Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes.
BACKGROUND
Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the hybrid-cluster protein, A-type flavoprotein, glucosamine-6-phosphate isomerase, and alcohol dehydrogenase E. These four genes have a limited distribution among sequenced prokaryotic and eukaryotic genomes and were previously implicated in gene transfer events affecting eukaryotes. If our previous contention that these genes were introduced by LGT independently into the diplomonad and Entamoeba lineages were true, we expect that the number of putative transfers and the phylogenetic signal supporting LGT should be stable or increase, rather than decrease, when novel eukaryotic and prokaryotic homologs are added to the analyses.


RESULTS
The addition of homologs from phagotrophic protists, including several Entamoeba species, the pelobiont Mastigamoeba balamuthi, and the parabasalid Trichomonas vaginalis, and a large quantity of sequences from genome projects resulted in an apparent increase in the number of putative transfer events affecting all three domains of life. Some of the eukaryotic transfers affect a wide range of protists, such as three divergent lineages of Amoebozoa, represented by Entamoeba, Mastigamoeba, and Dictyostelium, while other transfers only affect a limited diversity, for example only the Entamoeba lineage. These observations are consistent with a model where these genes have been introduced into protist genomes independently from various sources over a long evolutionary time.


CONCLUSIONS
Phylogenetic analyses of the updated datasets using more sophisticated phylogenetic methods, in combination with the gene distribution analyses, strengthened, rather than weakened, the support for LGT as an important mechanism affecting the evolution of these gene families. Thus, gene transfer seems to be an on-going evolutionary mechanism by which genes are spread between unrelated lineages of all three domains of life, further indicating the importance of LGT from non-organellar sources into eukaryotic genomes.
Andersson
Jan O
JO
Institute of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, S-751 24 Uppsala, Sweden. jan.andersson@icm.uu.se
Hirt
Robert P
RP
Foster
Peter G
PG
Roger
Andrew J
AJ
D000426:Alcohol Dehydrogenase / Q000235:genetics; D000445:Aldehyde Oxidoreductases / Q000235:genetics; D019747:Aldose-Ketose Isomerases / Q000235:genetics; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D044822:Biodiversity; D005075:Biological Evolution; D016054:DNA, Protozoan / Q000737:chemistry; D004463:Ecology; D004747:Entamoeba / Q000145:classification / Q000235:genetics; D029968:Escherichia coli Proteins; D056890:Eukaryota / Q000145:classification / Q000235:genetics*; D005247:Feeding Behavior / Q000502:physiology; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D007506:Iron-Sulfur Proteins / Q000235:genetics; D008390:Markov Chains; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009097:Multienzyme Complexes / Q000235:genetics; D009247:NADH, NADPH Oxidoreductases / Q000235:genetics; D009253:Naegleria / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D014246:Trichomonas vaginalis / Q000145:classification / Q000235:genetics
D001426:Bacterial Proteins; D016054:DNA, Protozoan; D029968:Escherichia coli Proteins; D007506:Iron-Sulfur Proteins; D009097:Multienzyme Complexes; C075199:prismane protein, Desulfovibrio vulgaris; D000426:Alcohol Dehydrogenase; C068383:adhE protein, E coli; C464438:FprA protein, M tuberculosis; D000445:Aldehyde Oxidoreductases; D009247:NADH, NADPH Oxidoreductases; C020582:glucosamine-6-phosphate isomerase; D019747:Aldose-Ketose Isomerases