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PMID: 17355171 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

PLoS biology ·Vol. 5 ·No. 3 ·2007-03-00 ·Pages e16

Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC

Abstract

Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature.

MeSH Terms
Expressed Sequence Tags Oceans and Seas Proteins/chemistry,genetics Water Microbiology
Chemicals
Proteins
Authors & Affiliations
33 authors, click to expand affiliations / ORCID
Yooseph Shibu
J. Craig Venter Institute, Rockville, Maryland, United States of America. Shibu.Yooseph@venterinstitute.org
Sutton Granger
Rusch Douglas B
Halpern Aaron L
Williamson Shannon J
Remington Karin
Eisen Jonathan A
Heidelberg Karla B
Manning Gerard
Li Weizhong
Jaroszewski Lukasz
Cieplak Piotr
Miller Christopher S
Li Huiying
Mashiyama Susan T
Joachimiak Marcin P
van Belle Christopher
Chandonia John-Marc
Soergel David A
Zhai Yufeng
Natarajan Kannan
Lee Shaun
Raphael Benjamin J
Bafna Vineet
Friedman Robert
Brenner Steven E
Godzik Adam
Eisenberg David
Dixon Jack E
Taylor Susan S
Strausberg Robert L
Frazier Marvin
Venter J Craig
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Article Info
Journal
PLoS biology
Abbr.
PLoS Biol
ISSN
1545-7885
DOI
10.1371/journal.pbio.0050016
Email
shibu.yooseph@venterinstitute.org
Published
2007-03-00
Pages
e16
Language
English
Region
United States
NLM ID
101183755
PMCID
PMC1821046
Subset
IM
Grants
NHGRI NIH HHS · T32 HG000047 · United States
NIGMS NIH HHS · R01 GM073109 · United States
NCRR NIH HHS · 5U54 RR020843-02 · United States
NHGRI NIH HHS · 5T32 HG00047 · United States
NHGRI NIH HHS · K22 HG000056 · United States
NHGRI NIH HHS · K22 HG00056 · United States
NIGMS NIH HHS · P20 GM068136 · United States
NCRR NIH HHS · U54 RR020843 · United States
NCI NIH HHS · P30 CA014195 · United States
Corrections
CommentIn
PMID: 17355178
CommentIn
PMID: 20076663
External Links
PubMed source DOI: 10.1371/journal.pbio.0050016 PMC Full Text View journal details
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