Toolbox model of evolution of prokaryotic metabolic networks and their regulation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 24, 2009, Pages 9743-9748

  Maslov, Sergei ^a   Krishna, Sandeep ^b   Pang, Tin Yau ^a,c   Sneppen, Kim ^b  

^a BROOKHAVEN NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c STONY BROOK UNIVERSITY   (United States)

Author keywords

Functional genome analysis; Horizontal gene transfer; Transcriptional regulatory networks

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BIOLOGICAL ACTIVITY; CONTROLLED STUDY; ESCHERICHIA COLI; GENOME; GENOME ANALYSIS; HORIZONTAL GENE TRANSFER; METABOLIC PARAMETERS; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE;

EVOLUTION; GENE EXPRESSION REGULATION; MODELS, GENETIC; PROKARYOTIC CELLS; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI; PROKARYOTA;

EID: 67649872627     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0903206106     Document Type: Article

References (30)

1. Madan Babu M, Teichmann SA (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 31(4):1234-1244. (Pubitemid 36284965)
2. Anantharaman V, Koonin E, Aravind L (2001) Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. JMol Biol 307(5):1271-1292. (Pubitemid 33027639)
3. Stover C, et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406(6799):959-964. (Pubitemid 30690454)
4. van Nimwegen E (2003) Scaling laws in the functional content of genomes. Trends Genet 19(9):479-484. (Pubitemid 37101085)
5. Cases I, de Lorenzo V, Ouzounis C (2003) Transcription regulation and environmental adaptation in bacteria. Trends Microbiol 11(6):248-253. (Pubitemid 36725012)
6. Konstantinidis K, Tiedje J (2004) Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci USA 101(9):3160-3165. (Pubitemid 38327751)
7. Thieffry D, Huerta A, Perez-Rueda E, Collado-Vides J (1998) From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli. BioEssays 20(5):433-440. (Pubitemid 28259735)
8. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28(1):27-30. (Pubitemid 30047706)
9. Spirin V, Gelfand M, Mironov A, Mirny L (2006) A metabolic network in the evolutionary context: Multiscale structure and modularity. Proc Natl Acad Sci USA 103(23):8774-8779. (Pubitemid 43878095)
10. von Mering C, et al. (2003) STRING: A database of predicted functional associations between proteins. Nucleic Acids Res 31(1):258-261. (Pubitemid 36150379)
11. Pal C, Papp B, Lercher M (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37(12):1372-1375. (Pubitemid 41722195)
12. Beiko R, Harlow T, Ragan M (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA 102(40):14332-14337.
13. Savageau M (1977) Design of molecular control mechanisms and the demand for gene expression. Proc Natl Acad Sci USA 74(12):5647-5651.
14. Handorf T, Ebenhoh O (2007) MetaPath Online: A web server implementation of the network expansion algorithm. Nucleic Acids Res 35:W613-W618.
15. Salgado H, et al. (2004) Regulon DB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 3:D303. (Pubitemid 38081663)
16. van Nimwegen E (2004) in Power Laws, Scale-Free Networks and Genome Biology, eds Koonin EV, Wolf YI, Karev GP (Landes Bioscience, Georgetown) pp 236-261.
17. Molina N, van Nimwegen E (2008) Universal patterns of purifying selection at noncoding positions in bacteria. Genome Res 18(1):148.
18. Shen-Orr S, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31(1):64-68. (Pubitemid 34887640)
19. Cosentino Lagomarsino M, Jona P, Bassetti B, Isambert H (2007) Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc Natl Acad Sci USA 104(13):5516-5520. (Pubitemid 47175712)
20. Chin C, Chubukov V, Jolly E, DeRisi J, Li H (2008) Dynamics and design principles of a basic regulatory architecture controlling metabolic pathways. PLoS Biol 6:e416. (Pubitemid 351888316)
21. Koonin EV, Wolf YI (2008) Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world. Nucleic Acids Res 236(21):6688-6719.
22. Foster D, Kauffman S, Socolar J (2006) Network growth models and genetic regulatory networks. Phys Rev E 73(3):31912.
23. Enemark J, Sneppen K (2007) Gene duplication models for directed networks with limits on growth. J Stat Mechan P11007.
24. Price M, Dehal P, Arkin A (2008) Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli. Genome Biol 9(1):R4. (Pubitemid 351911943)
25. Lawrence J, Roth JR (1996) Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143(4):1843-1860. (Pubitemid 26286959)
26. Gelfand M (2006) Evolution of transcriptional regulatory networks in microbial genomes. Curr Opin Struct Biol 16(3):420-429. (Pubitemid 43831639)
27. Handorf T, Ebenhoh O, Heinrich R (2005) Expanding metabolic networks: Scopes of compounds, robustness, and evolution. J Mol Evol 61:498-512. (Pubitemid 41416893)
28. Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA (2008) DBD - Taxonomically broad transcription factor predictions: New content and functionality. Nucleic Acids Res 36:D88-D92. (Pubitemid 351149701)
29. Maslov S, Sneppen K (2004) in Power Laws, Scale-Free Networks and Genome Biology, eds Koonin EV, Wolf YI, Karev GP (Landes Bioscience, Georgetown, TX), pp 25-37.
30. Handorf T, Ebenhoh O, Heinrich R (2005) Expanding metabolic networks: Scopes of compounds, robustness, and evolution. J Mol Evol 61:498-512. (Pubitemid 41416893)