Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications.
BACKGROUND
Determining the complete repertoire of protein structures for all soluble, globular proteins in a single organism has been one of the major goals of several structural genomics projects in recent years.


RESULTS
We report that this goal has nearly been reached for several "minimal organisms"--parasites or symbionts with reduced genomes--for which over 95% of the soluble, globular proteins may now be assigned folds, overall 3-D backbone structures. We analyze the structures of these proteins as they relate to cellular functions, and compare conservation of fold usage between functional categories. We also compare patterns in the conservation of folds among minimal organisms and those observed between minimal organisms and other bacteria.


CONCLUSIONS
We find that proteins performing essential cellular functions closely related to transcription and translation exhibit a higher degree of conservation in fold usage than proteins in other functional categories. Folds related to transcription and translation functional categories were also overrepresented in minimal organisms compared to other bacteria.
Chandonia
John-Marc
JM
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Kim
Sung-Hou
SH
D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D017124:Conserved Sequence; D030562:Databases, Protein; D019143:Evolution, Molecular; D005916:Globulins / Q000737:chemistry / Q000378:metabolism; D017510:Protein Folding; D017433:Protein Structure, Secondary; D020543:Proteome; D040901:Proteomics; D013559:Symbiosis / Q000235:genetics
D001426:Bacterial Proteins; D005916:Globulins; D020543:Proteome