Predicting the Proteins of Angomonas deanei, Strigomonas culicis and Their Respective Endosymbionts Reveals New Aspects of the Trypanosomatidae Family

Endosymbiont-bearing trypanosomatids have been considered excellent models for the study of cell evolution because the host protozoan co-evolves with an intracellular bacterium in a mutualistic relationship. Such protozoa inhabit a single invertebrate host during their entire life cycle and exhibit special characteristics that group them in a particular phylogenetic cluster of the Trypanosomatidae family, thus classified as monoxenics. in an effort to better understand such symbiotic association, we used DNA pyrosequencing and a reference-guided assembly to generate reads that predicted 16,960 and 12,162 open reading frames (ORFs) in two symbiont-bearing trypanosomatids, Angomonas deanei (previously named as Crithidia deanei) and Strigomonas culicis (first known as Blastocrithidia culicis), respectively. Identification of each ORF was based primarily on TriTrypDB using tblastn, and each ORF was confirmed by employing getorf from EMBOSS and Newbler 2.6 when necessary. the monoxenic organisms revealed conserved housekeeping functions when compared to other trypanosomatids, especially compared with Leishmania major. However, major differences were found in ORFs corresponding to the cytoskeleton, the kinetoplast, and the paraflagellar structure. the monoxenic organisms also contain a large number of genes for cytosolic calpain-like and surface gp63 metalloproteases and a reduced number of compartmentalized cysteine proteases in comparison to other TriTryp organisms, reflecting adaptations to the presence of the symbiont. the assembled bacterial endosymbiont sequences exhibit a high A+T content with a total of 787 and 769 ORFs for the Angomonas deanei and Strigomonas culicis endosymbionts, respectively, and indicate that these organisms hold a common ancestor related to the Alcaligenaceae family. Importantly, both symbionts contain enzymes that complement essential host cell biosynthetic pathways, such as those for amino acid, lipid and purine/pyrimidine metabolism. These findings increase our understanding of the intricate symbiotic relationship between the bacterium and the trypanosomatid host and provide clues to better understand eukaryotic cell evolution.Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)ERC AdG SISYPHEUniv Fed Rio de Janeiro, Inst Biofis Carlos Chagas Filho, Lab Ultraestrutura Celular Hertha Meyer, BR-21941 Rio de Janeiro, BrazilUniv Fed Rio de Janeiro, Inst Biofis Carlos Chagas Filho, Lab Metab Macromol Firmino Torres de Castro, BR-21941 Rio de Janeiro, BrazilLab Bioinformat, Lab Nacl Computacao Cient, Rio de Janeiro, BrazilINRIA Grenoble Rhone Alpes, BAMBOO Team, Villeurbanne, FranceUniv Lyon 1, CNRS, UMR5558, Lab Biometrie & Biol Evolut, F-69622 Villeurbanne, FranceUniv Estadual Campinas, Inst Biol, Dept Genet Evolucao & Bioagentes, São Paulo, BrazilUniv São Paulo, Fac Ciencias Farmaceut Ribeirao Preto, Dept Ciencias Farmaceut, São Paulo, BrazilLab Nacl Ciencia & Tecnol Bioetano, São Paulo, BrazilUniv Fed Minas Gerais, Inst Ciencias Biol, Dept Bioquim & Imunol, Belo Horizonte, MG, BrazilUniv Fed Goias, Inst Ciencias Biol, Mol Biol Lab, Goiania, Go, BrazilFundacao Oswaldo Cruz, Inst Carlos Chagas, Lab Biol Mol Tripanossomatideos, Curitiba, Parana, BrazilFundacao Oswaldo Cruz, Inst Carlos Chagas, Lab Genom Func, Curitiba, Parana, BrazilUniv Estadual Campinas, Ctr Pluridisciplinar Pesquisas Quim Biol & Agr, São Paulo, BrazilUniv Fed Minas Gerais, Inst Ciencias Biol, Dept Parasitol, Belo Horizonte, MG, BrazilUniv Fed Santa Catarina, Dept Microbiol Imunol & Parasitol, Ctr Ciencias Biol, Lab Protozool & Bioinformat, Florianopolis, SC, BrazilUniv Fed Vicosa, Dept Bioquim & Biol Mol, Ctr Ciencias Biol & Saude, Vicosa, MG, BrazilInst Butantan, Lab Especial Ciclo Celular, São Paulo, BrazilUniv São Paulo, Dept Biol, Fac Filosofia Ciencias & Letras Ribeirao Preto, São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, São Paulo, BrazilUniversidade Federal de São Paulo, Escola Paulista Med, Dept Microbiol Imunol & Parasitol, São Paulo, BrazilWeb of Scienc

The Bacterium Endosymbiont of Crithidia deanei Undergoes Coordinated Division with the Host Cell Nucleus

In trypanosomatids, cell division involves morphological changes and requires coordinated replication and segregation of the nucleus, kinetoplast and flagellum. In endosymbiont-containing trypanosomatids, like Crithidia deanei, this process is more complex, as each daughter cell contains only a single symbiotic bacterium, indicating that the prokaryote must replicate synchronically with the host protozoan. In this study, we used light and electron microscopy combined with three-dimensional reconstruction approaches to observe the endosymbiont shape and division during C. deanei cell cycle. We found that the bacterium replicates before the basal body and kinetoplast segregations and that the nucleus is the last organelle to divide, before cytokinesis. In addition, the endosymbiont is usually found close to the host cell nucleus, presenting different shapes during the protozoan cell cycle. Considering that the endosymbiosis in trypanosomatids is a mutualistic relationship, which resembles organelle acquisition during evolution, these findings establish an excellent model for the understanding of mechanisms related with the establishment of organelles in eukaryotic cells

Numbers of ORFs identified in <i>A. deanei</i> and <i>S. culicis</i> and their symbionts, according to the mechanisms of DNA replication and repair, signal transduction, transcription and translation.

<p>Numbers of ORFs identified in <i>A. deanei</i> and <i>S. culicis</i> and their symbionts, according to the mechanisms of DNA replication and repair, signal transduction, transcription and translation.</p

Members of the Fts family and PBPs that are present in endosymbionts of <i>A. deanei</i> and <i>S. culicis</i>.

<p>nd: not determined.</p

Protein Reference Sequence-Guided Assembly data of <i>A. deanei</i> and <i>S. culicis</i> genomes.

<p>Protein Reference Sequence-Guided Assembly data of <i>A. deanei</i> and <i>S. culicis</i> genomes.</p

Phylogenetic of histones of <i>A. deanei, S. culicis,</i> and other trypanosomatids.

<p>Histone protein (panel A) and nucleotide (panel B) sequences were generated by MUSCLE tool using 10 iterations in the Geneious package <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060209#pone.0060209-Drummond1" target="_blank">[120]</a>. Trees were constructed using the Geneious Tree Builder, by employing Jukes-Cantor genetic distance model with a neighbor-joining method and no out-groups. The consensus trees were generated from 100 bootstrap replicates of all detected histone genes, as shown below. Scale bars are indicated for each consensus tree. The trees in panel A are based in a collection of sequences of all trypanosomatids. The nucleotide sequences used for dihydrofolate reductase-thymidylate synthase are: <i>T. cruzi,</i> XM_810234; <i>T. brucei</i>, XM_841078; <i>T. vivax,</i> HE573023; <i>L. mexicana</i>, FR799559; <i>L. major</i>, XM_001680805; <i>L. infantum</i>, XM_001680805; and <i>C. fasciculata</i>, M22852.</p

Summary of the origin of ORFs found in <i>A. deanei</i> and <i>S. culicis.</i>

*<p>Number of genes with identity to Prokaryotes.</p>**<p>Number of genes with identity to Eukaryotes.</p>***<p>Ratio of the number of genes with identity to Prokaryotes/Eukaryotes.</p

Purine production, acquisition, and utilization in <i>A. deanei</i> and <i>S. culicis.</i>

<p>The figure illustrates the production, acquisition and utilization of purines in the host trypanosomes considering the presence of endosymbiont enzymes. This model suggests that the trypanosomatid acquires purines from the symbiont, which synthesizes them <i>de novo</i>. Some ecto-localized proteins, such as apyrase (APY) and adenosine deaminase (ADA), could be responsible for the generation of extracellular nucleosides, nucleobases, and purines. Nucleobases and purines could be acquired by the parasite through membrane transporters (T) or diffusion and could be incorporated into DNA, RNA, and kDNA molecules after “purine salvage pathway” processing. Abbreviations: NTP (nucleoside tri-phosphate), NDP (nucleoside di-phosphate), NMP (nucleoside mono- phosphate), N (nucleobase), ADO (adenosine), INO (inosine).</p

Oxidative stress-related genes in the genomes of <i>A. deanei</i>, <i>S. culicis</i> and <i>L. major</i>.

<p>The figure shows the number of ORFs for the indicated enzymes for each species.</p

Kinase families identified in trypanosomatids.

<p>Kinase families identified in trypanosomatids.</p