 2002/ Accepted 3 July 2002
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Escherichia coli contains three enzyme complexes that require lipoic acid as a cofactor. The three enzymes are pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase, and glycine cleavage enzyme (29, 37). The most-studied lipoic acid-dependent enzyme is the pyruvate dehydrogenase complex (29) (Fig. 1). This very large protein complex (molecular weight of ca. 5 x 106) is required for the synthesis of the acetyl coenzyme A (acetyl-CoA) required for entry of carbon into the citric acid cycle and fatty acids plus a variety of other molecules (7). The closely related 2-oxoglutarate dehydrogenase complex is a key enzyme of the citric acid cycle, and its product, succinyl-CoA, is a precursor in the synthesis of lysine and methionine (the pyruvate and 2-oxoglutarate dehydrogenases are often collectively called the 2-oxo acid dehydrogenases). The required covalent attachment of lipoic acid is to specific lysine residues of these enzymes that are found on protein domains of highly conserved sequences called lipoyl domains. E. coli has two distinct enzyme systems that modify lipoyl domains (26) (Fig. 2A and B). The best-understood lipoylation enzyme is lipoate protein ligase (LplA), which utilizes exogenously supplied lipoic acid to modify the specific lysine of the lipoyl domain (25). In a reaction analogous to that of biotin ligase (which modifies a structurally similar protein domain), LplA utilizes ATP to activate lipoic acid to lipoyl-AMP (Fig. 1A). The lipoyl-AMP mixed anhydride is then attacked by the
amino group of the target lysine residue, resulting in an amide linkage (13) (Fig. 1A). LplA has been shown to be required for E. coli to utilize lipoic acid from the environment. However, lplA null mutants can be constructed without engendering a deficiency of lipoylated enzymes (25) or a nutritional requirement on minimal medium containing glucose due to the presence of a second, LplA-independent, pathway of lipoylation. This second pathway is dependent on lipB (26), which encodes a novel enzyme, lipoyl-[acyl carrier protein]-protein N-lipoyltransferase (20) (Fig. 2B) and lipA, which encodes lipoic acid synthase (24).
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FIG. 1. Pyruvate dehydrogenase reaction. The 2-oxoglutarate dehydrogenase reaction proceeds by the same mechanism as that for the pyruvate dehydrogenase reaction, except that 2-oxoglutarate replaces pyruvate and the product is succinyl-CoA. The E3 subunit is common to the two enzymes (7). The SH HS of E3 denotes the active-site cysteine residues. Abbreviations: ThDP, thiamine diphosphate; lip, lipoic acid; FAD, flavin adenine dinucleotide.
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FIG. 2. The two pathways of lipoic acid attachment in E. coli. The systematic names for lipoic acid and Se-lip are 1,2-dithiolane-3-pentanoic acid and 1,2-diselenolane-3-pentanoic acid, respectively. ACP, the acyl carrier protein of fatty acid biosynthesis.
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Another Se-lip-resistant mutant, a slr7 mutant, had a more complex and puzzling phenotype. Upon transductional introduction of lipA null mutation into the slr7 strain, the resulting strain remained a lipoic acid prototroph (32), although introduction of a lipA null mutation into wild-type strains results in lipoic acid auxotrophy (37). Therefore, it was proposed that the Se-lip resistance of the slr7 strain might be due to an activation of some unidentified cryptic lipoic acid biosynthetic pathway that synthesized sufficient lipoic acid to effectively compete with the selenium analog for incorporation into the 2-oxo acid dehydrogenase complexes (32). We report that this proposal is incorrect. The slr7 mutation is a duplication of the chromosomal segment that contains both lipA and lipB.
Cloning of the "lipA-complementing element." Prior work showed that a lipA null allele (lipA::Tn1000dkan) could be transduced into the slr7 strain without engendering the expected lipoate auxotrophy. This result led to the hypothesis that the Se-lip resistance phenotype of the slr7 mutant was due to a mutation activating some unidentified cryptic lipoic acid synthetic gene (32). We attempted to identify the putative gene by cloning a lipA-complementing fragment from the slr7 lipA::Tn1000dkan strain, strain KER279 (see Table 1 for detailed descriptions of bacterial strains and plasmids). We constructed a genomic library by digesting strain KER279 genomic DNA with EcoRI and ligating the resulting fragments into plasmid pSU19 (23), a vector of medium copy number. We then selected complementing clones after transforming this library into strain KER176 (lipA::Tn1000dkan) and selecting for growth on minimal medium containing glucose and chloramphenicol (media and genetic methods were as described previously [25, 26, 31, 32, 37]). On minimal medium, a lipA strain requires supplementation with either lipoic acid or acetate plus succinate (these supplements bypass the lipoic acid-dependent enzymes essential for aerobic growth on minimal medium containing glucose); thus, plasmid clones able to suppress lipA permitted growth on minimal medium containing glucose but lacking lipoate. A complementing plasmid (pSJ10) that contained a 4-kb chromosomal segment was obtained. Upon isolation and transformation, the plasmid was found to complement the lipA null mutation of strain KER176, but not the lipB null mutation of strain KER184. Plasmid pSJ10 failed to confer Se-lip resistance (see below). The segment of pSJ10 DNA responsible for lipA complementation was sequenced and found to be identical to the lip region of E. coli. The complementing DNA segment contained lipA but lacked the N-terminal portion of lipB. To determine the sequences responsible for complementation, we performed Tn1000 mutagenesis (14) of plasmid pSJ10. Plasmid pSJ10 was transformed into the F plasmid strain JA200 (the F plasmid carries Tn1000), this strain was mated with strain TVB127, and exconjugants resistant to chloramphenicol, kanamycin, and tetracycline were selected on Luria-Bertani (LB) medium. The exconjugants were screened for lipoic acid auxotrophy by streaking bacteria onto minimal E medium containing glucose with or without 5 ng of R-lipoic acid per ml. Twenty-four Tn1000-mutagenized isolates of pSJ10 were screened, of which 14 had lost the ability to complement lipA. All of the Tn1000 insertions lacking lipA complementation activity mapped to lipA, whereas all of the isolates that retained complementation activity had insertions outside lipA. These results demonstrated that the ability of a slr7 lipA::Tn1000dkan strain, KER279, to grow on minimal medium lacking lipoic acid was not due to a mutation of some unknown lipoic acid metabolic gene. Instead, the lipoic acid prototrophy was due to the presence of at least one functional copy of lipA on the chromosome. The intact copy was present despite the fact that a lipA::Tn1000dkan insertion was also present in the chromosome. These data strongly suggested that a chromosomal duplication of the lip region was present in strain KER279. This conclusion was strengthened by use of a second lipA null allele. A lipA::lacZ-CAT insertion constructed by T. Morris of this laboratory was transduced into strain KER270 (slr7), and the resulting strain SWJ9 (slr7 lipA::lacZ-CAT) did not require lipoic acid for growth on minimal medium containing glucose. Therefore, the result obtained was independent of the disruption allele used.
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TABLE 1. Bacterial strains and plasmids used in this study
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FIG. 3. Southern blots demonstrate duplication of the lip region of the chromosome. (A) Chromosomal DNAs from strains were prepared (strains given above the lanes). Strain JK1 is the wild-type strain, and strain KER270 is the original slr7 strain. Strains KER176 and TM257 carry the lipA::Tn1000dkan and lipA::lacZ-CAT null alleles, respectively, and are lipoate auxotrophs. Strains KER279 and SWJ9 are slr7 strains that carry a second lipA allele, either lipA:: Tn1000dkan or lipA::lacZ-CAT, respectively. These strains are lipoate prototrophs. The DNAs were digested with EcoRI. The Ladder lane contains molecular size standards. The sizes of the chromosomal fragments (in kilobases) are given to the right of the figure. (B) Southern blots demonstrate that the slr chromosomal duplication is at least 24 kb in length. The products obtained by digestion of the chromosomal DNAs of strains JK1 (wild type) and KER270 (slr7) with several different restriction enzymes are shown. Most of the band in the strain KER270 PstI lane was lost upon transfer. The sizes of the chromosomal fragments (in kilobases) are given to the left of the figure. A map of the chromosomal region of E. coli K-12 is shown at the bottom of panel B. Restriction site abbreviations: B, BamHI; P, PstI; V, EcoRV; H, HindIII; E, EcoRI.
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In this test, we analyzed the progeny of two transductional crosses. In the first cross, we used a phage P1vir lysate grown on strain TM257 (lipA::lacZ-CAT) to transduce strain KER279 (slr7 lipA:Tn1000dkan). In the second cross, we transduced kanamycin resistance into strain SWJ9 (lipA::lacZ-CAT slr7) by use of phage P1vir lysate from strain KER176 (lipA:Tn1000dkan). Transductants resistant to both chloramphenicol and kanamycin were selected in the presence of lipoic acid and then scored for lipoic acid auxotrophy. In both crosses, approximately half of the transductants required lipoic acid for growth, whereas the remaining half grew without lipoic acid. Two prototrophic strains (SWJ36 and SWJ37) and two auxotrophic strains (SWJ34 and SWJ35) were chosen at random and analyzed by Southern blot analysis (Fig. 4). This analysis clearly showed that the auxotrophic strains contained two lipA alleles (lipA::Tn1000dkan and lipA::lacZ-CAT), whereas the prototrophic strains contained three alleles (the two insertion null alleles plus the wild-type allele). Note that it is possible that transduction could remove a copy (or copies) of the amplified region through recombination of the ends of the transducing DNA fragment with the left end of one copy of the chromosomal segment and the right end of another copy. However, in transductions in which the lipA::Tn1000dkan or lipA::lacZ-CAT allele was transduced into the slr7 strain, all of the recombinants were prototrophic. If copies of the amplified region were efficiently removed by transduction, then lipoic acid auxotrophic recombinants should have resulted. Moreover, prior transductional analyses of chromosome duplications (4, 19) and triplications (4) also failed to detect such events. Finally, the branch migration step of current models of homologous recombination (35) would argue against this possibility. Therefore, it seems likely that in slr7 strains the lip region is in flux and some cells may contain two copies of the lip region while other cells contain at least three copies.
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FIG. 4. Variable degrees of lip region amplification in the cells of an slr7 culture. The figure is a Southern blot (EcoRI digestion done as described in the legend to Fig. 3A) analysis of the recombinants from transductional crosses in which a second tagged lipA null mutation was transduced into an slr7 strain that carried a tagged lipA null mutation (see text). Recombinants that grew (Y for yes) or failed to grow (N for no) on glucose-containing minimal medium were analyzed together with the parental strains (all strains grew when supplemented with 5 ng of lipoate per ml). The bands diagnostic for the Tn1000dkan allele, the lipA::lacZ-CAT allele, and the wild-type alleles are the 6.0-, 4.5-, and 4.0-kb bands, respectively. The presence (+) or absence (-) of the Tn1000dkan and lipA::lacZ-CAT alleles are shown under the blot. The smaller lipA null allele bands are not shown because they were indistinct in many lanes due to the high background and their low intensities. The sizes of the chromosomal fragments (in kilobases) are given to the right of the figure.
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TABLE 2. Abilities of various plasmids to confer resistance to Se-lip to two strainsa
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Conclusions. Our data clearly demonstrate that the presence of multiple copies of lipB confers resistance to Se-lip and explains the slr7 phenotype. Prior work from this laboratory showed that lipB was required for posttranslational modification of lipoyl domains using de novo-synthesized lipoate (26). The other characterized Se-lip resistance allele (slr1) is an allele of the lplA (26, 32) gene, which encodes the enzyme responsible for modifying lipoyl domains utilizing exogenously supplied lipoic acid (25, 26). The lipB gene encodes a lipoyl-[acyl carrier protein]-protein N-lipoyltransferase and is essential for the utilization of de novo-synthesized lipoic acid (unpublished data). The ability of extra copies of lipB to confer high-level resistance to Se-lip indicates that increased activity of the lipB gene product increases the level of lipoylation by endogenously synthesized lipoic acid. Upon amplification of this pathway, LipB must effectively compete with the utilization of exogenous Se-lip acid via the LplA-dependent pathway. This competition was demonstrated by the loss of the slr7 Se-lip resistance upon overproduction of LplA (Table 2). Moreover, it seems probable that the capacity of the lipoate synthetic pathway exceeds that of the lipB-mediated attachment to protein, since the presence of additional copies of lipA had no effect on Se-lip resistance (Table 2).
The F', transduction, and Southern blot data show that a very modest (two- to threefold) increase in the dosage of lipB resulted in resistance to levels of Se-lip that completely inhibited growth of the wild-type strain. The expected and more-conventional result was a linear relationship between gene dosage and the level of resistance, such as that seen with E. coli ampC. Progressive stepwise selection of ampicillin-resistant isolates results in strains carrying repetitions of ampC and the neighboring chromosomal markers that give a strict correspondence between the number of ampC copies and the level of ampicillin resistance (11, 12). In the case of Se-lip resistance, no such correspondence was seen. How can a modest increase in gene dosage result in a large increase in resistance to Se-lip? In the case of the slr7 mutation, we believe the answer lies in the unusual structural properties of the 2-oxo acid dehydrogenases. These enzymes are much more complicated than a simple monomeric hydrolyase such as AmpC. The 2-oxo acid dehydrogenases (Fig. 1) are very large protein complexes that catalyze several partial reactions involving three active sites present on three different subunits (28, 29). We believe that the behavior of the slr7 mutant results from the properties of these enzymes plus the fact that wild-type E. coli strains contain levels of the 2-oxo acid dehydrogenases that are in functional excess.
The structures and enzyme mechanism of the 2-oxo acid dehydrogenases are known to combine to give a highly nonlinear relationship between the degree of protein lipoylation and the in vitro activity of the 2-oxoacid dehydrogenase complex (1, 5, 6, 10, 15, 30, 36). The rate-limiting step in the reaction mechanism is decarboxylation of the 2-oxo acid (Fig. 1); thus, the overall rate of a 2-oxo acid dehydrogenase complex is unaffected by significant decreases in the levels of lipoic acid bound to the complex (the cofactor is not required until the subsequent partial reaction) (10). Moreover, a single lipoyl domain is able to productively access many active sites within these very large protein complexes. That is, the lipoyl domain of one E2 subunit can be acetylated by E1 subunits bound to different E2 subunits; therefore, there is only a weak dependence of the overall activity of the complex on the level of protein-bound lipoic acid (1, 5, 6, 10, 15, 30, 36). These conclusions result from a variety of experimental approaches in several laboratories that removed or inactivated major fractions of the lipoyl domains of a 2-oxo acid dehydrogenase complex. Until complete loss of functional lipoyl domains was approached, these manipulations had little or no effect on either the overall enzymatic activity of the complex or on the growth of E. coli strains that required function of the complex (1, 5, 6, 10, 15, 30, 36). The functional redundancy of the lipoyl domains plus the fact that lipoic acid is not involved in the rate-controlling step of the 2-oxo acid dehydrogenase reaction mechanism results in a strikingly nonlinear dependence of dehydrogenase activity on lipoic acid content. For example, a pyruvate dehydrogenase complex having only 2 to 5% of the wild-type level of lipoic acid attachment has been reported to retain about 20% of the activity of the enzyme complex (36). These data indicate that in the presence of Se-lip, virtually all of the lipoyl domains must be modified by the analog in order to inactivate the 2-oxo acid dehydrogenase complexes. Therefore, small increases in the level of lipoic acid attachment resulting from modest overexpression of LipB would be expected to give disproportionate increases in enzyme activity.
The second important factor in lipB-mediated Se-lip resistance is that E. coli does not require full activity of the 2-oxo acid dehydrogenases for growth on minimal medium containing glucose. Thus, the small increases in 2-oxo acid dehydrogenase enzyme activities resulting from lipB duplication would result in large increases in growth. Studies in which nonsense mutations in the genes that encode subunits of either of the dehydrogenase complexes were suppressed by tRNA suppressors of various efficiencies indicate that 10% of the wild-type 2-oxo acid dehydrogenase complex activity levels permits growth on glucose-containing minimal medium (9, 16, 17). Therefore, when the enzymatic and in vivo data are considered in context, they indicate that attachment of lipoic acid in place of Se-lip to a few percent of the 2-oxo acid dehydrogenase complexes would be sufficient for growth. This picture is not only consistent with the behavior of the slr7 mutant but argues strongly that the nonlinear mechanism proposed for the 2-oxo acid dehydrogenases (1, 5, 6, 10, 15, 30, 36) operates in vivo. In order to further test this argument, it would be advantageous to measure the extent of lipoic acid attachment in the slr7 mutant grown with Se-lip. However, lipoic acid is determined by a bioassay using a lipA strain of E. coli (18) and the lipoic acid released by hydrolysis of the 2-oxoacid dehydrogenase complexes would be contaminated with a large excess of Se-lip. Since Se-lip would inhibit growth of the assay strain, use of the bioassay is precluded.
It seems clear that the acquisition of Se-lip resistance in the slr7 strain arose by a recognized pathway. Anderson and Roth (2-4) and Roth et al. (33) argue that 10% of the cells of a culture carry a spontaneously arising duplication of some region of the chromosome. Therefore, within the population of cells spread on Se-lip-supplemented plates, a few cells would have an existing duplication of the lipB region and would survive incorporation of the inhibitor due to their increased ability to attach lipoic acid. We have not determined the maximal number of copies of the lip region in the slr7 mutant strain, but since a derivative carrying three copies can be constructed, the number is at least three. Moreover, the finding that introduction of a F' plasmid (F' plasmids have copy numbers of one or two per cell) carrying the lip chromosomal region results in Se-lip resistance indicates that a two- to threefold increase in lipB is sufficient to give the resistance phenotype.
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-uvrB. J. Bacteriol. 134:778-794.
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