Open Access Highly Accessed Research article

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

João MP Alves15*, Cecilia C Klein234, Flávia Maia da Silva5, André G Costa-Martins5, Myrna G Serrano1, Gregory A Buck1, Ana Tereza R Vasconcelos4, Marie-France Sagot23, Marta MG Teixeira5, Maria Cristina M Motta6 and Erney P Camargo5

Author Affiliations

1 Virginia Commonwealth University, Richmond, VA, USA

2 BAMBOO Team, INRIA Grenoble-Rhône-Alpes, Villeurbanne, France

3 Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France

4 Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil

5 Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil

6 Laboratório de Ultraestrutura Celular Hertha Meyer. Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil

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BMC Evolutionary Biology 2013, 13:190  doi:10.1186/1471-2148-13-190

Published: 9 September 2013

Additional files

Additional file 1:

Genomic context and GC content for candidate HGT genes in the Trypanosomatidae analyzed in this work. Arrows show TBLASTN alignments of the genome against UniRef100 and KEGG proteins. Alignment orientation is displayed in blue or red, except for the alignment for the gene currently in focus, which is colored black. Coordinates are in kilobases.

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Additional file 2:

Summary of phylogenetic and genome coverage analyses of the candidate HGT genes in the Trypanosomatidae analyzed in this work and a few other genes of interest.

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Additional file 3:

Methionine salvage pathway. Enzymes surrounded by a thick gray box were shown to be horizontally transferred from Bacteria (see main text). Metabolites – I: methionine; II: S-adenosylmethionine; III: S-adenosylmethioninamine; IV: S-methyl-5-thioadenosine; V: S-methyl-5-thioribose; VI: S-methyl-5-thioribose 1-phosphate; VII: S-methyl-5-thioribulose 1-phosphate; VIII: 2,3-diketomethylthiopentyl-1-phosphate; IX: 2-hydroxy-3-keto-5-methylthiopenctenyl-1-phosphate; X: 1,2-dihydroxy3-keto-5-methylthiopentene; XI: 4-methylthio-2-oxobutanoate. Enzymes – 2.5.1.6: methionine adenosyltransferase; 4.1.1.50: adenosylmethionine decarboxylase; 2.5.1.16: spermidine synthase; 3.2.2.9: adenosylhomocysteine nucleosidase; 3.2.2.16: methylthioadenosine nucleosidase; 2.7.1.100: S-methyl-5-thioribose kinase; 2.4.2.28: S-methyl-5’-thioadenosine phosphorylase; 5.3.1.23: S-methyl-5-thioribose-1-phosphate isomerase; 4.2.1.109: methylthioribulose 1-phosphate dehydratase; 3.1.3.77: acireductone synthase; 1.13.11.54: acireductone dioxygenase; 2.6.1.5: tyrosine transaminase; 2.6.1.57: aromatic-amino-acid transaminase. SHT: symbiont-harboring trypanosomatid; RT: regular trypanosomatid; TPE: trypanosomatid proteobacterial endosymbiont.

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Additional file 4:

Maximum likelihood phylogeny of diaminopimelate epimerase (EC:5.1.1.7). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 5:

Maximum likelihood phylogeny of diaminopimelate decarboxylase (EC:4.1.1.20). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 6:

Maximum likelihood phylogeny of serine O-acetyltransferase (EC:2.3.1.30). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 7:

Maximum likelihood phylogeny of cysteine synthase (EC:2.5.1.47). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 8:

Maximum likelihood phylogeny of homoserine O-succinyltransferase (EC:2.3.1.46). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 9:

Maximum likelihood phylogeny of DNA (cytosine-5-)-methyltransferase (EC:2.1.1.37). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 10:

Maximum likelihood phylogeny of cystathionine gamma-synthase, O-acetylhomoserine aminocarboxypropyltransferase, and cystathionine beta-lyase (EC:2.5.1.48, EC:2.5.1.49, and EC:4.4.1.8). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

Format: PNG Size: 2.8MB Download file

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Additional file 11:

Maximum likelihood phylogeny of homocysteine S-methyltransferase (EC:2.1.1.10). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 12:

Maximum likelihood phylogeny of 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase (EC:2.1.1.14). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

Format: PNG Size: 1.2MB Download file

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Additional file 13:

Maximum likelihood phylogeny of S-methyl-5-thioribose kinase (EC:2.7.1.100). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 14:

Maximum likelihood phylogeny of L-threonine aldolase (EC:4.1.2.5). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 15:

Maximum likelihood phylogeny of (EC:4.2.1.20). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 16:

Maximum likelihood phylogeny of aminoacylase (EC:3.5.1.14). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 17:

Maximum likelihood phylogeny of acetylornithine deacetylase (EC:3.5.1.16). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

Format: PNG Size: 1.1MB Download file

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Additional file 18:

Maximum likelihood phylogeny of argininosuccinate synthase (EC:6.3.4.5). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 19:

Maximum likelihood phylogeny of argininosuccinate lyase (EC:4.3.2.1). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 20:

Maximum likelihood phylogeny of arginase (EC:3.5.3.1). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 21:

Maximum likelihood phylogeny of ornithine cyclodeaminase (EC:4.3.1.12). Overall tree colored according to taxonomic affiliation of sequences. Values on nodes represent bootstrap support (only 50 or greater shown) and distance bar only applies to the overall tree and not to the detailed regions.

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Additional file 22:

Genbank accession numbers for Trypanosomatidae genes characterized in this study.

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Additional file 23:

GenBank locus tags for the Ca.Kinetoplastibacterium genes analyzed in this study.

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