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From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways

Svetlana Y. Gerdes, Michael D. Scholle, Mark D'Souza, Axel Bernal, Mark V. Baev, Michael Farrell, Oleg V. Kurnasov, Matthew D. Daugherty, Faika Mseeh, Boris M. Polanuyer, John W. Campbell, Shubha Anantha, Konstantin Y. Shatalin, Shamim A. K. Chowdhury, Michael Y. Fonstein, Andrei L. Osterman
Svetlana Y. Gerdes
Integrated Genomics Inc., Chicago, Illinois 60612
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Michael D. Scholle
Integrated Genomics Inc., Chicago, Illinois 60612
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Mark D'Souza
Integrated Genomics Inc., Chicago, Illinois 60612
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Axel Bernal
Integrated Genomics Inc., Chicago, Illinois 60612
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Mark V. Baev
Integrated Genomics Inc., Chicago, Illinois 60612
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Michael Farrell
Integrated Genomics Inc., Chicago, Illinois 60612
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Oleg V. Kurnasov
Integrated Genomics Inc., Chicago, Illinois 60612
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Matthew D. Daugherty
Integrated Genomics Inc., Chicago, Illinois 60612
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Faika Mseeh
Integrated Genomics Inc., Chicago, Illinois 60612
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Boris M. Polanuyer
Integrated Genomics Inc., Chicago, Illinois 60612
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John W. Campbell
Integrated Genomics Inc., Chicago, Illinois 60612
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Shubha Anantha
Integrated Genomics Inc., Chicago, Illinois 60612
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Konstantin Y. Shatalin
Integrated Genomics Inc., Chicago, Illinois 60612
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Shamim A. K. Chowdhury
Integrated Genomics Inc., Chicago, Illinois 60612
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Michael Y. Fonstein
Integrated Genomics Inc., Chicago, Illinois 60612
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Andrei L. Osterman
Integrated Genomics Inc., Chicago, Illinois 60612
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  • For correspondence: andrei@integratedgenomics.com
DOI: 10.1128/JB.184.16.4555-4572.2002
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  • FIG. 1.
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    FIG. 1.

    General scheme for E. coli genetic footprinting procedure.

  • FIG. 2.
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    FIG. 2.

    Detection and mapping of transposon insertions. (A) Primer strategy for nested PCR. Transposon-specific primers are shown in gray; chromosome-specific landmark primers are shown in black. (B) The gel image shows analysis of the three chromosomal loci: aspC (nonessential) and lpdA and ftsJ (essential) at time zero (lanes 1, 3, and 5) and after outgrowth (lanes 2, 4, and 6). ORF locations are marked relative to each pair of lanes. Several inserts are visible in lpdA and ftsJ at time zero, while none can be detected after outgrowth. The nonessential aspC contains insertions at both time points. (C to E) Examples of genetic footprints. Note that the scale is different in each panel. The length and direction of each gene are indicated by the large horizontal gray arrows. Black diamonds represent transposon inserts. The width of each diamond corresponds to the mapping error introduced by gel electrophoresis. The positions of the landmark PCR primers are shown by bows crossing the genes, as well as by arrows above the genes. (C) Genetic footprinting of the ftsK locus in MG1655. Only the 3′ half of this essential gene contains inserts. (D) Genetic footprinting of the coaD locus in MG1655. A transposon insertion immediately upstream of this essential gene apparently does not interfere with its expression. (E) Mapping of the Δ(ara-leu)7697 deletion in DH10B. The genetic footprint of the corresponding region in MG1655 is shown for comparison.

  • FIG. 3.
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    FIG. 3.

    Simplified diagrams, illustrating the biochemical transformations directly involved in the biosynthesis of NAD(P) (A), CoA (B), and FMN/FAD (C). Most of the pathways and genes shown are those present in E. coli, with the few exceptions marked by dashed lines. Recycling pathways and other transformations related to genes that remain unknown (such as NMN deamidase) are not included.

  • FIG. 4.
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    FIG. 4.

    Selection of antibacterial drug targets by a combination of genetic footprinting in E. coli and comparative analysis of reconstructed metabolic subsystems, pathways, and individual genes in pathogens and humans.

  • FIG. 5.
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    FIG. 5.

    Prioritization of potential broad-spectrum antibacterial drug targets in biosynthetic pathways of NAD(P), CoA, and FAD. Three criteria are shown for each target enzyme (marked by abbreviations along the x axis). (A) Range of pathogens. A number of pathogens (from the representative set) containing the given target enzyme (and included in building of the corresponding HMM) are represented by filled bars. Organisms not containing this target enzyme and therefore excluded from the spectrum are indicated inside open bars (by two-letter abbreviations). (B) Compact pathogen subsets and outliers. Negative logarithms of the E values indicate how closely each bacterial sequence is related to the probabilistic consensus of the corresponding profile HMM (larger values indicate higher similarity). Subsets of pathogens with target orthologs most closely related to the consensus are shown inside dotted boxes. Outliers are indicated by two-letter organism abbreviations. Organisms shown are P. aeruginosa (○) (PA), B. anthracis (▾) (BA), M. tuberculosis (▿) (MT), H. pylori (▪) (HP), S. pneumoniae (□) (PN), S. aureus (♦) (SA), M. genitalium (⋄) (MG), H. influenzae (▴) (HI), C. trachomatis (▵) (CT), and E. coli (•). The E. coli proteins are very similar to those of Yersinia pestis and Salmonella enterica serovar Typhi. (C) Human counterparts: distance from bacterial families. The negative logarithms of the E values of human counterpart sequences compared to the corresponding bacterial HMMs (smaller values indicate higher divergence of the human enzyme from the corresponding bacterial family). ∗∗, HMM E values for these human proteins are higher than the threshold (>10,000).

  • FIG. 6.
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    FIG. 6.

    General scheme of chemical transformations catalyzed by the three adenylyltransferases (ATse) in the biosynthesis of NAD(P), CoA, and FAD. These enzymes—NaMNAT (encoded in E. coli by nadD), PPAT (gene coaD), and FADS (ribF)—were selected as the most promising antibacterial drug targets within these pathways.

Tables

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  • TABLE 1.

    Genetic footprinting of E. coli genes related to metabolism of adenylate cofactors NAD(P), CoA, and FAD

    Biosynthetic subsystemGeneORF size (bp)No. of inserts in ORF in strain:Conclusionb
    MG1655DH10B
    NAD nadB 1,6209NDN
    nadA 1,04112NDN
    nadC 89114N
    ushA 1,6506NDN
    pnuC 7174NDN
    nadR 1,25164N
    pncA 6572NDN
    pncB 1,2008NDN
    nadD (ybeN)63914Ec
    nadE 82501E
    nadF (yfiB)87600E
    CoA panD 37820N
    panB 79213N
    panE 90952N
    panC 84915N
    coaA 94800E
    coaBC (dfp)1,29000E
    coaD (kdtB)47700E
    coaE (yacE)61800E
    acpS 37800E
    FMN/FAD ribA 58800E
    ribD 1,10100E
    ribB 65100E
    ribH 46800E
    ribE 63900E
    ribF (yaaC)93900E
    • a The number of transposon insertions per gene in strains MG1655 and DH10B detected after logarithmic aerobic outgrowth for 23 population doublings in rich medium is shown.

    • ↵ b Assessments of gene essentiality, based on results of genetic footprinting in strains MG1655 and DH10B. E, essential; N, nonessential; ND, not determined.

    • ↵ c nadD appeared to be nonessential in the two genetic footprinting experiments but was then shown to be essential by a directed-knockout technique.

  • TABLE 2.

    Functional reconstruction of metabolic pathways of NAD/NADP biosynthesisa

    NAD(P) biosynthesisEC no.Protein examplePresence of ortholog or pathway in genome of:
    E. colibP. aeruginosaB. anthracisM. tuberculosisH. pyloriS. pneumoniaeS. aureusM. genitaliumH. influenzaeC. trachomatisH. sapiens
    De novo pathways to NaMNYesYesYesYesYesNoNoNoNoNoYes
        (I) Tryptophan to quinolinate−−−−−−−−−−+
        (II) Aspartate to quinolinate
            Aspartate oxidase1.4.3.16gi|16130499 nadB ++++−−−−−−
            Quinolinate synthasegi|16128718 nadA ++++−−−−−−
        Quinolinate to NaMN
            Quinolinate phosphoribosyl transferase2.4.2.19gi|16128102 nadC ++++−−−−−+
    Salvage: from niacin to NaMN/NMNYesYesYesYeseNoYesYesYesNoNoYes
        (I) Nicotinamide to NaMN
            Nicotinamide deamidase3.5.1.19gi|140602 pncA +++−++−−−−
            Nicotinate phosphoribosyl transferase2.4.2.11gi|16128898 pncB +++−++−−−−
        (II) Nicotinamide to NMN
            Nicotinamide phosphoribosyl transferase (nadVc)2.4.2.12gi|13629024−−−−−−−+−−+
    Salvage: from exogenous NMN to NADYesYesNoNoNoNoNoNoYesNoNo
            NMN phosphohydrolase (extracellular) (nadNd)3.1.3.5gi|1573165 ushA −+−−−−−+−+
            Pyridine nucleoside transportergi|16273640 pnuC ++−++−−+−−
            Nicotinamide ribose kinasef2.7.1.22gi|16132207 nadR +− + −−−− + −−
            NMN adenylyltransferase
                (i) NMN specific (archaea, some bacteria)2.7.7.1gi‖16132207 nadR −− + −−−− + −−
                (ii) NaMN/NMN specific (eukarya)2.7.7.1/18gi|11245478−−−−−−−−−−+
    Common pathway to NAD/NADPYesYesYesYesYesYesYesYesYesNoYes
        NaMN to NAD
            NaMN adenylyltransferase
                (i) NaMN specific (most bacteria)2.7.7.18gi|1723307 nadD +++++++−−−
                (ii) NaMN/NMN specific (eukarya)2.7.7.1/18gi|11245478−−−−−−−−−−+
            NAD synthetase6.3.5.1gi|16129694 nadE +++++++−−+
        NAD to NADP
            NAD kinase2.7.1.23gi|8489010 nadF ++++++++−+
    • ↵ a Subsystems, pathways, and individual functional roles (specified by Enzyme Classification [EC] numbers) involved in adenylate cofactor biosynthesis in all relevant organisms are presented as nodes and branches (rows) of a hierarchical tree. Proteins are shown by representative examples (GenBank ID numbers). The presence (+) or absence (−) of an orthologous gene in a specific genome is marked in the column corresponding to this organism, except for E. coli, where actual gene names are given. Alternative pathways within a subsystem are indicated by uppercase roman numerals. Nonorthologous genes with the same functional role are shown in separate rows and indicated by lowercase roman numerals. Bifunctional (fused) proteins with more than one functional domain are shown in boldface type. “Yes” indicates that a particular subsystem can be asserted in a given organism by the presence of required genes (enzymatic functions) in its genome. “No” indicates that a particular subpathway cannot be asserted in an organism on the basis of genomic data alone. Functional roles inferred by metabolic context analysis but not associated with specific genes (“missing genes”) are indicated by question marks.

    • ↵ b Identical patterns of pathways with very similar genes are found in E. coli, Salmonella enterica serovar Typhi, and Yersinia pestis in all of the subsystems considered.

    • ↵ c Identified in Haemophilus ducreyi; present in V factor-independent Pasteurellaceae, but not in H. influenzae (62).

    • ↵ d Identified in H. influenzae (76); closest homolog in E. coli is ushA.

    • ↵ e Experimental data suggest that this pathway is not functional in M. tuberculosis (83).

    • ↵ f The corresponding function in E. coli and H. influenzae is catalyzed by the C-terminal domain of the multifunctional protein NadR (O. Kurnasov et al., unpublished data).

  • TABLE 3.

    Functional reconstruction of metabolic pathways of CoA biosynthesisa

    CoA biosynthesisEC no.Protein examplePresence of ortholog or pathway in genome of:
    E. colibP. aeruginosaB. anthracisM. tuberculosisH. pyloriS. pneumoniaeS. aureusM. genitaliumH. influenzaeC. trachomatisH. sapiens
    De novo pathway to pantothenateYesYesYesYesYesNoYesNoNoNoNo
        Aspartate to β-alanine
            Aspartate 1-decarboxylase4.1.1.11gi|1786323 panD ++++−+−−−−
        Ketovalerate to pantoate
            3-Methyl-2-oxobutanoate hydroxymethyl transferase2.1.2.11gi|1786326 panB ++++−+−−−−
            2-Dehydropantoate 2-reductase
                (i) 2-Dehydropantoate 2-reductase1.1.1.169gi|1100871 panE +++−−+−−−−
                (ii) Ketol-acid reductoisomerase1.1.1.86gi|146477 ilvC ++++++−+−−
        β-Alanine, pantoate to pantothenate
            Pantoate-β-alanine ligase6.3.2.1gi|1786325 panC ++++−+−−−−
    Pantothenate (vitamin B5) salvageYesYesYesYesYesYesYesNoYesNoYes
            Sodium/pantothenate symportergi|455654 panF ++++++−+−+
    Common pathway to CoAYesYesYesYesYesYesYesNoYesNoYes
            Pantothenate kinase?f?f
                (i) Most bacteria2.7.1.33gi|1790409 coaA −−+−+−−+−−
                (ii) Eukarya2.7.1.33gi|6320740c−−+−−−+−−−+
            Phosphopantothenoylcysteine synthetase6.3.2.5gi|1790070 coaB e + + + + + + − + −+
            Phosphopantothenoylcysteine decarboxylase4.1.1.36gi|1790070 coaC e + + + + + + − + −+
            Pantetheine-phosphate adenylyltransferase
                (i) Bacteria2.7.7.3gi|1790065 coaD ++++++−+−−
                (ii) Eukarya2.7.7.3gi|632171d−−−−−−−−−− +
            Dephospho-CoA kinase2.7.1.24gi|1786292 coaE +++++++++ +
    • ↵ a See Table 2, footnote a, for details.

    • ↵ b Identical patterns of pathways with very similar genes are found in E. coli, Salmonella enterica serovar Typhi, and Yersinia pestis in all of the subsystems considered.

    • ↵ c Eukaryotic pantothenate kinase (21), structurally unrelated to the corresponding E. coli enzyme (CoaA family).

    • ↵ d Eukaryotic pantetheine-phosphate adenylyltransferase is only distantly related to the corresponding bacterial enzymes (beyond recognition by Psi-Blast) (27); it forms a fusion protein with dephospho-CoA kinase in higher eukaryotes.

    • ↵ e In most bacteria (except S. pneumoniae in this set), CoaB is the C-terminal domain, and CoaC is the N-terminal domain of a bifunctional protein.

    • ↵ f Pantothenate kinase is still a “missing gene” in a number of bacterial pathogens.

  • TABLE 4.

    Functional reconstruction of metabolic pathways of FMN/FAD biosynthesisa

    FMN/FAD biosynthesisEC no.Protein examplePresence of ortholog or pathway in genome of:
    E. colibP. aeruginosaB. anthracisM. tuberculosisH. pyloriS. pneumoniaeS. aureusM. genitaliumH. influenzaeC. trachomatisH. sapiens
    De novo pathways to riboflavinYesYesYesYesYesYesYesNoYesYesNo
        Ribuloso-5-phosphate to l-3,4-dihydroxy-2-butanone-4-phosphate
            3,4-Dioxy-2-butanone-4-phosphate synthetase4.1.2.-gi|1789420 ribB c + + + + + + −+ + −
        GTP to 5-amino-6-ribitylamino-2,4-(1H,3H)-pyrimidinedione
            GTP cyclohydrolase II3.5.4.25gi|16129238 ribA c + + + + + + −+ + −
            Pyrimidine deaminase3.5.4.26gi|1786616 ribD d + + + + + + − + + −
            Pyrimidine reductase1.1.1.193gi|1786616 ribD d + + + + + + − + + −
            Pyrimidine phosphatase3.1.3???????−??−
        l-3,4-Dihydroxy-2-butanone-4-phosphate, 5-amino-6-ribitylamino-2,4-         (1H,3H)-pyrimidinedione to riboflavin
            6,7-Dimethyl-8-ribityl-lumazine synthase2.5.1.9gi|16128400 ribH ++++++−++−
            Riboflavin synthase2.5.1.9gi|16129620 ribE ++++++−++−
    Riboflavin (vitamin B2) salvageNoNoYesNoNoYesYesYesNoNoYes
            Riboflavin transporter (ypaA)egi|16079362−−+−−++?−−?
    Common pathway to FMN/FADYesYesYesYesYesYesYesYesYesYesYes
            Riboflavin kinase2.7.1.26gi|16128019 ribF f + + + + + + + + + +
            FAD synthetase2.7.7.2
                (i) Bacteriagi|16128019 ribFf + + + + + + + + + −
                (ii) Eukaryagi|6320159g−−−−−−−−−−+
    • ↵ a See Table 2, footnote a, for details.

    • ↵ b Identical patterns of pathways with very similar genes are found in E. coli, Salmonella enterica serovar Typhi, and Yersinia pestis in all of the subsystems considered.

    • ↵ c RibA and RibB form a bifunctional (fused) protein in many bacteria and monofunctional separate proteins in E. coli and H. influenzae.

    • ↵ d RibD is a bifunctional (fused) protein in most bacteria.

    • ↵ e Riboflavin transporter originally identified in B. subtilis (56).

    • ↵ f RibF is a bifunctional (fused) protein in most bacteria.

    • ↵ g Eukaryotic FAD synthase originally identified in S. cerevisiae (100) has no detectable sequence similarity with corresponding bacterial enzymes.

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From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways
Svetlana Y. Gerdes, Michael D. Scholle, Mark D'Souza, Axel Bernal, Mark V. Baev, Michael Farrell, Oleg V. Kurnasov, Matthew D. Daugherty, Faika Mseeh, Boris M. Polanuyer, John W. Campbell, Shubha Anantha, Konstantin Y. Shatalin, Shamim A. K. Chowdhury, Michael Y. Fonstein, Andrei L. Osterman
Journal of Bacteriology Aug 2002, 184 (16) 4555-4572; DOI: 10.1128/JB.184.16.4555-4572.2002

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From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways
Svetlana Y. Gerdes, Michael D. Scholle, Mark D'Souza, Axel Bernal, Mark V. Baev, Michael Farrell, Oleg V. Kurnasov, Matthew D. Daugherty, Faika Mseeh, Boris M. Polanuyer, John W. Campbell, Shubha Anantha, Konstantin Y. Shatalin, Shamim A. K. Chowdhury, Michael Y. Fonstein, Andrei L. Osterman
Journal of Bacteriology Aug 2002, 184 (16) 4555-4572; DOI: 10.1128/JB.184.16.4555-4572.2002
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KEYWORDS

Coenzyme A
Escherichia coli
Flavin-Adenine Dinucleotide
NADP

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