Abstract
BackgroundLateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. Here we present a study of the occurrence of the latter gene replacement phenomenon in the four gene families encoding different classes of glutamate dehydrogenase (GDH), to evaluate and compare the patterns and rates of lateral gene transfer (LGT) in prokaryotes and eukaryotes.ResultsWe extend the taxon sampling of gdh genes with nine new eukaryotic sequences and examine the phylogenetic distribution pattern of the various GDH classes in combination with maximum likelihood phylogenetic analyses. The distribution pattern analyses indicate that LGT has played a significant role in the evolution of the four gdh gene families. Indeed, a number of gene transfer events are identified by phylogenetic analyses, including numerous prokaryotic intra-domain transfers, some prokaryotic inter-domain transfers and several inter-domain transfers between prokaryotes and microbial eukaryotes (protists).ConclusionLGT has apparently affected eukaryotes and prokaryotes to a similar extent within the gdh gene families. In the absence of indications that the evolution of the gdh gene families is radically different from other families, these results suggest that gene transfer might be an important evolutionary mechanism in microbial eukaryote genome evolution.
Highlights
Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs
As noted before [12,14], glutamate dehydrogenase (GDH)-1 is found in eubacteria and eukaryotes, GDH-2 is found in all domains of life, and GDH-4 is only found in eubacteria
GDH-1 and GDH2 cDNA clones from the red alga Porphyra yezoensis, GDH1 cDNA clones the oomycete Phytophthora infestans, the diplomonad Spironucleus barkhanus, and the parabasalid Trichomonas vaginalis, and a GDH-2 cDNA clone from the green alga Chlamydomonas reinhardtii were kindly made available from the various EST projects [15,16,17] and fully sequenced
Summary
Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. We present a study of the occurrence of the latter gene replacement phenomenon in the four gene families encoding different classes of glutamate dehydrogenase (GDH), to evaluate and compare the patterns and rates of lateral gene transfer (LGT) in prokaryotes and eukaryotes. We recently presented an analysis which showed a number of transfers involving eukaryotes, mostly in the prokaryoteto-eukaryote direction, and between different eukaryotic lineages [9]. These examples indicate that LGT does affect protists, the quantitative importance of the process in eukaryotic genome evolution remains unclear [10,11]. We have selected the glutamate dehydrogenase (gdh) gene families to investigate the (page number not for citation purposes)
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