title: Transmembrane protein oxygen content and compartmentalization of cells.
abstract: Recently, there was a report that explored the oxygen content of transmembrane proteins over macroevolutionary time scales where the authors observed a correlation between the geological time of appearance of compartmentalized cells with atmospheric oxygen concentration. The authors predicted, characterized and correlated the differences in the structure and composition of transmembrane proteins from the three kingdoms of life with atmospheric oxygen concentrations in geological timescale. They hypothesized that transmembrane proteins in ancient taxa were selectively excluding oxygen and as this constraint relaxed over time with increase in the levels of atmospheric oxygen the size and number of communication-related transmembrane proteins increased. In summary, they concluded that compartmentalized and non-compartmentalized cells can be distinguished by how oxygen is partitioned at the proteome level. They derived this conclusion from an analysis of 19 taxa. We extended their analysis on a larger sample of taxa comprising 309 eubacterial, 34 archaeal, and 30 eukaryotic complete proteomes and observed that one can not absolutely separate the two groups of cells based on partition of oxygen in their membrane proteins. In addition, the origin of compartmentalized cells is likely to have been driven by an innovation than happened 2700 million years ago in the membrane composition of cells that led to the evolution of endocytosis and exocytosis rather than due to the rise in concentration of atmospheric oxygen.
authors.affiliation: Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Rajkumar
authors.initials: R
authors.lastname: Sasidharan
authors.forename: Andrew
authors.initials: A
authors.lastname: Smith
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D003593:Cytoplasm / Q000378:metabolism; D016678:Genome; D007425:Intracellular Membranes / Q000378:metabolism; D008055:Lipids / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry*; D008954:Models, Biological; D010100:Oxygen / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D008055:Lipids; D008565:Membrane Proteins; D011506:Proteins; D010100:Oxygen