NDLI: Molecular signatures for the Crenarchaeota and the Thaumarchaeota

Content Provider	Springer Nature Link
Author	Gupta, Radhey S. Shami, Ali
Copyright Year	2010
Abstract	Crenarchaeotes found in mesophilic marine environments were recently placed into a new phylum of Archaea called the Thaumarchaeota. However, very few molecular characteristics of this new phylum are currently known which can be used to distinguish them from the Crenarchaeota. In addition, their relationships to deep-branching archaeal lineages are unclear. We report here detailed analyses of protein sequences from Crenarchaeota and Thaumarchaeota that have identified many conserved signature indels (CSIs) and signature proteins (SPs) (i.e., proteins for which all significant blast hits are from these groups) that are specific for these archaeal groups. Of the identified signatures 6 CSIs and 13 SPs are specific for the Crenarchaeota phylum; 6 CSIs and >250 SPs are uniquely found in various Thaumarchaeota (viz. Cenarchaeum symbiosum, Nitrosopumilus maritimus and a number of uncultured marine crenarchaeotes) and 3 CSIs and ~10 SPs are found in both Thaumarchaeota and Crenarchaeota species. Some of the molecular signatures are also present in Korarchaeum cryptofilum, which forms the independent phylum Korarchaeota. Although some of these molecular signatures suggest a distant shared ancestry between Thaumarchaeota and Crenarchaeota, our identification of large numbers of Thaumarchaeota-specific proteins and their deep branching between the Crenarchaeota and Euryarchaeota phyla in phylogenetic trees shows that they are distinct from both Crenarchaeota and Euryarchaeota in both genetic and phylogenetic terms. These observations support the placement of marine mesophilic archaea into the separate phylum Thaumarchaeota. Additionally, many CSIs and SPs have been found that are specific for different orders within Crenarchaeota (viz. Sulfolobales—3 CSIs and 169 SPs, Thermoproteales—5 CSIs and 25 SPs, Desulfurococcales—4 SPs, and Sulfolobales and Desulfurococcales—2 CSIs and 18 SPs). The signatures described here provide novel means for distinguishing the Crenarchaeota and the Thaumarchaeota and for the classification of related and novel species in different environments. Functional studies on these signature proteins could lead to discovery of novel biochemical properties that are unique to these groups of archaea.
Starting Page	133
Ending Page	157
Page Count	25
File Format	PDF
ISSN	00036072
Journal	Antonie van Leeuwenhoek
Volume Number	99
Issue Number	2
e-ISSN	15729699
Language	English
Publisher	Springer Netherlands
Publisher Date	2010-08-14
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Mesophilic crenarchaea Thaumarchaeota Crenarchaeota Archaeal phylogeny Conserved signature indels Signature proteins Korarchaeum Sulfolobales Thermoproteales Desulfurococcales Medical Microbiology Soil Science & Conservation Plant Sciences Microbiology
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Microbiology

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