From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways
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Published in | Journal of Bacteriology Vol. 184; no. 16; pp. 4555 - 4572 |
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Main Authors | , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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United States
American Society for Microbiology
01.08.2002
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Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens, and comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. Gerdes et al describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. We describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Our strategy is based on genetic footprinting in Escherichia coli followed by metabolic context analysis of essential gene orthologs in various species. Genes required for viability of E. coli in rich medium were identified on a whole-genome scale using the genetic footprinting technique. Potential target pathways were deduced from these data and compared with a panel of representative bacterial pathogens by using metabolic reconstructions from genomic data. Conserved and indispensable functions revealed by this analysis potentially represent broad-spectrum antibacterial targets. Further target prioritization involves comparison of the corresponding pathways and individual functions between pathogens and the human host. The most promising targets are validated by direct knockouts in model pathogens. The efficacy of this approach is illustrated using examples from metabolism of adenylate cofactors NAD(P), coenzyme A, and flavin adenine dinucleotide. Several drug targets within these pathways, including three distantly related adenylyltransferases (orthologs of the E. coli genes nadD , coaD , and ribF ), are discussed in detail. ABSTRACT Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. We describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Our strategy is based on genetic footprinting in Escherichia coli followed by metabolic context analysis of essential gene orthologs in various species. Genes required for viability of E. coli in rich medium were identified on a whole-genome scale using the genetic footprinting technique. Potential target pathways were deduced from these data and compared with a panel of representative bacterial pathogens by using metabolic reconstructions from genomic data. Conserved and indispensable functions revealed by this analysis potentially represent broad-spectrum antibacterial targets. Further target prioritization involves comparison of the corresponding pathways and individual functions between pathogens and the human host. The most promising targets are validated by direct knockouts in model pathogens. The efficacy of this approach is illustrated using examples from metabolism of adenylate cofactors NAD(P), coenzyme A, and flavin adenine dinucleotide. Several drug targets within these pathways, including three distantly related adenylyltransferases (orthologs of the E. coli genes nadD , coaD , and ribF ), are discussed in detail. Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. We describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Our strategy is based on genetic footprinting in Escherichia coli followed by metabolic context analysis of essential gene orthologs in various species. Genes required for viability of E. coli in rich medium were identified on a whole-genome scale using the genetic footprinting technique. Potential target pathways were deduced from these data and compared with a panel of representative bacterial pathogens by using metabolic reconstructions from genomic data. Conserved and indispensable functions revealed by this analysis potentially represent broad-spectrum antibacterial targets. Further target prioritization involves comparison of the corresponding pathways and individual functions between pathogens and the human host. The most promising targets are validated by direct knockouts in model pathogens. The efficacy of this approach is illustrated using examples from metabolism of adenylate cofactors NAD(P), coenzyme A, and flavin adenine dinucleotide. Several drug targets within these pathways, including three distantly related adenylyltransferases (orthologs of the E. coli genes nadD, coaD, and ribF), are discussed in detail. |
Author | Mark V. Baev Boris M. Polanuyer Michael D. Scholle Svetlana Y. Gerdes Konstantin Y. Shatalin Axel Bernal Andrei L. Osterman Oleg V. Kurnasov Mark D'Souza Faika Mseeh Shubha Anantha Shamim A. K. Chowdhury Michael Farrell Matthew D. Daugherty Michael Y. Fonstein John W. Campbell |
AuthorAffiliation | Integrated Genomics Inc., Chicago, Illinois 60612 |
AuthorAffiliation_xml | – name: Integrated Genomics Inc., Chicago, Illinois 60612 |
Author_xml | – sequence: 1 givenname: Svetlana Y surname: Gerdes fullname: Gerdes, Svetlana Y organization: Integrated Genomics Inc., Chicago, Illinois 60612, USA – sequence: 2 givenname: Michael D surname: Scholle fullname: Scholle, Michael D – sequence: 3 givenname: Mark surname: D'Souza fullname: D'Souza, Mark – sequence: 4 givenname: Axel surname: Bernal fullname: Bernal, Axel – sequence: 5 givenname: Mark V surname: Baev fullname: Baev, Mark V – sequence: 6 givenname: Michael surname: Farrell fullname: Farrell, Michael – sequence: 7 givenname: Oleg V surname: Kurnasov fullname: Kurnasov, Oleg V – sequence: 8 givenname: Matthew D surname: Daugherty fullname: Daugherty, Matthew D – sequence: 9 givenname: Faika surname: Mseeh fullname: Mseeh, Faika – sequence: 10 givenname: Boris M surname: Polanuyer fullname: Polanuyer, Boris M – sequence: 11 givenname: John W surname: Campbell fullname: Campbell, John W – sequence: 12 givenname: Shubha surname: Anantha fullname: Anantha, Shubha – sequence: 13 givenname: Konstantin Y surname: Shatalin fullname: Shatalin, Konstantin Y – sequence: 14 givenname: Shamim A K surname: Chowdhury fullname: Chowdhury, Shamim A K – sequence: 15 givenname: Michael Y surname: Fonstein fullname: Fonstein, Michael Y – sequence: 16 givenname: Andrei L surname: Osterman fullname: Osterman, Andrei L |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/12142426$$D View this record in MEDLINE/PubMed |
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Notes | ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 Corresponding author. Mailing address: Integrated Genomics, Inc., 2201 W. Campbell Park Dr., Chicago, IL 60612. Phone: (312) 491-0846, ext. 213. Fax: (312) 491-0856. E-mail: andrei@integratedgenomics.com. |
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PublicationTitle | Journal of Bacteriology |
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Mendeley... Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for... ABSTRACT Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new... Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens, and comparative genomics provides new opportunities for... |
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SubjectTerms | Anti-Bacterial Agents Antibiotics Bacteriology Coenzyme A - biosynthesis DNA Footprinting DNA Transposable Elements Drug Design Drug Resistance, Bacterial Escherichia coli - drug effects Escherichia coli - genetics Escherichia coli - metabolism Flavin Mononucleotide - biosynthesis Flavin-Adenine Dinucleotide - biosynthesis Genes Genetics Genome, Bacterial Meeting Presentations Mutagenesis, Insertional NADP - biosynthesis Nicotinamide-Nucleotide Adenylyltransferase - metabolism Pathogens Phosphotransferases (Alcohol Group Acceptor) - genetics Substrate Specificity |
Title | From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways |
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