Stoichiogenomics: The evolutionary ecology of macromolecular elemental composition

Trends in Ecology and Evolution

Volumn 26, Issue 1, 2011, Pages 38-44

  Elser, James J ^a   Acquisti, Claudia ^a,b   Kumar, Sudhir ^a,b  

^a ARIZONA STATE UNIVERSITY   (United States)

^b ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CHEMICAL COMPOSITION; DATA SET; EVOLUTIONARY BIOLOGY; GENOMICS; NUCLEIC ACID; PROTEIN; PROTEOMICS;

ANIMAL; ECOSYSTEM; EVOLUTION; GENETIC SELECTION; GENOMICS; PLANT; REVIEW; STATISTICS;

ANIMALS; BIOLOGICAL EVOLUTION; ECOSYSTEM; GENOMICS; PLANTS; SELECTION, GENETIC; STOCHASTIC PROCESSES;

ANIMALIA;

EID: 78650306221     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2010.10.006     Document Type: Review

References (27)

1. Eyre-Walker A., Keightley P.D. The distribution of fitness effects of new mutations. Nat. Rev. Genet. 2007, 8:610-618.
2. Kimura M. The Neutral Theory of Molecular Evolution 1983, Cambridge University Press.
3. Subramanian S., Kumar S. Higher intensity of natural selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol. Biol. Evol. 2006, 23:2283-2287.
4. Bohlin J., Skjerve E. Examination of genome homogeneity in prokaryotes using genomic signatures. PLoS ONE 2009, 4:e8113.
5. Wang H.-C., et al. On the correlation between genomic G1C content and optimal growth temperature in prokaryotes: data quality and confounding factors. Biochem. Biophys. Res. Commun. 2006, 342:681-684.
6. Bragg J.G., et al. Variation among species in proteomic sulphur content is related to environmental conditions. Proc. R. Soc. B. 2006, 273:1293-1300.
7. Elser J.J., Hamilton A.L. Stoichiometry and the new biology: the future is now. PLoS Biol. 2007, 5:e181. doi: 110.1371/journal.pbio.0050181.
8. Akashi H., Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:3695-3700.
9. Scheibel T., et al. S. cerevisiae and sulfur: a unique way to deal with the environment. FASEB J. 1997, 11:917-921.
10. Baudouin-Cornu P., et al. Molecular evolution of protein atomic composition. Science 2001, 293:297-300.
11. Bragg J.G., Wagner A. Protein material costs: single atoms can make an evolutionary difference. Trends Genet. 2009, 25:5-8.
12. Carlson R.P. Metabolic systems cost-benefit analysis for interpreting network structure and regulation. Bioinformatics 2007, 23:1258-1264.
13. Elser J.J., et al. Signatures of ecological resource availability in the animal and plant proteomes. Mol. Biol. Evol. 2006, 23. 10.1093.
14. Li N., et al. Low contents of carbon and nitrogen in highly abundant proteins: evidence of selection for the economy of atomic composition. J. Mol. Evol. 2009, 68:248-255.
15. Acquisti C., et al. Ecological nitrogen limitation shapes the DNA composition of plant genomes. Mol. Biol. Evol. 2009, 26:953-956.
16. Acquisti C., et al. From elements to biological processes: signatures of nitrogen limitation in the elemental composition of the catabolic apparatus. Proc. R. Soc. B. 2009, 276:2605-2610.
17. Bragg J.G., Hyder C.L. Nitrogen versus carbon use in prokaryotic genomes and proteomes. Proc. R. Soc. B. 2004, 271:S374-S377.
18. Hessen D.O., et al. Genome streamlining and the elemental costs of growth. Trends Ecol. Evol. 2010, 25:75-80.
19. Sterner R.W., Elser J.J. Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere 2002, Princeton University Press.
20. DeLong E.F. The microbial ocean from genomes to biomes. Nature 2009, 459:200-206.
21. Riesenfeld C.S., et al. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 2004, 38:525-552.
22. Jones N. Undersea project delivers data flood. Nature 2010, 464.
23. Van Mooy B., et al. Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature 2009, 458:69-72.
24. Lv J., et al. Association between the availability of environmental resources and the atomic composition of organismal proteomes: evidence from Prochlorococcus strains living at different depths. Biochem. Biophys. Res. Commun. 2008, 375:241-246.
25. Burke J., et al. Crop evolution: from genetics to genomics. Curr. Opin. Genet. Dev. 2007, 17:525-532.
26. Stark A., et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007, 450:219-232.
27. Kumar S., Dudley J. Bioinformatics software for biologists in the genomics era. Bioinformatics 2007, 23:1713-1717.