The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

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.

Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae

“…The detection of inteins from all of our samples in this study, the presence of a variety of putative inteins from every station from the Global Ocean Survey data set (Yooseph et al, 2007) and the presence of DNA polymerase I motif C inteins in the phycodnavirus isolates HaV (Nagasaki et al, 2005) and CeV (Monier et al, 2008) all suggest that inteins are common among marine viruses. This raises the question of how DNA polymerase I motif C inteins are acquired by phycodnaviruses.…”

“…The designations for sequences retrieved in this study are in bold type and begin with 'KB' for Kāne'ohe Bay. Sequences starting with 'JCVI' are environmental sequences from the Global Ocean Survey (Yooseph et al, 2007). A blue circle adjacent to a sequence indicates the intein encodes a homing endonuclease.…”

Protein function space: viewing the limits or limited by our view?

“…On the other hand, uncharacterized 'singletons' are rarely saturating, that is, each genome or environment contains a lot of uncharacterizable ORFs (or ORF fragments). That novel families grow linearly if more ocean samples are added was also a major conclusion of a recent metagenomics ocean survey [63 • ], when applying a similar method to that described in [49 • ,50]. However, this observed 'novelty', based on the absence of homology to anything we know, could also be inflated by gene fragments that are too short to be recognized or by spurious gene predictions (although stringent criteria were applied in this study [63 • ]).…”

Microbiotes et métagénomique

“…L'inventaire des gènes est encore plus impressionnant que celui des espèces rencontrées [25][26][27]. Mais que peut-on en dire ?…”