Molecular signatures for the main phyla of photosy

Authors: Radhey S Gupta

Publish Date: 2010/04/23

Volume: 104, Issue: 2-3, Pages: 357-372

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Abstract

The bacterial groups corresponding to different photosynthetic prokaryotes are presently identified mainly on the basis of their branching in phylogenetic trees The availability of genome sequences is enabling identification of many molecular signatures that are specific for different groups of photosynthetic bacteria Our recent work has identified large numbers of signatures consisting of conserved inserts or deletions indels in widely distributed proteins as well as whole proteins that are specific for various sequenced species/strains from Cyanobacteria Chlorobi and Proteobacteria phyla Based upon these signatures it is now possible to identify/distinguish bacteria from these phyla of photosynthetic bacteria as well as their major subclades in clear molecular terms The use of these signatures in conjunction with phylogenomic analyses summarized here is leading to a holistic picture concerning the branching order and evolutionary relationships among the above groups of photosynthetic bacteria Although detailed studies in this regard have not yet been carried on Chloroflexi and Heliobacteriaceae we have identified some conserved indels that are specific for these groups Some of the conserved indels for the photosynthetic bacteria are present in photosynthesisrelated proteins These include a 4 aa insert in the pyruvate flavodoxin/ferridoxin oxidoreductase that is specific for the genus Chloroflexus a 2 aa insert in magnesium chelatase that is uniquely shared by all Cyanobacteria except the deepest branching Clade A Gloebacterales a 6 aa insert in an Atype flavoprotein that is specific for various marine unicellular Cyanobacteria a 2 aa insert in heme oxygenase that is specific for various Prochlorococcus strains/isolates and 1 aa deletion in the protein protochlorophyllide oxidoreductase that is commonly shared by various Prochlorococcus strains except the deepest branching isolates MIT 9303 and MIT 9313 The identified CSIs are located in the structures of these proteins in surface loops indicating that they may be important in mediating protein–protein interactions The cellular functions of these conserved indels or most of the signature proteins are presently unknown but they provide valuable means for discovering novel properties that are unique to different groups of photosynthetic bacteria

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