Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi
- Published
- Accepted
- Subject Areas
- Biochemistry, Genomics, Molecular Biology, Parasitology, Infectious Diseases
- Keywords
- Chagas disease, Metabolic Regulation, Trypanosoma cruzi, Surface Proteins, RNA-seq
- Copyright
- © 2017 Berná et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi. PeerJ Preprints 5:e2782v1 https://doi.org/10.7287/peerj.preprints.2782v1
Abstract
American trypanosomiasis is a chronic and endemic disease, which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi, amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to the different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vector, showed higher expression on genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also a general down regulation of surface glycoproteins was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, an also express a specific subset of surface glycoproteins coding genes. In addition, these results allowed to improve the annotation of Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Table S1. Highly expressed genes and GO analyses
Comparison of 500 highest expressed genes among stages and Gene Ontology analysis
Table S2. Differentially expressed genes
Result of differentially expression analysis. Gene ontology of stage specific DEGs
Table S3. Oxidative metabolism
Normalized read counts of Krebs cycle and respiratory chain genes
Table S4. Antioxidant genes
Normalized read counts of antioxidant genes
Table S5. Lipid metabolism
Normalized read counts of genes related to different lipid related metabolic processes: fatty acid, steroid and phospholipid
Table S6. Carbohydrate metabolism
Normalized read counts of glycolytic and pentose phosphate pathway genes
Table S7. Protein metabolism
Normalized read counts of genes coding general protein metabolic pathways including protein degradation, protein synthesis, amino acid transport and metabolism
Table S8. New genes prediction
Characterization of putative new transcripts predicted for Dm28c. Statistical description of the validation by HMM and Blast searches
Table S9. Raw and normalized counts
Raw transcript levels from ERANGE. Normalized counts were obtained from DESeq2
Figure S1. Stage specific TS examination
Representation of predicted molecular weights of trans-sialidases specific from amastigotes (aTS, green), epimastigotes (eTS, blue) and trypomastigotes (tTS, orange). T test was performed, ** represents p-value<0.01.
Figure S2. Surface gene composition in different T. cruzi stages
A) Expression of each gene in normalized read counts is shown for the different group of membrane component. At the X axis each gene is plotted at the same order,for the three stages. B) Sum of total normalized read counts per gene Kb of each family group in the three stages. Different cycle stages are represented: amastigote (green), epimastigote (blue) and trypomastigote (orange).
Figure S3. GP63 philogeny
Neighbor-joining tree of the protein sequences of GP63 genes; numbers correspond to gene ID. Differentially up-regulated in A (green), differentially up-regulated in T (orange)
Figure S4. Gene expression patterns
Comparison to known protein expression profiles. A) flagellum associated genes down-regulated in amastigotes. B) genes related to conversion of histidine to glutamate up-regulated in epimastigotes. C) mucins up regulated in trypomastigotes.