Trypanosoma cruzi transcriptome during axenic epimastigote growth curve

<div><p> BACKGROUND Trypanosoma cruzi is an important protozoan parasite and the causative agent of Chagas disease. A critical step in understanding T. cruzi biology is the study of cellular and molecular features exhibited during its growth curve. OBJECTIVES We aimed to acquire a global view of the gene expression profile of T. cruzi during epimastigote growth. METHODS RNA-Seq analysis of total and polysomal/granular RNA fractions was performed along the 10 days T. cruzi epimastigote growth curve in vitro, in addition to cell viability and cell cycle analyses. We also analysed the polysome profile and investigated the presence of granular RNA by FISH and western blotting. FINDINGS We identified 1082 differentially expressed genes (DEGs), of which 220 were modulated in both fractions. According to the modulation pattern, DEGs were grouped into 12 clusters and showed enrichment of important gene ontology (GO) terms. Moreover, we showed that by the sixth day of the growth curve, polysomal content declined greatly and the RNA granules content appeared to increase, suggesting that a portion of mRNAs isolated from the sucrose gradient during late growth stages was associated with RNA granules and not only polyribosomes. Furthermore, we discuss several modulated genes possibly involved in T. cruzi growth, mainly during the stationary phase, such as genes related to cell cycle, pathogenesis, metabolic processes and RNA-binding proteins.</p></div

Cellular localization of tagged Hel45 in <i>Trypanosoma cruzi</i>.

<p>(A) Detection of exogenous Hel45 and a Hel45 NES deletion mutant (Hel45ΔNES) (both tagged with PTP at the NT) by indirect immunofluorescence microscopy with an anti-ProtA antibody. DAPI = DNA stained with DAPI. Hel45 =  localization of tagged Hel45 or Hel45ΔNES. MERGE = merged images for DAPI staining and Hel45 localization. N = nucleus. K = kinetoplast. Arrows = parasites with nuclear accumulation of tagged Hel45. Bar = 5 µm. (B and C) Western blot of total extract from wild-type epimastigotes (WT) and epimastigotes expressing recombinant Hel45 (B) or Hel45ΔNES (C) tagged with a PTP at the N-terminus (NT). Lane 1 =  detection with anti-Hel45 antibodies. Lane 2 =  detection with anti-ProtA antibodies.</p

Localization of Hel45 after actinomycin D treatment in <i>T. cruzi</i>.

<p>Detection of exogenous Hel45 (A) tagged with PTP at the NT by indirect immunofluorescence with an anti-ProtA antibody and of mRNA (B) by fluorescence <i>in situ</i> hybridization (FISH) with a digoxigenin-conjugated oligo(dT) probe in <i>T. cruzi</i> after treatment with 50 µg/ml actinomycin D (ACTD) for 24 hours. Probe detection was carried out by indirect immunofluorescence with anti-DIG mouse monoclonal antibodies (Sigma-Aldrich, 1∶300 dilution) followed by secondary Alexa Fluor 488-conjugated antibodies (1∶600 dilution). As a control, 100 µg/ml RNase A was incubated with the parasites before probe hybridization (RNase A). DAPI = DNA stained with DAPI. Hel45 =  localization of tagged Hel45. MERGE = merged images for DAPI staining and Hel45 or mRNA localization. N = nucleus. K = kinetoplast. Arrows = parasites with nuclear accumulation of tagged Hel45. Bar = 5 µm.</p

Multiple sequence alignment and prediction of the structure of Hel45.

<p>(A) Multiple sequence alignment of the diagnostic conserved region of the DEAD-box helicase family (positions 25–365 according to Hel45). The nine putative conserved motifs (<i>Q</i>, <i>I</i> (WalkerA), <i>Ia, Ib, II</i> (WalkerB), <i>III, IV, V, VI</i>) are marked with orange boxes. Alignment columns displaying 100%, more than 90%, and more than 80% of similarity are highlighted in black, dark grey, and light grey, respectively. Sequences are identified with organism abbreviation and gene name, except Hel45. The organism abbreviations are: Sc: <i>Saccharomyces cerevisiae</i>, Hs: <i>Homo sapiens</i>, Pf: <i>Plasmodium falciparum</i>. The sequences have the following GenBank Identifiers (GIs): Hel45 (71418343), Sc_TIF2 (6322323), Sc_FAL1 (398365053), Sc_DBP5 (6324620), Hs_EIF4A1 (4503529), Hs_EIF4A2 (83700235), Hs_EIF4A3 (7661920), Hs_DDX19A (8922886), Pf_PFD1070w (124505577), Pf_H45 (124810293), Pf_DBP5 (6324620). (B) Schematic representation showing the nine conserved helicase motifs are boxed in orange. The N-terminal domain (NTD) contains the motifs Q, I and II for ATP-binding, Ia and Ib for RNA-binding, and III for ATP hydrolysis <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109521#pone.0109521-Cordin1" target="_blank">[44]</a>. The C-terminal domain (CTD) contains the motifs IV and V for RNA-binding, and VI for ATPase and unwinding activities <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109521#pone.0109521-Cordin1" target="_blank">[44]</a>. The predicted nuclear export signal (NES) in the LYDTLTI sequence (255–261 position) is shown in yellow. (C) Molecular modeling of Hel45. The nine motifs are highlighted in orange, the predicted NES (yellow) is close to the CT extremity (green). A zoom of this region (box) shows the side chains of amino-acids D257, T258 and D393, and the interactions that maintain the structure at its C-terminal extremity. The organization of the NES in the CT is shown in the inset (upper right corner).</p

Oligonucleotides used for PCR.

<p>Restriction endonuclease sites are underlined and attB recombination sites are shown in bold.</p><p>Oligonucleotides used for PCR.</p

Hel45 is a component of ribonucleoprotein complexes in the cytoplasm.

<p>Polysome fractionation by sucrose density gradient. The fractions (1–22) were collected after the sedimentation of cytoplasmic extract from <i>T. cruzi</i> treated with 100 µg/ml cycloheximide (A), 2 mM puromycin (B), or 500 U/ml micrococcal nuclease in the presence of 2 mM CaCl₂ (C). The 40S and 60S ribosomal subunits, the 80S ribosome monomer and polysomes are indicated. A western blot was performed with an anti-Hel45 antibody for each fraction. S7, a small ribosomal subunit protein, was used as a control. (D) mRNP isolation assay. Western-blot analysis with anti-Hel45 and anti-S7 antibodies and mRNPs obtained from the <i>T. cruzi</i> cytoplasmic fraction after elution from oligo(dT)-conjugated magnetic beads (El). As a control, cytoplasmic extract was treated with 10 µg/ml RNaseA before mRNP capture. FT = flow-through from cytoplasmic extract not bound to the oligo(dT). El = eluted fraction.</p

Localization of Hel45 after leptomycin B treatment in <i>T. cruzi</i> and localization of the ortholog of Hel45 (TbHel46) in <i>T. brucei</i> after Mex67 RNAi induction.

<p>(A) Detection of exogenous Hel45 tagged with PTP at the NT by indirect immunofluorescence with an anti-ProtA antibody. <i>T. cruzi</i> parasites were treated with 500 ng/ml leptomycin B (LMB) for 24 hours or were untreated (control). (B) Growth curve of <i>T. cruzi</i> parasites after treatment with 500 ng/ml leptomycin B (LMB). (C) Growth curve of <i>T. brucei</i> parasites after the induction of RNAi against Mex67 with 2 µg/ml tetracycline (RNAi-induced). (B) and (C) represent graphics of a biological replica which the density of cells in the culture was determined by counting in triplicate with a particle counter (Beckman Coulter). (D) Western-blot analysis of total protein extracts from parasites 48 (I_{48 h}) or 72 (I_{72 h}) hours after the induction of Mex67 RNAi. Non-induced (NI) parasites are shown as a control. The assay was carried out with anti-Mex67 antibodies. Anti-GAPDH antibodies were used as loading control. (E.1) Cellular localization of mRNA by fluorescence <i>in situ</i> hybridization (FISH) with a digoxigenin-conjugated oligo(dT) probe and localization of TbHel46 by indirect immunofluorescence Cells were fixed 48 hours after the induction of Mex67 RNAi (+TET). Images were processed by deconvolution software Leica AF6000. DAPI = DNA stained with DAPI. Hel45 =  localization of tagged Hel45. TbHel46 =  endogenous TbHel46 localized with anti-Hel45 antibodies. MERGE = merged images for DAPI staining and Hel45 localization (A) or DAPI staining, FISH and TbHel46 localization (E.1). N = nucleus. K = kinetoplast. (E.2 and E.3) Graphs show the quantification of fluorescence intensity of DAPI (blue), FISH (green), and TbHel46 (red) labelling that was detected across the dotted line in E.1. Fluorescence intensity was plotted in the y-axis for Mex67 RNAi-induced parasites (+TET, Figure E.2) and non-induced parasites (−TET, Figure E.3).</p