Compensatory evolution in response to a novel RNA polymerase: Orthologous replacement of a central network gene

Molecular Biology and Evolution

Volumn 24, Issue 4, 2007, Pages 900-908

  Bull, J J ^a   Springman, R ^a   Molineux, I J ^a  

^a UNIVERSITY OF TEXAS   (United States)

Author keywords

Adaptation; Bacteriophage; Evolution; Experimental; Genomics

Indexed keywords

BACTERIAL PROTEIN; RNA POLYMERASE;

ARTICLE; BACTERIAL GROWTH; BACTERIOPHAGE; BIOENGINEERING; CONTROLLED STUDY; DNA REPLICATION; EVOLUTIONARY ADAPTATION; EXPERIMENTAL STUDY; GENE CONTROL; GENE EXPRESSION; GENE MUTATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME; HOST; LYSIS; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PROGENY; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

BACTERIOPHAGE T3; BACTERIOPHAGE T7; BASE SEQUENCE; DNA-DIRECTED RNA POLYMERASES; EVOLUTION, MOLECULAR; MUTATION; PROMOTER REGIONS (GENETICS); TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

BACTERIA (MICROORGANISMS);

EID: 34047202740     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm006     Document Type: Article

References (26)

1. Atsumi S, Little JW. 2006. Role of the lytic repressor in prophage induction of phage lambda as analyzed by amodule-replacement approach. Proc Natl Acad Sci USA. 103:4558-4563.
2. Atkinson MR, Savageau MA, Myers JT, Ninfa AJ. 2003. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell. 597-607.
3. Bailey JN, Klement JF, McAllister WT. 1983. Relationship between promoter structure and template specificities exhibited by the bacteriophage T3 and T7 RNA polymerases. Proc Natl Acad Sci USA. 80:2814-2818.
4. Bull JJ, Badgett MR, Springman R, Molineux IJ. 2004. Genome properties and the limits of adaptation in bacteriophages. Evol Int J Org Evol. 58:692-701.
5. Crooks GE, Hon G., Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res. 14:1188-1190.
6. Endy D, You L, Yin J, Molineux IJ. 2000. Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proc Natl Acad Sci USA. 97:5375-5380.
7. Golomb M, Chamberlin MJ. 1977. T7- and T3-specific RNA polymerases: characterization and mapping of the in vitro transcripts read from T3 DNA. J Virol. 21:743-752.
8. Heineman RH, Molineux IJ, Bull JJ. 2005. Evolutionary robustness of an optimal phenotype: re-evolution of lysis in a bacteriophage deleted for its lysin gene. J Mol Evol. 61:181-191.
9. Klement JF, Moorefield MB, Jorgensen E, Brown JE, Risman S, McAllister WT. 1990. Discrimination between bacteriophage T3 and T7 promoters by the T3 and T7 RNA polymerases depends primarily upon a three base-pair region located 10 to 12 base-pairs upstream from the start site. J Mol Biol. 215:21-29.
10. MacDonald L. 1993. Termination by T7 RNA polymerase. Brooklyn (NY): State University of New York.
11. McAdams HH, Arkin A. 1998. Simulation of prokaryotic genetic circuits. Annu Rev Biophys Biomol Struct. 27:199-224.
12. McAdams HH, Arkin A. 2000. Towards a circuit engineering discipline. Curr Biol. 10:R318-R320.
13. McAdams HH, Srinivasan B, Arkin AP. 2004. The evolution of genetic regulatory systems in bacteria. Nat Rev Genet. 5:169-178.
14. Molineux I. 2005. The T7 group. In: Calendar R, editor. The Bacteriophages. Oxford: Oxford University Press. p. 277-301.
15. Morris CE, Klement JF, McAllister WT. 1986. Cloning and expression of the bacteriophage T3 RNA polymerase gene. Gene. 41:193-200.
16. Pajunen MI, Elizondo MR, Skurnik M, Kieleczawa J, Molineux IJ. 2002. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. J Mol Biol. 319:1115-1132.
17. Raskin CA, Diaz G, Joho K, McAllister WT. 1992. Substitution of a single bacteriophage T3 residue in bacteriophage T7 RNA polymerase at position 748 results in a switch in promoter specificity. J Mol Biol. 228:506-515.
18. Rokyta D, Badgett MR, Molineux IJ, Bull JJ. 2002. Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus. Mol Biol Evol. 19:230-238.
19. Sadowski PD. 1974. Suppression of a mutation in gene 3 of bacteriophage T7 (T7 endonuclease I) by mutations in phage and host polynucleotide ligase. J Virol. 13:226-229.
20. Savageau MA. 1998. Rules for the evolution of gene circuitry. Pac Symp Biocomput. 54-65.
21. Savageau MA. 2001. Design principles for elementary gene circuits: elements, methods, and examples. Chaos. 11:142-159.
22. Springman R, Badgett MR, Molineux IJ, Bull JJ. 2005. Gene order constrains adaptation in bacteriophage T7. Virology. 341:141-152.
23. Studier FW, Moffatt BA. 1986. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol. 189:113-130.
24. Wall ME, Hlavacek WS, Savageau MA. 2003. Design principles for regulator gene expression in a repressible gene circuit. J Mol Biol. 332:861-876.
25. Wall ME, Hlavacek WS, Savageau MA. 2004. Design of gene circuits: lessons from bacteria. Nat Rev Genet. 5:34-42.
26. Zhang X, Studier FW. 1995. Isolation of transcriptionally active mutants of T7 RNA polymerase that do not support phage growth. J Mol Biol. 250:156-168.