Phylogenetic analysis of the triterpene cyclase protein family in prokaryotes and eukaryotes suggests bidirectional lateral gene transfer

Abstract

Functional constraints to modifications in triterpene cyclase amino acid sequences make them good candidates for evolutionary studies on the phylogenetic relatedness of these enzymes in prokaryotes as well as in eukaryotes. In this study, we used a set of identified triterpene cyclases, a group of mainly bacterial squalene cyclases and a group of predominantly eukaryotic oxidosqualene cyclases, as seed sequences to identify 5288 putative triterpene cyclase homologues in publicly available databases. The Cluster Analysis of Sequences software was used to detect groups of sequences with increased pairwise sequence similarity. The sequences fall into two main clusters, a bacterial and a eukaryotic. The conserved, informative regions of a multiple sequence alignment of the family were used to construct a neighbour-joining phylogenetic tree using the AsaturA and maximum likelihood phylogenetic tree using the PhyML software. Both analyses showed that most of the triterpene cyclase sequences were similarly grouped to the accepted taxonomic relationships of the organism the sequences originated from, supporting the idea of vertical transfer of cyclase genes from parent to offspring as the main evolutionary driving force in this protein family. However, a small group of sequences from three bacterial species (Stigmatella, Gemmata and Methylococcus) grouped with an otherwise purely eukaryotic cluster of oxidosqualene cyclases, while a small group of sequences from seven fungal species and a sequence from the fern Adiantum grouped consistently with a cluster of otherwise purely bacterial squalene cyclases. This suggests that lateral gene transfer may have taken place, entailing a transfer of oxidosqualene cyclases from eukaryotes to bacteria and a transfer of squalene cyclase from bacteria to an ancestor of the group of Pezizomycotina fungi.

Hopanoid lipids: from membranes to plant–bacteria interactions

“…For example, several members of the Polypodiales (polypod) order of ferns encode an SHC enzyme 24 that seems to exclusively produce the C 30 hopanoid diplopterol in vitro 27 . It is likely that these ferns acquired shc by horizontal transfer from bacteria 28 . Other hopanoid-like molecules in plants contain additional accessory groups not observed in bacterial hopanoids (FIG.…”

Squalene-Hopene Cyclases

“…Both enzyme types share a 16-amino-acid-long nontandem repeat known as the QW motif (see below) in addition to the presence of a large catalytic cavity in the protein center. Frickey and Kannenberg proposed that TTCs originate from a common ancestor from whom the majority of TTCs diverged in two major groups: the bacterial group, whose members use squalene as a substrate, and the eukaryotic group, cyclizing 2,3-oxidosqualene (26). For most of the proteins, vertical gene transfer from the common ancestor is assumed.…”

“…However, some lateral gene transfer seems to have taken place. For example, a eukaryote-like OSC sequence is present in the translated genome of the myxobacterium Stigmatella, and a typical bacterial SHC-like sequence is present in an ancestral Pezizomycotina fungus (26). The planctomycete Gemmata obscuriglobus even produces sterols as well as hopanoids.…”

“…Biosynthesis of sterols is also derived from squalene that is epoxidized to 2,3-oxidosqualene prior to the cyclization reaction by 2,3-oxidosqualene cyclases (OSCs) in a reaction similar to that of SHCs. SHCs and OSCs are distantly related in amino acid sequences, and both contain five to eight copies of a so-called QW motif, which seems to be unique to this enzyme class (26). Both can cyclize a variety of substrate analogs.…”

Hopanoids as functional analogues of cholesterol in bacterial membranes

“…Importantly, hopanoid synthesis does not require molecular oxygen, and hopanoids have been reported in sediments predating the enrichment of oxygen in Earth's atmosphere (6,7). Their discovery led to the proposal that they might serve as sterol surrogates in bacteria (8), especially because hopanoids and sterols share common structural features and are cyclized by closely related enzymes (9,10).…”