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

Background Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont’s contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here. Results Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes. Conclusion We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of experimental results. We uncovered the remarkable plasticity in essential amino acid biosynthesis pathway evolution in these protozoans, demonstrating heavy influence of horizontal gene transfer events, from Bacteria to trypanosomatid nuclei, in the evolution of these pathways.

We would like to thank Marta Campaner and Carmen C. Takata (USP), Vladimir Lee, Andrey Matveyev, and Yingping Wang (VCU) for technical support, and Carlisle G. Childress Jr. and J. Michael Davis (VCU Center for High-Performance Computing). Sequencing was performed in the Nucleic Acids Research Facilities, and analyses were performed in the Bioinformatics Computational Core Lab and the Center for High Performance Computing at VCU. The research leading to these results was funded by: the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement n° [247073]10; the French project ANR MIRI BLAN08-1335497; FAPERJ grant coordinated by Dr. Cristina Motta and the FAPERJ-INRIA project RAMPA; by the Laboratoire International Associé (LIA) LIRIO co-coordinated by Ana Tereza R. de Vasconcelos (Labinfo, LNCC, Brazil) and Marie-France Sagot (LBBE, UCBL-CNRS-INRIA, France); the National Science Foundation [USA, grant number NSF DEB-0830056 to Gregory Buck]; and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Brazil) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Brazil) to Cristina Motta, Marta M.G. Teixeira and Erney P. Camargo.