Origin and evolution of overlapping genes in the family Microviridae

References

1. Bläsi U., Lubitz W. 1985; Influence of C-terminal modifications of ϕ X174 lysis gene E on its lysis-inducing properties. J Gen Virol 66:1209–1213 [CrossRef]
   [Google Scholar]
2. Bozarth C. S., Weiland J. J., Dreher T. W. 1992; Expression of ORF-69 of turnip yellow mosaic virus is necessary for viral spread in plants. Virology 187:124–130 [CrossRef]
   [Google Scholar]
3. Brentlinger K. L., Hafenstein S., Novak C. R., Fane A. B., Borgon R., McKenna R., Agbandje-McKenna M. 2002; Microviridae , a family divided: isolation, characterization, and genome sequence of ϕ MH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus . J Bacteriol 184:1089–1094 [CrossRef]
   [Google Scholar]
4. Bull J. J., Badgett M. R., Wichman H. A. 2000; Big-benefit mutations in a bacteriophage inhibited with heat. Mol Biol Evol 17:942–950 [CrossRef]
   [Google Scholar]
5. Dokland T., McKenna R., Ilag L. L., Bowman B. R., Incardona N. L., Fane B. A., Rossmann M. G. 1997; Structure of a viral procapsid with molecular scaffolding. Nature 389:308–313 [CrossRef]
   [Google Scholar]
6. Gibbs A., Keese P. K. 1995; In search of the origins of viral genes. In Molecular Basis of Virus Evolution pp  76–90 Edited by Gibbs A., Calisher C. H., García-Arenal F. Cambridge: Cambridge University Press;
   [Google Scholar]
7. Gillam S., Atkinson T., Markham A., Smith M. 1985; Gene K of bacteriophage ϕ X174 codes for a protein which affects the burst size of phage production. J Virol 53:708–709
   [Google Scholar]
8. Godson G. N., Barrell B. G., Staden R., Fiddes J. C. 1978; Nucleotide sequence of bacteriophage G4 DNA. Nature 276:236–247 [CrossRef]
   [Google Scholar]
9. Guyader S., Ducray D. G. 2002; Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J Gen Virol 83:1799–1807
   [Google Scholar]
10. Hughes A. L., Westover K., da Silva J., O'Connor D. H., Watkins D. I. 2001; Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus. J Virol 75:7966–7972 [CrossRef]
    [Google Scholar]
11. Hutchinson C. A. III, Sinsheimer R. L. 1966; The process of infection with bacteriophage ϕ X174. X. Mutations in a ϕ X lysis gene. J Mol Biol 18:429–447 [CrossRef]
    [Google Scholar]
12. Jordan I. K., Sutter B. A. IV, McClure M. A. 2000; Molecular evolution of the paramyxoviridae and rhabdoviridae multiple-protein-encoding P gene. Mol Biol Evol 17:75–86 [CrossRef]
    [Google Scholar]
13. Keese P. K., Gibbs A. 1992; Origin of genes: “big bang” or continuous creation?. Proc Natl Acad Sci U S A 89:9489–9493 [CrossRef]
    [Google Scholar]
14. Kodaira K., Nakano K., Okada S., Taketo A. 1992; Nucleotide sequence of the genome of the bacteriophage α 3: interrelationship of the genome structure and the gene products with those of the phages, ΦX174, G4 and ΦK. Biochim Biophys Acta 1130277–288 [CrossRef]
    [Google Scholar]
15. Krakauer D. C. 2000; Stability and evolution of overlapping genes. Evolution 54:731–739 [CrossRef]
    [Google Scholar]
16. Miyata T., Yasunaga T. 1978; Evolution of overlapping genes. Nature 272:532–535 [CrossRef]
    [Google Scholar]
17. Mizokami M., Orito E., Ohba K., Ikeo K., Lau J. Y. N., Gojobori T. 1997; Constrained evolution with respect to gene overlap of hepatitis B virus. J Mol Evol 44 (Suppl. 1):S83–S90 [CrossRef]
    [Google Scholar]
18. Morrison D. F. 1976 Multivariate Statistical Methods New York: McGraw-Hill;
    [Google Scholar]
19. Narechania A., Terai M., Burk R. D. 2005; Overlapping reading frames in closely related human papillomaviruses result in modular rates of selection within E2. J Gen Virol 86:1307–1313 [CrossRef]
    [Google Scholar]
20. Nei M., Gojobori T. 1986; Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426
    [Google Scholar]
21. Pavesi A. 2000; Detection of signature sequences in overlapping genes and prediction of a novel overlapping gene in hepatitis G virus. J Mol Evol 50:284–295
    [Google Scholar]
22. Pavesi A., De Iaco B., Granero M. I., Porati A. 1997; On the informational content of overlapping genes in prokaryotic and eukaryotic viruses. J Mol Evol 44:625–631 [CrossRef]
    [Google Scholar]
23. Renaudin J., Pascarel M.-C., Bové J.-M. 1987; Spiroplasma virus 4: nucleotide sequence of the viral DNA, regulatory signals, and proposed genome organization. J Bacteriol 169:4950–4961
    [Google Scholar]
24. Sander C., Schulz G. E. 1979; Degeneracy of the information contained in amino acid sequences: evidence from overlaid genes. J Mol Evol 13:245–252 [CrossRef]
    [Google Scholar]
25. Sanger F., Air G. M., Barrell B. G., Brown N. L., Coulson A. R., Fiddes C. A., Hutchinson C. A., Slocombe P. M., Smith M. 1977; Nucleotide sequence of bacteriophage ΦX174 DNA. Nature 265:687–695 [CrossRef]
    [Google Scholar]
26. Sharp P. M., Li W.-H. 1987; The codon adaptation index – a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295 [CrossRef]
    [Google Scholar]
27. Spiropoulou C. F., Nichol S. T. 1993; A small highly basic protein is encoded in overlapping frame within the P gene of vesicular stomatitis virus. J Virol 67:3103–3110
    [Google Scholar]
28. Storey C. C., Lusher M., Richmond S. J. 1989; Analysis of the complete nucleotide sequence of Chp1, a phage which infects avian Chlamydia psittaci . J Gen Virol 70:3381–3390 [CrossRef]
    [Google Scholar]
29. Tessman E. S., Tessman I., Pollock T. J. 1980; Gene K of bacteriophage ϕ X174 codes for a nonessential protein. J Virol 33:557–560
    [Google Scholar]
30. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
31. Walewski J. L., Keller T. R., Stump D. D., Branch A. D. 2001; Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame. RNA 7:710–721 [CrossRef]
    [Google Scholar]