Equally parsimonious pathways through an RNA sequence space are not equally likely

Journal of Molecular Evolution

Volumn 45, Issue 3, 1997, Pages 278-284

  Lee, Youn Hyung ^a   DSouza, Lisa M ^a   Fox, George E ^a  

^a UNIVERSITY OF HOUSTON   (United States)

Author keywords

5S rRNA; Evolutionary paths; Parsimony; Sequence space; Shape space; Vibrio proteolyticus

Indexed keywords

RNA 5S;

ARTICLE; ESCHERICHIA COLI; EVOLUTION; NONHUMAN; RNA SEQUENCE; VIBRIO;

NASA DISCIPLINE EXOBIOLOGY; NON-NASA CENTER;

BASE SEQUENCE; ESCHERICHIA COLI; EVOLUTION; MODELS, THEORETICAL; MOLECULAR SEQUENCE DATA; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 5S; VARIATION (GENETICS); VIBRIO;

ESCHERICHIA COLI; VIBRIO; VIBRIO PROTEOLYTICUS;

EID: 0030876370     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006231     Document Type: Article

References (24)

1. Brosius J (1984) Toxicity of an overproduced foreign gene in Escherichia coli and its use in plasmid vectors for the selection of transcription terminators. Gene 27:161-172
2. Chao L, McBroom SM (1985) Evolution of transposable elements: an IS10 insertion increases fitness in Escherichia coli. Mol Biol Evol 2:359-369
3. Dallas A, Rycyna R, Moore P (1995) A proposal for the conformation of loop E in Escherichia coli 5SrRNA. Biochem Cell Biol 73:887-897
4. Dykhuizen DE, Hartl DL (1983) Selection in chemostats. Microbiol Rev 47:150-168
5. Eigen M, Winkler-Oswalitsch R, Dress A (1988) Statistical geometry in sequence space: a method of quantitative comparative sequence analysis. Proc Natl Acad Sci USA 85:5913-5917
6. Gautheret D, Damberger SH, Gutell RR (1995) Identification of base-triples in RNA using comparative sequence analysis. J Mol Biol 248:27-43
7. Godson GN, Sinsheimer RL (1967) Use of Brij lysis as a general method to prepare polysomes from Escherichia coli. Biochim Biophys Acta 159:489-495
8. Gutell RR (1993) Comparative studies of RNA: inferring higher-order structure from patterns of sequence variation. Curr Opin Struct Biol 3:313-322
9. Hartl DL, Dykhuizen DE, Miller RD, Green L, de Framond J (1983) Transposable element IS50 improves growth rate of E. coli cells without transposition. Cell 188:503-510
10. Hedenstierna KOF, Lee Y-H, Yang Y, Fox GE (1993) A prototype stable RNA identification cassette for monitoring plasmids of genetically engineered microorganisms. System Appl Microbiol 16: 280-286
11. Hillis DM, Bull JJ, White ME, Badgett MR, Molieux IJ (1992) Experimental phylogenetics: generation of a known phylogeny. Science 255:589-592
12. Jermann TM, Opitz JG, Stackhouse J, Benner SA (1995) Reconstructing the evolutionary history of the artiodactyl ribonuclease super-family. Nature 374:57-59
13. Lee Y-H, DSouza L, Fox GE (1993) Experimental investigation of an RNA sequence space. Orig Life & Evol Biosphere 23:365-372
14. Lenski RE (1988a) Experimental study of pleiotropy and epistasis in Escherichia coli. I. Variation in competitive fitness among mutants resistant to virus T4. Evolution 42:425-432
15. Lenski RE (1988b) Experimental study of pleiotropy and epistasis in Escherichia coli. II. Compensation for maladaptive effects associated with resistance to virus T4. Evolution 42:433-440
16. MacDonell MT, Colwell RR (1985) Phylogeny of the Vibrionaceae and recommendation for two new genera, Listonella and Shewanella. System Appl Microbiol 6:171-182
17. Ninio J (1983) Molecular approach to evolution. Princeton University, Princeton, NJ
18. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
19. Schuster P, Fontana W, Stadler PF, Hofacker, IL (1994) From sequencing to shapes and back: a case study in RNA secondary structures. Proc R Soc Lond B Biol Sci 255:279-284
20. Smith JM (1970) Natural selection and concept of a protein space. Nature 225:563-564
21. Szeberenyi J, Apirion D (1984) Synthesis and processing of 5S rRNA from an rrnB minigene in a plasmid. Biochim Biophy Acta 783: 15-25
22. Vandeyar MA, Weiner MP, Hutton CJ, Batt CA (1988) A simple and rapid method for the selection of oligonucleotide-directed mutants. Gene 65:129-133
23. Wallace DM (1987) Large- and small-scale phenol extraction. Methods Enzymol 152:33-41
24. Zoller MJ, Smith M (1984) Oligonucleotide-directed mutagenesis: a simple method using two oligonucleotide primers and a single-stranded DNA template. DNA 3:479-488