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

Gerdes, Svetlana; Scholle, Michael D.; D’Souza, Mark; Bernal, Axel; Baev, Mark V.; Farrell, Michael; Kurnasov, Oleg V.; Daugherty, Matthew D.; Mseeh, Faika; Polanuyer, Boris; Campbell, John W.; Anantha, Shubha; Shatalin, Konstantin; Chowdhury, Shamim; Fonstein, Michael; Osterman, Andrei L.

doi:10.1128/jb.184.16.4555-4572.2002

Cited by 255 publications

(279 citation statements)

References 87 publications

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“…With specific reference to CoASH biosynthesis in B. anthracis, Gerdes et al (50) published an analysis of potential broadspectrum antimicrobial drug targets among cofactor biosynthetic pathways; all four coa gene products in E. coli were concluded to be individually "essential," as was the acpS gene product which synthesizes the holo-acyl carrier protein from CoASH + apo-acyl carrier protein (51). Using the ERGO database and the B. anthracis Ames genome sequence, the predicted CoASH biosynthetic pathway for the anthrax pathogen was analyzed with the aid of the known E. coli pathway (50). All components of the de novo Pan biosynthetic pathway, as well as the Na + /Pan transporter, were identified (presence of the orthologous gene); similar results were found for the pathway from Pan→CoASH, except for the type I PanK.…”

Section: Panks In B Anthracismentioning

confidence: 99%

Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 Å Resolution: Implications for Coenzyme A-Dependent Redox Biology^,

Parsonage

Paige

et al. 2007

Biochemistry

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Coenzyme A (CoASH) is the major low-molecular weight thiol in Staphylococcus aureus and a number of other bacteria; the crystal structure of the S. aureus coenzyme A-disulfide reductase (CoADR), which maintains the reduced intracellular state of CoASH, has recently been reported [Mallett, T.C., Wallen, J.R., Karplus, P.A., Sakai, H., Tsukihara, T., and Claiborne, A. (2006) Biochemistry 45, 11278-11289]. In this report we demonstrate that CoASH is the major thiol in Bacillus anthracis; a bioinformatics analysis indicates that three of the four proteins responsible for † This work was supported by National Institutes of Health (NIH) Grants GM-35394 (A.C), AI-49174 (R.C.F.), and GM-62896 (S.J.), by a grant from the Southeast Regional Center of Excellence for Biodefense and Emerging Infections (SERCEB, to A.C.), and by Cancer Center (CORE) Support Grant CA21765 and ALSAC (S.J.). C.P. was the recipient of a Graduate Fellowship from the U.S. Department of Homeland Security (DHS). SERCEB is supported by an award from the NIH (National Institute of Allergy and Infectious Diseases; NIAID). The DHS Scholarship and Fellowship Program is administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement with the U.S. Department of Energy (DOE). ORISE is managed by Oak Ridge Associated Universities under DOE contract number DE-AC05-06OR23100. The findings, opinions, and recommendations expressed in this paper are those of the authors and are not necessarily those of NIAID, SERCEB, NIH, DHS, DOE, or ORISE. Data for this study were measured at beamline X12C of the National Synchrotron Light Source. With the identification of two distinct new bacterial pantothenate kinase classes in 2005, different investigators have used either type I, -II, and -III CoaAs (e.g., type II Staphylococcus aureus CoaA) or PanK-I, -II, and -III nomenclature to identify the three bacterial enzyme classes. In this report we refer to the three bacterial enzyme classes as bacterial type I, type II, and type III PanKs; CoaA is synonymous with the type I PanK. 5 J. Ravel, personal communication. Supporting Information Available A figure depicting a structure-based alignment of 13 type III PanK sequences ( Figure S1) is included as Supporting Information (one page). This material is available free of charge via the Internet at http://pubs.acs.org NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2009 January 5. In contrast, a novel type III pantothenate kinase (PanK) catalyzes the first committed step in the biosynthetic pathway in B. anthracis; unlike the E. coli type I PanK, this enzyme is not subject to feedback inhibition by CoASH. The crystal structure of B. anthracis PanK (BaPanK), solved using multiwavelength anomalous dispersion data and refined at a resolution of 2.0 Å, demonstrates that BaPanK is a new member of the Acetate and Sugar Kinase/Hsc70/Actin (ASKHA) superfamily. The Pan and ATP substrates have been modeled into the active-site cleft; in addition to prov...

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Section: Panks In B Anthracismentioning

confidence: 99%

Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 Å Resolution: Implications for Coenzyme A-Dependent Redox Biology^,

Parsonage

Paige

et al. 2007

Biochemistry

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“…These include several cofactors such as biotin, pantothenate, and riboflavin, as well as the electron carriers flavin mononucleotide and flavin adenine dinucleotide. These unavailable nutrients are particularly interesting from a therapeutic perspective, because bacteria-specific pathways for biosynthesis of these metabolites may represent novel therapeutic targets (31,32). Thus, although CF sputum is an amino acid-rich environment our comparative Tn-seq approach reveals that it is relatively cofactor-poor.…”

Section: The Essential Genomes Of Multiple P Aeruginosa Strains In Cmentioning

confidence: 99%

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum

Turner

Wessel

Palmer

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

366

491

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Defining the essential genome of bacterial pathogens is central to developing an understanding of the biological processes controlling disease. This has proven elusive for Pseudomonas aeruginosa during chronic infection of the cystic fibrosis (CF) lung. In this paper, using a Monte Carlo simulation-based method to analyze high-throughput transposon sequencing data, we establish the P. aeruginosa essential genome with statistical precision in laboratory media and CF sputum. Reconstruction of the global requirements for growth in CF sputum compared with defined growth conditions shows that the latter requires several cofactors including biotin, riboflavin, and pantothenate. Comparison of P. aeruginosa strains PAO1 and PA14 demonstrates that essential genes are primarily restricted to the core genome; however, some orthologous genes in these strains exhibit differential essentiality. These results indicate that genes with similar molecular functions may have distinct genetic roles in different P. aeruginosa strains during growth in CF sputum. We also show that growth in a defined growth medium developed to mimic CF sputum yielded virtually identical fitness requirements to CF sputum, providing support for this medium as a relevant in vitro model for CF microbiology studies.

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“…Nonetheless, this version of pantothenate kinase is also inhibited by N5-Pan and N7-Pan, and the analogs are toxic to S. aureus (31). Other bacteria such as Pseudomonas aeruginosa and Helicobacter pylori do not have a recognizable pantothenate kinase gene in their chromosomes, although they clearly have the other four genes that comprise the CoA biosynthetic pathway (32,33). In these organisms, the gene for pantothenate kinase needs to be identified, and its ability to use the pantothenamides as substrates should be examined.…”

Section: Formation Of Faster Migrating Acps In Cells Treated With Thementioning

confidence: 99%

Acyl Carrier Protein Is a Cellular Target for the Antibacterial Action of the Pantothenamide Class of Pantothenate Antimetabolites

Zhang

Frank

Virga

et al. 2004

Journal of Biological Chemistry

124

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Pantothenate is the precursor of the essential cofactor coenzyme A (CoA). Pantothenate kinase (CoaA) catalyzes the first and regulatory step in the CoA biosynthetic pathway. The pantothenate analogs N-pentylpantothenamide and N-heptylpantothenamide possess antibiotic activity against Escherichia coli. Both compounds are substrates for E. coli CoaA and competitively inhibit the phosphorylation of pantothenate. The phosphorylated pantothenamides are further converted to CoA analogs, which were previously predicted to act as inhibitors of CoA-dependent enzymes. Here we show that the mechanism for the toxicity of the pantothenamides is due to the inhibition of fatty acid biosynthesis through the formation and accumulation of the inactive acyl carrier protein (ACP), which was easily observed as a faster migrating protein using conformationally sensitive gel electrophoresis. E. coli treated with the pantothenamides lost the ability to incorporate [1-14 C]acetate to its membrane lipids, indicative of the inhibition of fatty acid synthesis. Cellular CoA was maintained at the level sufficient for bacterial protein synthesis. Electrospray ionization time-of-flight mass spectrometry confirmed that the inactive ACP was the product of the transfer of the inactive phosphopantothenamide moiety of the CoA analog to apo-ACP, forming the ACP analog that lacks the sulfhydryl group for the attachment of acyl chains for fatty acid synthesis. Inactive ACP accumulated in pantothenamide-treated cells because of the active hydrolysis of regular ACP and the slow turnover of the inactive prosthetic group. Thus, the pantothenamides are pro-antibiotics that inhibit fatty acid synthesis and bacterial growth because of the covalent modification of ACP.CoA is the major acyl group carrier in living systems and is synthesized by a universal series of reactions beginning with the vitamin (B 5 ) pantothenate (1). All of the genes and enzymes involved in the CoA biosynthetic pathway have been identified in Escherichia coli (Fig. 1). The first step in the pathway is catalyzed by the key rate-controlling pantothenate kinase (CoaA) 1 (ATP:D-pantothenate 4Ј-phosphotransferase; EC 2.7.1.33). Cysteine is next added to the phosphopantothenate by 4Ј-phosphopantothenoylcysteine synthase and rapidly decarboxylated to phosphopantetheine. These two steps are carried out by a bifunctional polypeptide, phosphopantothenoylcysteine synthetase decarboxylase (denoted CoaBC, formally Dfp) (2). The last two steps are carried out by two separate enzymes, namely phosphopantetheine adenylyltransferase (CoaD) (3, 4) followed by the addition of the 3Ј-ribose phosphate by dephospho-CoA kinase (CoaE) (5). E. coli is capable of de novo pantothenate biosynthesis (1) or can import pantothenate from the medium via a sodium-dependent active transport process (6-8). CoA is also required for the synthesis of ACP, the acyl group carrier in bacterial fatty acid synthesis. The phosphopantetheine moiety of CoA is transferred to serine 36 of apo-ACP by [ACP]synthase (AcpS) (9, 10), and ...

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

Cited by 255 publications

References 87 publications

Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 Å Resolution: Implications for Coenzyme A-Dependent Redox Biology^,

Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 Å Resolution: Implications for Coenzyme A-Dependent Redox Biology^,

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum

Acyl Carrier Protein Is a Cellular Target for the Antibacterial Action of the Pantothenamide Class of Pantothenate Antimetabolites

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

Cited by 255 publications

References 87 publications

Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 Å Resolution: Implications for Coenzyme A-Dependent Redox Biology,

Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 Å Resolution: Implications for Coenzyme A-Dependent Redox Biology,

Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum

Acyl Carrier Protein Is a Cellular Target for the Antibacterial Action of the Pantothenamide Class of Pantothenate Antimetabolites

Contact Info

Product

Resources

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Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 Å Resolution: Implications for Coenzyme A-Dependent Redox Biology^,

Structure of the Type III Pantothenate Kinase from Bacillus anthracis at 2.0 Å Resolution: Implications for Coenzyme A-Dependent Redox Biology^,