Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes

BMC Research Notes

Volumn 5, Issue , 2012, Pages

  Tiessen, Axel ^a   Pérez Rodríguez, Paulino ^b   Delaye Arredondo, Luis ^a  

^a DEPARTAMENTO DE INGENIERÍA GENÉTICA   (Mexico)

^b Colegio de Posgraduados ^*  (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

ALVEOLATA; AMOEBOZOA; ANIMALIA; ARCHAEA; BACTERIA (MICROORGANISMS); DIPLOMONADIDA GROUP; EQUUS ASINUS; EUKARYOTA; EUMETAZOA; FUNGI; PLACOZOA; PROKARYOTA; STRAMENOPILES; VIRIDIPLANTAE;

EID: 84856377506     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-5-85     Document Type: Article

References (52)

1. Lehninger. Principles of Biochemistry. Nelson DL, Cox MM, Freeman WH, 4 2004
2. The Classification and Origins of Protein Folding Patterns. Chothia C, Finkelstein AV, Annu Rev Biochem 1990 59 1007 1039 10.1146/annurev.bi.59.070190. 005043 2197975
3. Protein Structure and Function. Petsko GA, Ringe D, New Science Press, Ltd 2003 111
4. Protein-length distributions for the three domains of life. Zhang JZ, Trends Genet 2000 16 3 107 109 10.1016/S0168-9525(99)01922-8 10689349 (Pubitemid 30122341)
5. Protein length in eukaryotic and prokaryotic proteomes. Brocchieri L, Karlin S, Nucleic Acids Res 2005 33 10 3390 3400 10.1093/nar/gki615 15951512 (Pubitemid 41199547)
6. Amino-Acid Composition of Proteins-Selection against Genetic Code. Jukes TH, Holmquist R, Moise H, Science 1975 189 4196 50 51 10.1126/science.237322 237322
7. A relationship between GC content and coding-sequence length. Oliver JL, Marin A, J Mol Evol 1996 43 3 216 223 10.1007/BF02338829 8703087 (Pubitemid 26315123)
8. Some hints on open reading frame statistics-How ORF length depends on selection. Gierlik A, Mackiewicz P, Kowalczuk M, Cebrat S, Dudek MR, Int J Mod Phys C 1999 10 4 635 643 10.1142/S0129183199000474
9. Evolution of Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences. Eck RV, Dayhoff MO, Science 1966 152 3720 363 & 10.1126/science.152.3720.363 17775169
10. Repeating sequences and gene duplication in proteins. McLachlan A, J Mol Biol 1972 64 417 437 10.1016/0022-2836(72)90508-6 5023183
11. Implications of RNA-RNA splicing in evolution of eukaryotic cells. Darnell J, Science 1978 202 1257 1260 10.1126/science.364651 364651 (Pubitemid 9116080)
12. The limited universe of exons. Dorit RL, Gilbert W, Cur Opinion Struc Biol 1991 1 973 977 10.1016/0959-440X(91)90093-9 (Pubitemid 121002690)
13. How big is the universe of exons? Dorit R, Schoenbach L, Gilbert W, Science 1990 250 1377 1382 10.1126/science.2255907 2255907 (Pubitemid 120031849)
14. The evolution of proteins from random amino-acid-sequences. 1. Evidence from the lengthwise distribution of amino-acids in modern protein sequences. White SH, Jacobs RE, J Mol Evol 1993 36 1 79 95 10.1007/BF02407307 8433379 (Pubitemid 23018098)
15. Statistical distribution of hydrophobic residues along the length of protein chains-implications for protein folding and evolution. White SH, Jacobs RE, Biophys J 1990 57 4 911 921 10.1016/S0006-3495(90)82611-4 2188687 (Pubitemid 20111250)
16. Theory for protein mutability and biogenesis. Lau KF, Dill KA, P Natl Acad Sci USA 1990 87 2 638 642 10.1073/pnas.87.2.638
17. Implications of thermodynamics of protein folding for evolution of primary sequences. Shakhnovich EI, Gutin AM, Nature 1990 346 6286 773 775 10.1038/346773a0 2388698 (Pubitemid 20251095)
18. The Evolution of proteins from random amino-acid-sequences. 2. Evidence from the statistical distributions of the lengths of modern protein sequences. White SH, J Mol Evol 1994 38 4 383 394 10.1007/BF00163155 8007006 (Pubitemid 24096438)
19. Infinite allele model with varying mutation rate. Nei M, Chakraborty R, Fuerst P, P Natl Acad Sci USA 1976 73 4164 4168 10.1073/pnas.73.11.4164
20. The size distributions of proteins, mRNA, and nuclear RNA. Sommer S, Cohen J, J Mol Evol 1980 15 37 57 10.1007/BF01732582 6154144 (Pubitemid 10070427)
21. Stochastic dynamics modeling of the protein sequence length distribution in genomes: implications for microbial evolution. Jain R, Ramakumar S, Physica A 1999 273 3-4 476 485 10.1016/S0378-4371(99)00370-2 (Pubitemid 129590929)
22. Introduction to Probability models. Ross SM, San Diego: Academic press 4 1989
23. compositional nonrandomness-quantitatively conserved evolutionary invariant. Holmquist R, Moise H, J Mol Evol 1975 6 1 1 14 10.1007/BF01732670 1185793
24. Eukaryota, Organisms with nucleated cells. The Tree of Life Web Project, Version 28. http://tolweb.org/Eukaryotes/3/2009.10.28
25. Molecular phylogeny of eukaryotes. Schlegela M, Trends in Ecology & Evolution 1994 9 9 330 335 10.1016/0169-5347(94)90153-8 22282460 (Pubitemid 2125706)
26. On the origin and highly likely completeness of single-domain protein structures. Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J, P Natl Acad Sci USA 2006 103 8 2605 2610 10.1073/pnas.0509379103
27. The protein folds as platonic forms: New support for the pre-Darwinian conception of evolution by natural law. Denton MJ, Marshall CJ, Legge M, J Theor Biol 2002 219 3 325 342 10.1006/jtbi.2002.3128 12419661 (Pubitemid 35341072)
28. The theory of the folding and stability of globular proteins. Dill KA, Biochemistry 1985 24 1501 1509 10.1021/bi00327a032 3986190
29. The amino acid preferences of small proteins: implications for protein stability and evolution. White SH, J Mol Biol 1992 227 4 991 995 10.1016/0022-2836(92)90515-L 1433304
30. Exons-Present from the Beginning. Blake C, Nature 1983 306 5943 535 537 10.1038/306535a0 6646232
31. The objects of selection. Mayr E, P Natl Acad Sci USA 1994 94 2091 2094
32. Selective pressures on the olfactory receptor repertoire since the human-chimpanzee divergence. Gimelbrant AA, Skaletsky H, Chess A, P Natl Acad Sci USA 2004 101 24 9019 9022 10.1073/pnas.0401566101 (Pubitemid 38781603)
33. Comparative genomics and structural biology of the molecular innovations of eukaryotes. Aravind L, Iyer LM, Koonin EV, Curr Opin Struc Biol 2006 16 3 409 419 10.1016/j.sbi.2006.04.006 (Pubitemid 43831642)
34. Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications. Chandonia JM, Kim SH, BMC Structural Biology 2006 6 7 10.1186/1472-6807-6-7 16566839 (Pubitemid 44019885)
35. Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Kolodny R, Petrey D, Honig B, Curr Opin Struc Biol 2006 16 3 393 398 10.1016/j.sbi.2006.04.007 (Pubitemid 43831645)
36. New-Protein Folds. Murzin AG, Curr Opin Struc Biol 1994 4 3 441 449 10.1016/S0959-440X(94)90114-7 (Pubitemid 24195861)
37. Protein structure: evolutionary bridges to new folds. Yeates TO, Curr Biol 2007 17 2 48 R50 10.1016/j.cub.2006.12.003 17240325 (Pubitemid 46107829)
38. Average proteins and genetic code. Jukes TH, Holmquist R, Moise H, Science 1976 194 4265 642 643 10.1126/science.982033 982033
39. Generation of overlapping open reading frames. Cebrat S, Dudek MR, Trends Genet 1996 12 1 12 12 10.1016/0168-9525(96)81376-X 8741854
40. Relationship between the total size of exons and introns in protein-coding genes of higher eukaryotes. Naora H, Deacon NJ, P Natl Acad Sci-Biol 1982 79 20 6196 6200 10.1073/pnas.79.20.6196 (Pubitemid 13219832)
41. How many protein-coding genes are there in the Saccharomyces cerevisiae genome? Mackiewicz P, Kowalczuk M, Mackiewicz D, Nowicka A, Dudkiewicz M, Laszkiewicz A, Dudek MR, Cebrat S, Yeast 2002 19 619 629 10.1002/yea.865 11967832 (Pubitemid 34521063)
42. Missing genes in the annotation of prokaryotic genomes. Warren AS, Archuleta J, Feng WC, Setubal JC, BMC Bioinformatics 2010 11 131 10.1186/1471-2105-11-131 20230630
43. 4-oxalocrotonate tautomerase, an enzyme composed of 62 amino-acid-residues per monomer. Chen LH, Kenyon GL, Curtin F, Harayama S, Bembenek ME, Hajipour G, Whitman CP, J Biol Chem 1992 267 25 17716 17721 1339435
44. Cost-minimization of amino acid usage. Seligmann H, J Mol Evol 2003 56 2 151 161 10.1007/s00239-002-2388-z 12574861 (Pubitemid 36169683)
45. Metabolic efficiency and amino acid composition in the proteomes of escherichia coli and bacillus subtilis. Akashi H, Gojobori T, P Natl Acad Sci USA 2002 99 6 3695 3700 10.1073/pnas.062526999 (Pubitemid 34252168)
46. The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms. Kiraga J, Mackiewicz P, Mackiewicz D, Kowalczuk M, Biecek P, Polak N, Smolarczyk K, Dudek MR, Cebrat S, BMC Genomics 2007 8 8 10.1186/1471-2164-8-8 17210083 (Pubitemid 46210967)
47. Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution. Nandi S, Mehra N, Lynn AM, Bhattacharya A, BMC Genomics 2005 6 116 10.1186/1471-2164-6-116 16150155 (Pubitemid 41372423)
48. R: A language and environment for statistical computing. R Development Core Team, Vienna, Austria 2011
49. protein classification by stochastic modeling and optimal filtering of amino-acid-sequences. White JV, Stultz CM, Smith TF, Math Biosci 1994 119 1 35 75 10.1016/0025-5564(94)90004-3 8111135
50. Modern applied statistics with S. Venables WN, Ripley BD, New York: Springer 2002
51. A unified approach to model selection using the likelihood ratio test. Lewis F, Butler A, Gilbert L, Methods in Ecology and Evolution 2010 2041 2210
52. A new look at the statistical model identification. Akaike H, IEEE Transactions on Automatic Control 1974 19 6 716 723 10.1109/TAC.1974.1100705