Identification, substrate specificity, and inhibition of the Streptococcus pneumoniae beta-ketoacyl-acyl carrier protein synthase III (FabH).

In the bacterial type II fatty acid synthase system, beta-ketoacyl-acyl carrier protein (ACP) synthase III (FabH) catalyzes the condensation of acetyl-CoA with malonyl-ACP. We have identified, expressed, and characterized the Streptococcus pneumoniae homologue of Escherichia coli FabH. S. pneumoniae FabH is approximately 41, 39, and 38% identical in amino acid sequence to Bacillus subtilis, E. coli, and Hemophilus influenzae FabH, respectively. The His-Asn-Cys catalytic triad present in other FabH molecules is conserved in S. pneumoniae FabH. The apparent K(m) values for acetyl-CoA and malonyl-ACP were determined to be 40.3 and 18.6 microm, respectively. Purified S. pneumoniae FabH preferentially utilized straight short-chain CoA primers. Similar to E. coli FabH, S. pneumoniae FabH was weakly inhibited by thiolactomycin. In contrast, inhibition of S. pneumoniae FabH by the newly developed compound SB418011 was very potent, with an IC(50) value of 0.016 microm. SB418011 also inhibited E. coli and H. influenzae FabH with IC(50) values of 1.2 and 0.59 microm, respectively. The availability of purified and characterized S. pneumoniae FabH will greatly aid in structural studies of this class of essential bacterial enzymes and facilitate the identification of small molecule inhibitors of type II fatty acid synthase with the potential to be novel and potent antibacterial agents active against pathogenic bacteria.

rho is not essential for viability or virulence in Staphylococcus aureus.

We have identified the gene for transcription termination factor Rho in Staphylococcus aureus. Deletion of rho in S. aureus reveals that it is not essential for viability or virulence. We also searched the available bacterial genomic sequences for homologs of Rho and found that it is broadly distributed and highly conserved. Exceptions include Streptococcus pneumoniae, Streptococcus pyogenes, Mycoplasma genitalium, Mycoplasma pneumoniae, Ureaplasma urealyticum, and Synechocystis sp. strain PCC6803, all of which appear not to possess a Rho homolog. Complementation studies indicate that S. aureus Rho possesses the same activity as Escherichia coli Rho and that the Rho inhibitor bicyclomycin is active against S. aureus Rho. Our results explain the lack of activity of bicyclomycin against many gram-positive bacteria and raise the possibility that the essentiality of rho may be the exception rather than the rule.

The impact of genomics on novel antibacterial targets.

Antibiotic discovery has remained primarily focused on improving versions of existing classes of antibiotics which work on a limited set of bacterial targets. In addition, the characterization of these targets has focused almost entirely on Escherichia coli homologs. The advancing problems associated with resistant pathogens has driven a critical need for the discovery of new classes of antibiotics which will target novel bacterial functions required for viability and pathogenicity. Recent advances in DNA sequencing technology have now made it possible to elucidate the entire genomes of pathogenic bacteria. Comparative analysis of these genome sequences, driven by advancements in the availability of bioinformatic tools, is dramatically increasing our ability to interrogate the spectrum and selectivity of novel antibacterial target areas. In this review, we present an update on the antibiotic target areas of tRNA synthetases, two-component signal transduction systems, peptidoglycan biosynthesis, fatty acid biosynthesis and chorismate biosynthesis. We illustrate how the availability of genomes from a range of clinically important pathogens has enabled valid considerations of the limitations and advantages of particular targets based on their predicted spectrum and selectivity. Furthermore, we demonstrate how genomics is facilitating the characterization of targets from relevant pathogens and how these data, coupled with genomic-based technologies, provide new approaches for drug discovery.

Isolation and characterization of a sigB deletion mutant of Staphylococcus aureus.

The sigB gene of Staphylococcus aureus, coding for the alternate sigma factor B, has been deleted by allelic replacement mutagenesis. The mutant grew as well as the parent in vitro, although it was deficient in clumping factor, coagulase, and pigment. In two murine and one rat infection model the mutant showed no reduction in virulence.

Mutational analysis of the Escherichia coli spoT gene identifies distinct but overlapping regions involved in ppGpp synthesis and degradation.

The spoT gene of Escherichia coli encodes a guanosine 3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (ppGppase) as well as an apparent guanosine 3',5'-bis(diphosphate) synthetase (designated PSII). To determine the regions of the SpoT protein that are required for these two competing activities, we analysed plasmid-borne deletion mutations for their ability to complement chromosomal mutations defective in each activity. We found that a region containing the first 203 amino acids of the 702-amino-acid SpoT protein was sufficient for ppGppase activity while an overlapping region containing residues 67-374 was sufficient for PSII activity. These data indicate that the catalytic sites involved in the two activities are separate but closely linked in the primary sequence of the SpoT protein. A ppGppase-defective delta 1-58 deletion mutant strain failed to synthesize ppGpp in response to nutrient limitation, also supporting the notion that PSII activity from wild-type SpoT does not increase in response to nutrient limitation. Using a strain lacking PSII activity but retaining ppGppase activity, we determined the contribution of the RelA protein (ppGpp synthetase I, PSI) to ppGpp synthesis following glucose starvation. We found that the RelA protein activity accounts for the initial burst of ppGpp synthesis at the onset of glucose starvation but that this source of synthesis is absent when amino acids are present during glucose starvation.

Cellular localization of the Escherichia coli SpoT protein.

The SpoT protein of Escherichia coli serves as a source of degradation as well as an apparent source of synthesis of (p)ppGpp. Since the subcellular localization of SpoT might be a clue to its function, we have used SpoT-specific antisera to analyze cell extracts fractionated on sucrose gradients. We find that the SpoT protein is not bound to ribosomes or to either inner or outer membrane fractions. Although the SpoT protein is found in large aggregates, its localization is probably cytosolic.

Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp.

Strains of Escherichia coli which lack detectable guanosine 3',5'-bispyrophosphate (ppGpp) display a pleiotropic phenotype that in some respects resembles that of rpoS (katF) mutants. This led us to examine whether ppGpp is a positive regulator of sigma s synthesis. sigma s is a stationary-phase-specific sigma factor that is encoded by the rpoS gene. We found that a ppGpp-deficient strain is defective in sigma s synthesis as cells enter stationary phase in a rich medium, as judged by immunoblots. Under more-defined conditions we found that the stimulation of sigma s synthesis following glucose, phosphate, or amino acid starvation of wild-type strains is greatly reduced in a strain lacking ppGpp. The failure of ppGpp-deficient strains to synthesize sigma s in response to these starvation regimens could indicate a general defect in gene expression rather than a specific dependence of rpoS expression on ppGpp. We therefore tested the effect of artificially elevated ppGpp levels on sigma s synthesis either with mutations that impair ppGpp decay or by gratuitously inducing ppGpp synthesis with a Ptac::relA fusion. In both instances, we observed enhanced sigma s synthesis. Apparently, ppGpp can activate sigma s synthesis under conditions of nutrient sufficiency as well as during entry into stationary phase. This finding suggests that changes in ppGpp levels function both as a signal of imminent stationary phase and as a signal of perturbations in steady-state growth.

In vitro functional characterization of overproduced Escherichia coli katF/rpoS gene product.

The katF/rpoS gene product (sigma s), a central regulator of stationary-phase gene expression in Escherichia coli, has been purified from an overproducing strain. sigma s was used as an immunogen for the production of monoclonal antibodies. Previous sequence analysis of sigma s strongly indicated homology to the sigma factor family. We show biochemically in this paper that sigma s is a sigma factor. This protein can bind to core RNA polymerase (E), and this binding can be competed effectively by the major E. coli transcription initiation factor, sigma 70. Immunopurified sigma s holoenzyme (E sigma s) transcribes the promoters of the bolAp1 gene and the xthA gene. Interestingly, both promoters can also be transcribed by sigma 70 holoenzyme (E sigma 70).

Cross-linking of Escherichia coli RNA polymerase subunits: identification of beta' as the binding site of omega.

The omega protein is a peptide found in near-stoichiometric levels in highly purified Escherichia coli RNA polymerase. In order to determine the binding site of omega to RNA polymerase, we cross-linked omega to RNA polymerase with the hetero-bifunctional cross-linker N-hydroxysuccinimidyl 4-azidobenzoate and analyzed for cross-linked partners using antibodies raised against each of the subunits. Our analysis indicates that omega cross-links predominantly with the beta' subunit, while a very low level of cross-linking was detected to the alpha subunit. We did not detect cross-linking to either the sigma 70 or the beta subunits. This report demonstrates the utility of combining cross-linking and immunological techniques to determine interactions between RNA polymerase subunits.

Characterization of the Escherichia coli K12 gltS glutamate permease gene.

The gltS gene is known to encode a sodium-dependent, glutamate-specific permease. We have localized the Escherichia coli K12 gltS gene with respect to the spoT gene, sequenced it, and recombined a null insertion-deletion allele into the chromosome without loss of viability. The gltS null allele gives a Glt- phenotype, i.e. it abolishes the ability of a gltCc host to grow on glutamate as sole carbon and nitrogen source and also confers alpha-methylglutamate resistance. A multicopy plasmid expressing the gltS gene can reverse the Glt- phenotype of gltS- or wild-type strains while other plasmids show host-dependent complementation patterns. Induction of gltS gene overexpression under control of isopropyl-beta-D-thiogalactoside (IPTG)-inducible promoters severely inhibits growth. The GltS protein is deduced to be a 42425 dalton hydrophobic protein with 2 sets of 5 possible integral protein domains, each flanking a central hydrophilic, flexible region.

Overproduction and purification of the omega subunit of Escherichia coli RNA polymerase.

This paper reports the construction of plasmids which direct the overproduction of the omega subunit of Escherichia coli RNA polymerase and the subsequent purification of omega. Useful overproduction is achieved only if the natural ribosomal binding site region of rpoZ is replaced with the ribosomal binding site region of bacteriophage T7 gene 10. Overproduction is directed by T7 RNA polymerase which is provided on a separate plasmid. omega is purified by three column steps either from the insoluble inclusion body fraction or from the soluble fractions of lysates. The final yield is approximately 2 mg omega per 10 g cells wet wt. Additionally, we found that recombinant omega is readily cleaved by an endogenous protease. Sequence analysis of the most prevalent proteolytic fragment suggested that the protease responsible was the product of the ompT gene. Cleavage of omega is greatly reduced in ompT- strains.

rpoZ, encoding the omega subunit of Escherichia coli RNA polymerase, is in the same operon as spoT.

Highly purified Escherichia coli RNA polymerase contains a small subunit termed omega. This subunit consists of 91 amino acids with a molecular weight of 10,105. We previously reported the cloning and sequencing of the gene encoding omega, which we call rpoZ (D. R. Gentry and R. R. Burgess, Gene 48:33-40, 1986). We constructed an rpoZ insertion mutation by placing a kanamycin resistance cassette into the coding region of the rpoZ gene. Purified RNA polymerase from strains carrying this mutation lacked detectable omega. We found that the insertion mutation conferred a slow-growth phenotype when introduced into most strains. We mapped the position of rpoZ on the E. coli chromosome by genetic techniques and by examining the restriction map of the whole chromosome and found that rpoZ maps around 82 min, very close to spoT. We determined that the slow-growth phenotype of the insertion mutant is suppressed in relA mutants and that the rpoZ insertion results in a classical SpoT- phenotype. This finding strongly suggests that rpoZ is upstream of spoT in the same operon and that the slow-growth phenotype elicited by the insertion mutation is due to polarity on spoT.

The cloning and sequence of the gene encoding the omega subunit of Escherichia coli RNA polymerase.

Omega is a small protein found associated with Escherichia coli RNA polymerase. The role of omega, if any, in transcription is not known. We have cloned the omega-encoding gene (rpoZ) so that we can produce large amounts of omega by over-production and to introduce mutations in its gene. We determined the N-terminal amino acid (aa) sequence of omega by aa microsequencing. Using the sequence we synthesized an eight-fold ambiguous 14-mer oligodeoxynucleotide probe and screened an E. coli genomic library using the base composition independent method of hybridization reported by Wood et al. [Proc. Natl. Acad. Sci. USA 82 (1985) 1585-1588]. With this method we isolated a clone that contained part of rpoZ which we used as a probe to isolate the complete gene. The sequence of the region containing the rpoZ gene predicts a highly charged protein of 91 aa with an Mr of 10 105. In addition, upstream from the gene is a good promoter-like sequence. We have verified by S1 mapping that in vivo transcripts originate from this promoter and possibly from a second promoter farther upstream.