Lateral gene transfer in gut ciliate: parallel evolution or gene re-acquisition?

CJ Newbold, N McEwan & A Meade

There is strong evidence that all gut living ciliates are derived from a monophyletic line, furthermore whilst free living ciliates like plasmodium and tetrahymena do not contain fibrolytic genes there is growing evidence that many of the ciliates living in the gut of herbivorous insects, birds and mammals are able to degrade cellulose. Recently, based on phylogeny and codon amelioration, we have shown that the rumen ciliates have acquired their fibrolytic enzymes by lateral gene transfer from rumen bacteria in the recent evolutionary past (McEwan et al., 2008). Given the deep evolutionary branching between the ciliate containing insects, birds and even within the herbivorous mammals this suggest two non-mutually exclusive putative hypotheses:

1. All gut ciliates are derived from a non fibrolytic ancestor and acquired fibrolytic genes by parallel lateral gene transfer within their respective ecosystems (parallel evolution).
2. All gut ciliates are derived from a fibrolytic ancestor but some have lost this activity and reacquired it at a later date through lateral gene transfer (gene reacquisition).

This study aims to evaluate these hypotheses in ciliate protozoa from different gut environments.

Genomic and cDNA libraries (Devillard et al., 2003, Newbold et al., 2005, Boxma et al 2008) from rumen ciliates and Nyctotherus from the mid gut of cockroaches will be screened for functional CMCase and xylanase activity, active clones will be sequenced and the resultant sequences used for phylogenetic comparison with other ruminal and non ruminal activities [this will provide both training, in all the laboratory and bio-computing techniques required for the project,and novel information; utilising resources that have proven to contain function genes ; Ricard et al, 2006, Boxma et al 2008].

New metagenomic cDNA libraries will be constructed from ciliates recovered from the hindgut of horses, again active cellulases and xylanases will be recovered and sequenced. [This will be the 1st ever report of the cloning and characterisation of activities from ciliates in the equid gut.] Thereafter sequences will undergo bioinformatical analysis as we seek to establish if ciliates in the horse gut also obtained their fibrolytic enzymes by lateral gene transfer and, via an analysis of codon amelioration, how recently [when combined with the information on lateral gene transfer in the rumen ciliates this will provide the 1st available comparison of acquisition of genes in different gut ciliates].