Low-complexity segments in Plasmodium falciparum proteins are primarily nucleic acid level adaptations

Molecular and Biochemical Parasitology

Volumn 128, Issue 1, 2003, Pages 21-32

  Xue, H Y ^a   Forsdyke, D R ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

Base composition; Codons; Complexity; Introns; Malaria

Indexed keywords

ADENINE; CYTOSINE; GUANINE; NUCLEIC ACID; PROTOZOAL PROTEIN;

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; ARTICLE; CODON; DNA BASE COMPOSITION; EVOLUTIONARY ADAPTATION; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMODIUM FALCIPARUM; PRESSURE; PRIORITY JOURNAL; PROTOZOAL GENETICS;

PLASMODIUM FALCIPARUM;

EID: 0037466436     PISSN: 01666851     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-6851(03)00039-2     Document Type: Article

References (42)

1. Naora H., Deacon N.J. Relationship between the total size of exons and introns in protein-coding genes of higher eukaryotes. Proc. Natl. Acad. Sci. U.S.A. 79:1982;6196-6200.
2. Blake C. Exons - present from the beginning? Nature. 306:1983;535-537.
3. Smith M.W. Structure of vertebrate genes: a statistical analysis implicating selection. J. Mol. Evol. 27:1988;45-55.
4. Traut T.W. Do exons code for structural or functional units in proteins? Proc. Natl. Acad. Sci. U.S.A. 85:1988;2944-2948.
5. Sakharkar M., Passetti F., de Souza J.E., Long M., de Souza S.J. ExInt: an exon intron database. Nucleic Acids Res. 30:2002;191-194.
6. Pizzi E., Frontali C. Low-complexity regions in Plasmodium falciparumproteins. Genome Res. 11:2001;218-229.
7. Wan H., Wootton J.C. A global complexity measure for biological sequences. AT-rich and GC-rich genomes encode less complex proteins. Comput. Chem. 24:2000;71-94.
8. Sueoka N. Compositional correlation between deoxyribonucleic acid and protein. Cold. Spring Harb. Symp. Quant. Biol. 26:1961;35-43.
9. Kimura M. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature. 267:1977;275-276.
10. Forsdyke D.R., Mortimer J.R. Chargaff's legacy. Gene. 261:2000;127-137.
11. Forsdyke DR. Functional constraint and molecular evolution. In: Encyclopedia of life sciences, vol. 7. London: Nature Publishing Group; 2001. p. 396-403.
12. Forsdyke DR. The origin of species, revisited. Montreal: McGill-Queen's University Press; 2001.
13. Lao P.J., Forsdyke D.R. Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res. 10:2000;228-236.
14. Cristillo A.D., Mortimer J.R., Barrette I.H., Lillicrap T.P., Forsdyke D.R. Double-stranded RNA as a not-self alarm signal: to evade, most viruses purine-load their RNAs, but some (HTLV-1, Epstein-Barr) pyrimidine-load. J. Theor. Biol. 208:2001;475-491.
15. Forsdyke D.R. Selective pressures that decrease synonymous mutations in Plasmodium falciparum. Trends Parasitol. 18:2002;411-418.
16. Gardner M.J., Tettelin H., Carucci D.J.et al. Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science. 282:1998;1126-1132.
17. Bowman S., Lawson D., Basham D.et al. The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature. 400:1999;532-538.
18. Baer R., Bankier A.T., Biggin M.D.et al. DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature. 310:1984;207-211.
19. Konopka AK. Towards mapping functional domains in indiscriminantly sequenced nucleic acids: a computational approach. In: Sarma RH, Sarma MH, editors. Human genome initiative and DNA recombination, vol. 1. New York: Adenine Press; 1990. p. 113-25.
20. Nakamura Y., Gojobori T., Ikemura T. Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28:2000;292.
21. Bell S., Forsdyke D.R. Accounting units in DNA. J. Theor. Biol. 197:1999;51-61.
22. Zuker M. Calculating nucleic acid secondary structure. Curr. Opin. Struct. Biol. 10:2000;303-310.
23. Forsdyke D.R. A stem-loop "kissing" model for the initiation of recombination and the origin of introns. Mol. Biol. Evol. 12:1995;949-958.
24. Forsdyke D.R. Conservation of stem-loop potential in introns of snake venom phospholipase A2 genes. Mol. Biol. Evol. 12:1995;1157-1165.
25. Forsdyke D.R. Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection. J. Mol. Evol. 41:1995;1022-1037.
26. Forsdyke D.R. An alternative way of thinking about stem-loops in DNA. J. Theor. Biol. 192:1998;489-504.
27. Seffens W., Digby D. mRNAs have greater negative folding free energies than shuffled or codon-choice randomized sequences. Nucleic Acids Res. 27:1999;1578-1584.
28. Musto H., Caccio S., Rodriguez-Maseda H., Bernardi G. Compositional constraints on the extremely GC-poor genome of Plasmodium falciparum. Memoria do Instituto Oswaldo Cruz. 92:1997;835-841.
29. Eigen M., Schuster P. The hypercycle. A principle of natural self organization. Part C. The realistic hypercycle. Naturwissenschaften. 65:1978;341-369.
30. Bell S., Forsdyke D.R. Deviations from Chargaff's second parity rule correlate with direction of transcription. J. Theor. Biol. 197:1999;63-76.
31. Kurtis J.D., Hollingdale M.R., Luty A.J.F., Lanar D.E., Krzych U., Duffy P.E. Pre-erythocytic immunity to Plasmodium falciparum: the case for an LSA1 vaccine. Trends. Parasitol. 17:2001;219-223.
32. Stoltzfus A., Spencer D.F., Zuker M., Logsdon J.M., Doolittle W.F. Testing the exon theory of genes: the evidence from protein structure. Science. 265:1994;202-207.
33. Weber K., Kabsch W. Intron positions in actin genes seem unrelated to the secondary structure of the protein. EMBO J. 13:1994;1280-1286.
34. Saul A., Battistuta D. Codon usage in Plasmodium falciparum. Mol. Biochem. Parasitol. 27:1988;35-42.
35. Mrázek J., Kypr J. Biased distribution of adenine and thymine in gene nucleotide sequences. J. Mol. Evol. 39:1994;439-447.
36. Barrette I.H., McKenna S., Taylor D.R., Forsdyke D.R. Introns resolve the conflict between base order-dependent stem-loop potential and the encoding of RNA or protein: further evidence from overlapping genes. Gene. 270:2001;181-189.
37. Bossi L., Roth J.R. The influence of codon context on genetic code translation. Nature. 286:1980;123-127.
38. Simonson A.B., Lake J.A. The transorientation hypothesis for codon recognition during protein synthesis. Nature. 416:2002;281-284.
39. Tchavtchitch M., Fischer K., Huestis R., Saul A. The sequence of a 200 kb portion of a Plasmodium vivax chromosome reveals a high degree of conservation with chromosome 3. Mol. Biochem. Parasitol. 118:2001;211-222.
40. Wu H., Kapoor P., Frappier L. Separation of the DNA replication, segregation, and transcriptional functions of Epstein-Barr nuclear antigen 1. J. Virol. 76:2002;2480-2490.
41. Tellam J., Sherritt M., Thomson S.et al. Targeting of EBNA1 for rapid intracellular degradation overrides the inhibitory effects of the gly-ala repeat domain and restores CD8+ T cell recognition. J. Biol. Chem. 276:2001;33353-33360.
42. Heessen S., Leonchiks A., Issaeva N.et al. Functional p53 chimeras containing the Epstein-Barr virus Gly-Ala repeat are protected from Mdm2- and HPV-E6-induced proteolysis. Proc. Natl. Acad. Sci. U.S.A. 99:2002;1532-1537.