Influence of the lifestyle on horizontal gene transfer in free-living, symbiont-harboring, and parasitic protozoa Sabrina Ellenberger, Lisa Siegmund, and Johannes Wöstemeyer Chair of General Microbiology and Microbial Genetics, Friedrich Schiller University Jena, Neugasse 24, 07743 Jena, Germany
[email protected]
Introduction Lifestyles of protozoa induce differences in frequency of horizontal gene transfer Phagotrophic protozoa are able to replace ancient eukaryotic genes by prokaryotic genes from food bacteria. Physical contact, which is needed for HGT, can also occur in symbiotic or host-parasite relationships. A third mediator for gene transfer between prokaryotes and eukaryotes are virus infections. Amoeba: free-living (Dictyostelium discoideum) or parasitic (Entamoeba histolytica) Ciliates: non-parasitic (Paramecium tetraurelia, Tetrahymena thermophila) Trypanosomatids: symbiont-harboring (Strigomonas culicis) or pathogenic (Leishmania major) Apicomplexa: parasitic (Cryptosporidium parvum, Plasmodium falciparum, Toxoplasma gondii)
Andersson, 2005
Methods
Phylogenetic trees on three levels Multilevel analysis of phylogenetic trees of malate dehydrogenase: Single tree consists of the sequences of one organism (protozoon) plus one sequence of a fungus (Saccharomyces cerevisiae), a plant (Arabidopsis thaliana), a metazoon (Homo sapiens), and one bacterial sequence per eukaryotic protein subtype. Small tree includes all eukaryotic sequences plus one bacterial sequence per eukaryotic protein subtype. Large tree contains all prokaryotic and eukaryotic sequences. All trees provide clear evidence for HGT in MDH_3 variant of malate dehydrogenase in Apicomplexa (labeled with ellipses).
The HGT Calculator is a Java application for detection of HGT between prokaryotes and protozoa. We developed an algorithm combining four approaches for the detection of HGT events in a score-based application.
i. protein domain-based information in InterPro [1] ii. BLAST search via UniProtJAPI [2] and alien index [3] iii. GC content and codon adaptation index [4] iv. multilevel analysis of Neighbor-Joining trees [5] This approach works without the requirement for complete genomes or any species trees. The HGT Calculator runs with the protozoa sequences and some reference sequences from Saccharomyces, Arabidopsis, Homo, and a set of prokaryotes. We constructed a HGT score, which describes the probability for a sequence to be a horizontal gene transfer candidate. The HGT Calculator is able to distinguish between single, multiple, and endosymbiotic gene transfer (EGT) events. Single events have a score higher than 45 and appear as the only score for this protein, which is higher than zero. Multiple events show several scores higher than 30. EGT results in scores less than 30.
HGT score
L. major ICDH_1
L. major ICDH_2
Probable sources of foreign genetic material
Estimation of HGT in Protozoa AI = log ((Best E-value for eukaryotes) + E-200) – log ((Best E-value for prokaryotes) + E-200)
Dictyostelium
Dictyostelium
Entamoeba
Entamoeba
Paramecium
Paramecium Number of HGT known from literature Number of AI > 45 for genes from amino acid biosynthesis pathway
Tetrahymena Cryptosporidium Plasmodium
Tetrahymena Cryptosporidium Plasmodium
Toxoplasma
Toxoplasma
Leishmania
Leishmania
Strigomonas
Strigomonas 0
10
20
30
40
50
60
70
80
90
ASS: Argininosuccinate synthase [9, 10]; CS: Cysteine synthase [7]; FBP: Fructose-1,6-biphosphatase; FECH: Ferrochelatase [9]; Supported by references
Archaea Actinobacteria Bacteroidetes/Chlorobi Chloroflexi Cyanobacteria Firmicutes Proteobacteria Spirochaetes Other bacteria
0%
100
HDH: Homoserine dehydrogenase [10]; ICDH: Isocitrate dehydrogenase [9]; IPPI: Isopentenyl-diphosphate delta-isomerase [9]; IPT: Isopentenyl transferase [6];
20%
40%
60%
80%
100%
MDH: Malate dehydrogenase [8]; SAT: Serine acetyltransferase [7, 9, 10]; TK: Thymidine kinase [8]; TYMS: Thymidylate synthase [6];
Results HGT seems to occur more frequent in parasitic and pathogenic protozoa than in free-living ones. Parasitic protozoa often have reduced pathways and are dependent on their hosts. They can adapt transferred genes directly, if they show an immediate benefit to the protozoon. The pressure is higher for free-living organisms, because any new gene could disturb existing pathways and regulatory mechanisms, and reduce the fitness of the organism. They do not have the alternative to benefit from a host organism.
The ratio of potential sources of HGT is higher for proteobacteria than for all other groups of bacteria. The donors of ancient endosymbiotic gene transfers (EGT) were cyanobacteria or -proteobacteria. Many sequences, which have a sequence from a proteobacteria as best prokaryotic BLAST hit are mitochondrial genes or ancient EGT. Single HGT events between endosymbionts and their hosts yield the highest HGT scores, for example, homoserine dehydrogenase from Strigomonas culicis with a HGT score of 65.
References [1] Hunter et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucl. Acids Res., 40, D306-D312. [2] Patient et al. (2008) UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics, 24, 1321-1322. [3] Gladyshev et al. (2008) Massive horizontal gene transfer in Bdelloid rotifers. Science, 320, 1210-1213. [4] Xia (2007) An improved implementation of codon adaptation index. Evol. Bioinform. Online, 3, 53-58. [5] Larkin et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. [6] Eichinger et al. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature, 435, 43-57. [7] Loftus et al. (2005) The genome of the protist parasite Entamoeba histolytica. Nature, 433, 865-868.
[8] Huang et al. (2004) Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol., 5, R88. [9] Opperdoes and Michels (2007) Horizontal gene transfer in trypanosomatids. Trends Parasitol., 23, 470-476. [10] Alves et al. (2013) Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers. BMC Evol. Biol. 13, 190.
