Acetylation is a ubiquitous protein modification present in prokaryotic and eukaryotic cells that participates in the regulation of many cellular processes. The bromodomain is the only domain known to bind acetylated lysine residues. In the last few years, many bromodomain inhibitors have been developed in order to treat diseases caused by aberrant acetylation of lysine residues and have been tested as anti-parasitic drugs. In the present paper, we report the first characterization of Trypanosoma cruzi bromodomain factor 1 (TcBDF1). TcBDF1 is expressed in all life cycle stages, but it is developmentally regulated. It localizes in the glycosomes directed by a PTS2 (peroxisome-targeting signal 2) sequence. The overexpression of wild-type TcBDF1 is detrimental for epimastigotes, but it enhances the infectivity rate of trypomastigotes and the replication of amastigotes. On the other hand, the overexpression of a mutated version of TcBDF1 has no effect on epimastigotes, but it does negatively affect trypomastigotes' infection and amastigotes' replication.
Lysine acetylation is a reversible and highly regulated post-translational modification that is known to play a key role in regulating transcription and other DNA-dependent nuclear processes . Advancements in mass spectrometry have allowed characterization of the acetylomes in bacteria [2–10], yeast , the protozoan parasites Toxoplasma gondii  and Plasmodium falciparum , plants , Drosophila melanogaster , rats  and human cells [1,17,18]. These acetylomes consisted of hundreds to thousands of acetylated proteins distributed among the different cellular compartments and involved in several processes such as transcription, translation, cell cycle progression, apoptosis, stress response and metabolism. One of the most surprising findings has been that metabolic enzymes are highly represented among the acetylomes. This suggested that changes in acetylation status might alter enzymatic activity to allow the cell to respond to changes in metabolic demands by adjusting flux through critical nodes in the relevant pathways . Furthermore, the effects of acetylation appear to be co-ordinated to simultaneously shunt metabolic flux along specific pathways and away from others. These efforts have uncovered a stunning complexity of the acetylome that potentially rivals that of the phosphoproteome. The remarkably ubiquitous and conserved nature of protein acetylation revealed by these studies suggests the regulatory power of this dynamic modification.
The bromodomain is the only known protein domain involved in the recognition of acetylated lysine residues. It represents an evolutionarily conserved module, present mostly in nuclear proteins. It has an atypical left-handed four-helix bundle connected by two loops that form the surface-accessible hydrophobic pocket where the acetyl-lysine-binding site is located. Bromodomains are present in many transcription factors and chromatin regulators; they can also interact with other proteins in an acetylation-dependent manner and form multisubunit complexes . We have described previously in Trypanosoma cruzi a nuclear bromodomain (TcBDF2, Trypanosoma cruzi bromodomain factor 2), which binds H4K10 (Lys10 of histone H4) and H4K14 (Lys14 of histone H4) , and a cytoplasmic bromodomain (TcBDF3), which interacts with acetylated α-tubulin .
The trypanosomatid parasites Leishmania spp., Trypanosoma brucei and Trypanosoma cruzi (also known as ‘TriTryps’) are a group of early divergent flagellated protozoa that cause severe diseases in humans, including leishmaniasis, sleeping sickness and Chagas' disease. They constitute important public health problems in developing countries owing to the lack of vaccines and modern therapies (http://www.who.int/). The glycosome is a peroxisome-like organelle specific to trypanosomatids. It contains the first six or seven glycolytic enzymes together with some auxiliary pathways apparently involved in the reoxidation of NADH and in the regeneration of the ATP consumed in the activation of the glucose molecule [23,24]. In addition, the glycosome may harbour other enzymatic systems such as fatty acid β-oxidation , sterol synthesis [26,27] and isoprenoid synthesis.
Genes of glycosomal and peroxisomal proteins are encoded in the nucleus necessitating organellar protein import in a post-translational fashion. This import requires a routing signal. Two main topogenic signals (PTS or peroxisome-targeting signal) that direct the matrix proteins have been described and are well conserved between species. Most of these proteins use a PTS1, a tripeptide motif present at their C-terminus, which is recognized by the cytosolic peroxisome-import receptor called PEX5 (peroxin 5). The general consensus sequence of PTS1 is [SAC]-[KRH]-[LM]. The PTS2 consensus sequence, M-X0–20-[RK]-[LVI]-X5-[HKQR]-[LAIVFY], is a nonapeptide that resides near the N-terminus  and is recognized by PEX7. Other proteins are imported upon recognition of an I-PTS (polypeptide-internal signal) .
In the present paper, we describe the characterization of TcBDF1, one of the few bromodomain-containing proteins reported outside the nucleus. TcBDF1 is expressed in all life cycle stages, but it is developmentally regulated, being more abundant in the infective form (trypomastigotes) than in the replicative forms (epimastigotes and amastigotes). TcBDF1 localizes in the glycosomes and it possesses a PTS2 responsible for its import. The overexpression of wild-type TcBDF1 is deleterious for epimastigote growth and in vitro differentiation to metacyclic trypomastigotes; however, it increases trypomastigote infection of Vero cells and amastigote duplication. On the other hand, when we overexpressed a mutant version of TcBDF1, the infectivity of trypomastigotes decreased, but it caused no alteration to epimastigote replication.
MATERIALS AND METHODS
T. cruzi epimastigote forms (CL Brener) were cultured at 28°C in LIT (liver infusion tryptose) medium (5 g/l liver infusion, 5 g/l Bacto™ tryptose, 68 mM NaCl, 5.3 mM KCl, 22 mM Na2HPO4, 0.2% glucose and 0.002% haemin) supplemented with 10% (v/v) heat-inactivated FBS, 100 U/ml penicillin and 100 μg/ml streptomycin. Cell viability was assessed by direct microscopic examination.
Cell culture and infections
Vero cells were cultured in DMEM (Dulbecco's modified Eagle's medium) (Life Technologies), supplemented with 2 mM L-glutamine, 10% (v/v) FBS, 100 U/ml penicillin and 100 μg/ml streptomycin.
Metacyclic trypomastigotes were obtained by spontaneous differentiation of epimastigotes at 28°C. Cell-derived trypomastigotes were obtained by infection with metacyclic trypomastigotes of Vero cell monolayers. After two rounds of infections, the cell-derived trypomastigotes were used for the infection and intracellular amastigote proliferation experiments. Trypomastigotes were collected by centrifugation of the supernatant of previously infected cultures at 2000 g at room temperature for 10 min and incubated for 3 h at 37°C in order to allow the trypomastigotes to move from the pellet into the supernatant. After this period, the supernatant was collected and trypomastigotes were counted in a Neubauer chamber. The purified trypomastigotes were pre-incubated in the presence or absence of 0.25 μg/ml tetracycline for 3 h and then used to infect new monolayers of Vero cells at a ratio of 20 parasites per cell in DMEM supplemented with 2% (v/v) FBS. After 16 h of infection at 37°C, the free trypomastigotes were removed by successive washes with PBS. Cultures were incubated in complete medium with or without tetracycline (0.25 μg/ml) for 3 days post-infection. Cells were then fixed in methanol and the percentage of infected cells and the mean number of amastigotes per infected cell were determined by counting the slides after Giemsa staining using a Nikon Eclipse Ni-U microscope, by counting ∼1000 cells per slide. The significance of the results was analysed by a two-way ANOVA using GraphPad Prism version 6.0 for Mac. Results are expressed as means±S.E.M. of triplicates, and represent one of three independent experiments performed.
Cloning and expression of TcBDF1
DNA purified from T. cruzi CL Brener strain was used as a template for PCR with oligonucleotides: BDF1BamHIFw (5′-AAGGATCCATGACTGATTTTGTCTCTC-3′) and BDF1HA-XhoIRv (5′-AACTCGAGAGCATAATCCGGCACATCATAC-GGATAATCTCTTCTTCCTCCTCA-3′) using a proofreading polymerase. PCR product was inserted into a pCR®2.1-TOPO® vector (Invitrogen) and sequenced (Maine University facility, Orono, ME, U.S.A.). The TcBDF1 coding region was introduced into a pENTR3C vector (Gateway® system, Invitrogen) using the BamHI/XhoI restriction sites included in the oligonucleotides (underlined). It was then transferred into a destination vector pDEST17 (Gateway® system) by recombination using LR Clonase (Invitrogen) to express TcBDF1 as a His-tag fusion protein. This vector was transformed into Escherichia coli BL21 pLysS, and recombinant protein was obtained by expression-induction with 1 mM IPTG for 10 h at 37°C. The protein was purified under denaturing conditions by affinity chromatography using Ni-NTA (Ni2+-nitrilotriacetate) agarose (Qiagen) following the manufacturer's instructions.
The double mutant (TcBDF1-Y102A/V109A) was constructed using a PCR-based site-directed mutagenesis strategy with the following oligonucleotides: BDF1YxAFw (5′-GCTACGCGGCCAATGGTGAAG-3′), BDF1YxARv (5′-CTTCACCATTGGCCGCGTAGC-3′), BDF1VxAFw (5′-GTT-TCTCCAGCGGCAGCGTTG-3′) and BDF1VxARv (5′-CAACGCTGCCGCTGGAGAAAC-3′). Both resulting PCR products obtained were used simultaneously as templates in a new PCR with BDF1BamHIFw and BDF1HAXhoIRv. The TcBDF1 double mutant coding region was inserted into a pCR®2.1-TOPO® vector, sequenced (Maine University facility) and introduced into a pENTR3C vector (Gateway® system Invitrogen) using the BamHI/XhoI restriction sites included in the oligonucleotides (underlined). Wild-type TcBDF1 (TcBDF1wt) and TcBDF1 double mutant (TcBDF1dm) coding regions were transferred from pENTR3C vector to pTcINDEX-GW  by recombination using LR clonase II enzyme mixture (Invitrogen).
TcBDF1 fusion constructs
DNA purified from T. cruzi CL Brener strain was used as a template for PCR to amplify TcBDF1 with the oligonucleotides BDF1XbaIFw (5′-AATCTAGAATGACTGA-TTTTGTCTCTC-3′) and BDF1SalIRv (5′-AAGTCGACA-ATCTCTTCTTCCTCCTC-3′), TcBDF1ΔN with BDF1ΔN-XbaIFw (5′-AATCTAGAATGAATTCCTTCTACCGTGAGTG-3′) and BDF1SalIRv, and TcBDF1PTS-2 with BDF1XbaIFw and BDF1PTS2SalIRv (5′-AAGTCGACGAA-GGAATTCTCCAAGTG-3′) using a proofreading polymerase. PCR products were inserted into a pCR®2.1-TOPO® vector and sequenced. The coding regions were introduced into the vector pTREX-mCherry  using the XbaI/SalI restriction sites included in the oligonucleotides (underlined).
Rabbit and mouse polyclonal antisera against TcBDF1 were obtained by inoculating subcutaneously the recombinant protein emulsified in Freund's adjuvant. Formal animal ethics approval was given for this work by the Institutional Animal Care and Use Committee of the School of Biochemical and Pharmaceutical Sciences, National University of Rosario (Argentina). Animals were housed and maintained according to institutional guidelines. The animals were injected three times with 2-week intervals between each dose and bled 2 weeks after the final injection .
Transfection of parasites
Epimastigote forms of T. cruzi CL Brener were grown at 28°C in LIT medium, supplemented with 10% (v/v) FBS, to a density of approximately 3×107 cells/ml. Parasites were harvested by centrifugation at 4000 g for 5 min at room temperature, washed once in PBS and resuspended in 0.4 ml of electroporation buffer (140 mM NaCl, 25 mM Hepes and 0.74 mM Na2HPO4, pH 7.5) to a density of 108 cells/ml. Cells were then transferred to a 0.2-cm-gap cuvette (Bio-Rad Laboratories) and ∼50 μg of DNA was added. The mixture was placed on ice for 10 min and then subjected to two pulses of 450 V and 500 μF using GenePulser II (Bio-Rad Laboratories). After electroporation, cells were transferred into 3 ml of LIT medium containing 10% (v/v) FBS, where they were incubated at 28°C. After 24 h of incubation, the antibiotic (hygromycin or geneticin) was added to an initial concentration of 125 μg/ml. Then, 72–96 h after electroporation, cultures were diluted 1:10 and antibiotic concentration was doubled. Stable resistant cells were obtained approximately 20 days after transfection. The pTREXmCherry fusion transfectants were selected with geneticin (G418; Life Technologies).
For inducible expression of TcBDF1wt and TcBDF1dm in the parasite, we first generated a cell line expressing T7 RNA polymerase and tetracycline repressor genes by transfecting epimastigotes with the plasmid pLew13. After selection with G418, this parental cell line was then transfected with pTcINDEX-GW constructs and transgenic parasites were obtained after 3 weeks of selection with 100 μg/ml G418 and 200 μg/ml hygromycin B (Sigma).
In vitro metacyclogenesis
To quantify the metacyclogenesis rate of the transfected lines, epimastigotes were differentiated in vitro following the procedure described by Contreras et al.  using chemically defined conditions (TAU3AAG medium). Briefly, cells were washed with PBS and incubated in TAU medium (190 mM NaCl, 17 mM KCl, 2 mM MgCl2, 2mM CaCl2 and 8 mM phosphate buffer, pH 6.0) in the absence or presence of 0.25 μg/ml tetracycline, reaching a density of 5×108 parasites/ml at 28°C for 2 h. Then they were diluted 1:100 in TAU3AAG medium (TAU medium plus 10 mM glucose, 2 mM L-aspartic acid, 50 mM L-glutamic acid and 10 mM L-proline) and incubated at 28°C for 72 h, again in the absence or presence of tetracycline. Finally, the parasites were fixed, stained with Giemsa, visualized with a Nikon Eclipse Ni-U microscope and counted using ImageJ software (NIH). Only parasites with a fully elongated nucleus and a round kinetoplast at the posterior end of the parasite were considered to be metacyclic forms . A total 500 parasites from each triplicate were counted and the experiment was repeated three times.
T. cruzi protein extracts
Exponentially growing epimastigotes were washed twice with ice-cold PBS, and pellets were resuspended in urea lysis buffer (8 M urea, 20 mM Hepes, pH 8, 1 mM PMSF and Protease Inhibitor Cocktail set I, Calbiochem), incubated at room temperature for 20 min and boiled for 5 min with protein loading buffer. Insoluble debris was eliminated by centrifugation. The same procedure was applied to amastigote and trypomastigote cellular pellets.
Nuclear and non-nuclear extracts were prepared from 2×1010 exponentially growing parasites. After washing, parasites were lysed in hypotonic buffer A [10 mM Hepes, pH 8, 50 mM NaCl, 1 mM EDTA, 5 mM MgCl2, 1% (v/v) Nonidet P40, 1 mM PMSF, 10 μg/ml aprotinin and 0.25% Triton X-100], 5% (v/v) glycerol was added and the pellet was collected by centrifugation. The supernatant corresponded to the non-nuclear fraction. Pellets were washed with buffer B [10 mM Hepes, pH 8, 140 mM NaCl, 1 mM EDTA, 5 mM MgCl2, 5% (v/v) glycerol, 1 mM PMSF and 10 μg/ml aprotinin) and incubated for 10 min on ice. Nuclei were collected by centrifugation and resuspended in buffer C [10 mM Hepes, pH 8, 400 mM NaCl, 0.1 mM EDTA, 0.5 mM DTT, 5% (v/v) glycerol, 1 mM PMSF and 10 μg/ml aprotinin], incubated for 1 h on ice and sonicated. This extraction was repeated three times and supernatants were precipitated with 20% trichloroacetic acid overnight at 4°C.
Partial permeabilization by digitonin treatment
Parasites in exponential phase were collected, washed and suspended in buffer A (20 mM Tris/HCl, pH 7.2, with 225 mM sucrose, 20 mM KCl, 10 mM KH2PO4, 5 mM MgCl2, 1 mM sodium EDTA and 1 mM DTT) at a concentration of 1 mg/ml and fractionated in several tubes. The required amount of digitonin was added to each of these tubes (each tube contained a different digitonin concentration), and the suspensions were incubated at 28°C for 20 min before being centrifuged at 14000 g for 2 min at 4°C. The assayed enzymatic activities were determined in the supernatant and occasionally in the cell pellet in the presence of 0.1% Triton X-100 and 150 mM NaCl.
Subcellular fractionation by differential centrifugation
T. cruzi CL Brener epimastigotes in exponential growth phase were centrifuged at 2000 g for 10 min, and washed twice in homogenization buffer (25 mM Tris/HCl, pH 8, 1 mM EDTA, 0.25 M sucrose and 1 mM PMSF). The parasites were ground in a pre-chilled mortar with 1× wet weight silicon carbide until no intact cells were observed under the light microscope. The lysate was diluted and centrifuged at 100 g for 10 min to remove the silicon carbide. Unbroken cells, nuclei and debris were sedimented at 1000 g for 10 min (Fraction N). From the resulting soluble extract, a large-granule fraction (LG) was separated at 5000 g for 15 min, a small-granule fraction (SG) was separated at 20000 g for 20 min and microsomal fraction (M) was separated at 139000 g for 1 h . All of the sediments were resuspended in urea lysis buffer.
Western blot analysis
For Western blots, proteins of the diverse fractions were first separated by SDS/PAGE and transferred on to a nitrocellulose membrane. Proteins were visualized by Ponceau S staining. Membranes were treated with 10% (w/v) non-fat dried skimmed milk powder in PBS for 1 h, and then with specific antibodies diluted in PBS for 3 h. Bound antibodies were detected using horseradish peroxidase-labelled anti-mouse IgG, anti-rabbit IgG (GE Healthcare) or anti-rat IgG (Thermo Scientific) and developed using ECL Prime kit (GE Healthcare) according to the manufacturer's protocol.
The fractions obtained with the different subcellular fractionations were analysed by Western blotting with antibodies against TcBDF1 and several markers: anti-TAT (tyrosine aminotransferase), anti-MDHg (glycosomal malate dehydrogenase), anti-MDHm (mitochondrial malate dehydrogenase) isoforms, anti-HK (hexokinase), anti-bromodomain factor 2 and anti-bromodomain factor 3.
The parasites were centrifuged, washed twice in PBS, added to the poly-L-lysine-coated slides and then fixed with 4% (w/v) formaldehyde in PBS at room temperature for 20 min. Fixed parasites were washed with PBS and permeabilized with 0.1% Triton X-100 in PBS for 5 min. After washing with PBS, parasites were incubated with the indicated antibodies diluted in 1% (w/v) BSA in PBS for 1 h at room temperature. For co-localizations, both antibodies were used at the same time. The antibodies were washed with PBS, and the slides were incubated with anti-rabbit or anti-mouse IgG antibody fluorescent conjugates. The slides were mounted with VectaShield (Vector Laboratories) in the presence of 2 μg/ml DAPI in PBS. Images were acquired using Nikon Eclipse E300 and Nikon Eclipse TE-2000-E2 microscopes. The programs Adobe Photoshop CS Version 8.0.1. (Adobe Systems Incorporated) and Nikon EZ-C1 FreeViewer version 3.70 (Nikon Corporation) were used to analyse the images.
Parasites were washed twice in PBS and fixed in 2.5% (w/v) glutaraldehyde in 0.1 M cacodylate buffer (pH 7.2) for 1 h. Then, cells were washed in 0.1 M cacodylate buffer (pH 7.2) and post-fixed for 1 h in 1% (w/v) osmium tetroxide, 0.8% potassium ferrocyanide and 5 mM CaCl2 in 0.1 M cacodylate buffer. After post-fixation, cells were washed in the same buffer, dehydrated in a series of increasing acetone concentrations and embedded in Epon, first as a mixture of Epon and acetone (1:1) and then as pure Epon. Ultrathin sections were obtained using an Ultracut Reichert Ultramicrotome and mounted on 400-mesh copper grids. Samples were stained with uranyl acetate and lead citrate and then analysed using a Zeiss 900 transmission electron microscope.
T. cruzi bromodomain factor 1 (TcBDF1)
T. cruzi CDS TcCLB.506247.80 codes for a 295-amino-acid protein with a predicted molecular mass of 33.8 kDa and a pI of 9.18, which contains a bromodomain (pfam: PF00439) in the N-terminal half of the protein, from Phe30 to Met120. Orthologous genes are present in other trypanosomatids: the T. brucei (Tb927.10.8150) and Leishmania major (LmjF.36.6880) proteins have identities of 44% and 31% with TcBDF1 respectively (Supplementary Figure S1A). The C-terminal region does not show similarity with any other sequence present in databases, and it can be divided into a portion rich in glutamine residues (28.5% glutamine) and a portion rich in acidic amino acids, such as aspartic and glutamic acid residues (21.8% aspartic and glutamatic acid), and serine residues (10.9% serine). In general, these highly charged low complexity sequences are considered prone to participate in protein–protein interaction. In higher eukaryotes, bromodomains are usually found associated with other domains or enzymatic activities in the same polypeptide; however, this is not the situation with TcBDF1, or with TcBDF2 and TcBDF3.
A multiple alignment of TcBDF1 with other bromodomains (Supplementary Figure S1B) revealed the typical structure of a four-helix left-twisted bundle . Despite the low similarity among the aligned sequences, the amino acids shown previously to be involved in acetylated lysine binding are conserved or conservatively substituted.
TcBDF1’s three-dimensional structure was predicted using the I-TASSER  server based on homology with other known bromodomain-containing proteins and, as expected, the model with the highest score presents four α-helices (αA, αB, αC and αZ) and two loops (ZA and BC) characteristic of bromodomains (Supplementary Figure S1C). The conserved amino acids important for binding of acetyl-lysine are indicated.
TcBDF1 is differentially expressed throughout the life cycle
In order to evaluate TcBDF1 expression in T. cruzi, antibodies were raised against the recombinant protein and purified by affinity chromatography. After confirming the specificity of the antibodies, they were used in Western blots to test TcBDF1 expression in total lysates of epimastigotes, amastigotes and trypomastigotes and in immunofluorescence assays of fixed parasites (Figure 1). Figure 1(A) shows that the expression of TcBDF1 is developmentally regulated throughout the T. cruzi life cycle; its expression levels are higher in trypomastigotes than in amastigotes and epimastigotes. As can be seen in Figure 1(B), TcBDF1 is localized out of the nucleus in the three developmental stages.
The expression of TcBDF1 is developmentally regulated
TcBDF1 is a glycosomal protein
Several approaches were used to determine the localization of TcBDF1 in epimastigotes: three different subcellular fractionation methods followed by Western blotting (Figure 2) and fluorescence analysis (Figure 3). First, nuclear and non-nuclear extracts were prepared: unlike the nuclear marker TcBDF2, which was only observed at the nuclear fraction, TcBDF1 was observed in the non-nuclear fraction (Figure 2A). Secondly, a subcellular fractionation by differential centrifugation was performed: TcBDF1 was present in Fraction M, enriched for glycosomes, as was confirmed using the glycosomal markers MDHg and HK (Figure 2B). Finally, a progressive permeabilization of epimastigotes was performed in the presence of increasing amounts of digitonin. The fractions obtained at each digitonin concentration were analysed by Western blotting with antibodies against TcBDF1 and several markers (Figure 2C). The release of the cytosolic markers TAT and TcBDF3, was complete at ∼0.08 mg of digitonin/mg of protein. At this concentration, the glycosomal markers HK and MDHg were only partially detected and their release was complete at 0.20–0.24 mg of digitonin/mg of protein. The mitochondrial marker MDHm was completely released at ∼0.50 mg of digitonin/mg of protein. TcBDF1 was partially detected at 0.16 mg of digitonin/mg of protein and its liberation was complete at 0.28 mg of digitonin/mg of protein. TcBDF1 pattern was similar to the HK and MDHg patterns, both glycosomal proteins. All of these results strongly suggest that TcBDF1 is located in the glycosomes.
TcBDF1 localizes in the glycosomes
Furthermore, as can be seen in the immunofluorescence analysis (Figure 3A), TcBDF1 and HK co-localized in epimastigotes simultaneously stained with the polyclonal mouse anti-TcBDF1 and rabbit anti-TcHK antibodies. In order to confirm the glycosomal localization of TcBDF1, epimastigotes were co-transfected with pTEX-GFP-PTS1 and pTREX-TcBDF1-Cherry, and the transient parasites were analysed by confocal microscopy. As can be observed in Figure 3(B), TcBDF1-Cherry co-localized with the GFP directed to the glycosomes by the PTS1 importing signal .
Identification of TcBDF1 PTS2 signal
The amino acid sequence of TcBDF1 was analysed using the PeroxisomeDB server (http://www.peroxisomedb.org/target_signal.php) and by visual inspection. An alignment of the possible PTS2 present in the TcBDF1 N-terminus with known PTS2 sequences is shown in Supplementary Figure S2. PTS2 is less conserved and is found in fewer peroxisomal proteins than PTS1. However, both cytosolic receptors PEX5 and PEX7 have orthologues in all trypanosomatids.
To determine whether the N-terminus of TcBDF1 is responsible for its import into the glycosome, we transiently transfected epimastigotes with constructs encoding the whole protein (TcBDF1), a truncated version which lacks the first 27 amino acids (TcBDF1∆N) or only the N-terminus-targeting signal (TcBDF1PTS2), fused to Cherry fluorescent protein. The intracellular localization of the different fusion proteins was determined by confocal microscopy (Figure 4). Whereas TcBDF1-Cherry shows the typical glycosomal granular pattern observed previously by immunofluorescence for TcBDF1 and HK, TcBDF1∆N-Cherry is spread throughout the cytoplasm. In the case of TcBDF1PTS2-Cherry, in addition to the punctate pattern, some cytosolic fluorescence was also detected. The same phenomenon has been described for mammalian cells expressing the minimal PTS2 . As discussed by Blattner et al. , there are three possible explanations for this. One is that the PTS2 sequence does not function well as a consequence of joining to Cherry; probably some conformational effects may be reducing the accessibility of the signal sequence. Secondly, it is possible that two sequences are necessary for import. A third possibility is that we are observing ‘overflow’ from the glycosomes, because the PTS2 receptors may be saturated.
TcBDF1 is directed to the glycosomes by its N-terminal PTS2
Inducible expression of wild-type and mutant TcBDF1
In order to assess the function of TcBDF1 in Trypanosoma cruzi, parasites expressing wild-type and double mutant versions of TcBDF1 with a haemagglutinin (HA) tag (hereinafter TcBDF1wtHA and TcBDF1dmHA respectively) under the control of a tetracycline-regulated promoter were obtained as described above. The double mutant version of TcBDF1 was constructed as described above, changing Tyr102 and Val109 for alanine based on sequence alignments with human PCAF [p300/CREB (cAMP-response-element-binding protein)-binding protein-associated factor] bromodomain (Supplementary Figure S3). Homologous mutations in human PCAF were found to disrupt the bromodomain acetyl-lysine-binding capacity without altering its structure .
Overexpression was performed using the T. cruzi inducible vector pTcINDEXGW . The induction of the expression by tetracycline was tested by Western blotting (Figures 5A and 5B) and immunofluorescence (Figure 5C). Western blot analysis of whole-cell extracts with rat monoclonal anti-HA antibodies revealed the expression of both constructs after the addition of tetracycline, at their expected molecular masses. No leaky expression was observed in the uninduced parasite lines (Figure 5A). The Western blot with the specific antibodies against TcBDF1 shows a high degree of overexpression (∼10-fold) in the induced lines (Figure 5B).
Inducible expression of TcBDF1wtHA and TcBDF1dmHA
Wild-type TcBDF1 overexpression is deleterious for epimastigote replication and induces nuclear and glycosomal ultrastructural alterations
We monitored the effect of the overexpression on epimastigote growth by counting cell numbers daily after protein induction. Figure 6(A) shows a replication defect in CL Brener TcBDF1wtHA cell line that leads to growth arrest and death. These epimastigotes exhibit aberrant morphologies with multiple kinetoplasts and flagella (Figure 6B), as was already described for dysfunctional cell cycle parasites . When observed by electron microscopy, these induced parasites show nuclear alterations in comparison with uninduced cells (Figure 7A) such as condensation (Figure 7B) followed by dispersion (Figure 7C) of the nucleolus granular region, as well as nucleolar fragmentation (Figure 7E) and nuclear disorganization (Figure 7E). Furthermore, a hypercompaction of the chromatin situated at the nucleus periphery (Figure 7F) was observed and is compatible with an apoptotic process. Induced parasites also exhibit larger glycosomes that are less electrodense (Figures 7G–7I); this can be related to higher levels of protein importation. In contrast, parasites harbouring TcBDF1dmHA grew at similar rates in the absence and presence of tetracycline (Figure 6A) and presented a normal cellular ultrastructure (results not shown).
Overexpression of TcBDF1wtHA is deleterious for epimastigotes
Overexpression of TcBDF1wtHA triggers apoptosis
Effect of TcBDF1 overexpression on in vitro metacyclogenesis
In vitro metacyclic trypomastigotes were produced from epimastigotes using TAU medium, in the absence (−Tet) or presence (+Tet) of tetracycline. TcBDF1dmHA overexpression had no effect on the differentiation to trypomastigotes, whereas TcBDF1wtHA strain showed a meaningful decrease in metacyclogenesis, probably due to its deleterious effect in epimastigotes (Figure 8).
Effect of the overexpression of wild-type and mutant TcBDF1 on in vitro metacyclogenesis
Wild-type TcBDF1 enhances the infectivity of trypomastigotes
To study the importance of TcBDF1 expression in trypomastigotes' infectivity and in the replicative form present inside the mammalian host, we investigated how the transgenic lines induced with tetracycline performed in vitro for invasion and replication in host cells. Trypomastigotes were pre-incubated in the presence or absence of 0.25 μg/ml tetracycline and then used to infect Vero cells at a ratio of 20 parasites per cell. After 16 h of infection at 37°C, the free trypomastigotes were washed out and replaced by complete medium alone or with tetracycline (0.25 μg/ml) for 3 days post-infection. Microscopic quantification of Vero cells stained with Giemsa showed that the overexpression of TcBDF1wtHA improved the infective capacity of trypomastigotes [(+/−) compared with (−/−)] (Figure 9A) and the replication rate of intracellular amastigotes [(−/+) compared with (−/−)] (Figure 9B). In contrast, the overexpression of TcBDF1dmHA diminished the infectivity of trypomastigotes and slightly decreased the proliferation of amastigotes.
TcBDF1 overexpression affects Vero cells infection
In the present paper, we describe the first experimental characterization of T. cruzi bromodomain factor 1. The expression of this protein is developmentally regulated throughout the T. cruzi life cycle, being more abundant in the infective form than in the replicative forms.
One of the most remarkable features of TcBDF1 is its glycosomal localization. Even though it is not possible to be sure that this organelle is the only intracellular compartment where TcBDF1 is located, the experimental data presented supports the idea that most of the protein is placed at the glycosome where it is directed by a PTS2 signal peptide.
The existence of non-nuclear bromodomains is not a novelty in T. cruzi. As already mentioned, we recently described a cytoplasmic and flagellar TcBDF3 . Some bromodomain-containing proteins from mammals are also found in the cytoplasm, but all cases reported so far are of nuclear proteins that only localize in the cytoplasm under very particular situations, like ovarian folliculogenesis or spinal cord development [43–45]. On the other hand, there has been no bromodomain-containing protein reported to date that localizes in an organelle other than the nucleus. As we already proposed, the presence of non-nuclear bromodomains could be another ancient feature of trypanosomatids absent from mammalian host cells.
The presence of a bromodomain factor in the glycosome opens a number of new questions about the existence of acetylation and its function in this organelle. In a preliminary acetylome study of T. cruzi epimastigotes performed in our group, 150 acetylated proteins were identified. Of these, 30% were enzymes related to metabolic pathways. Among these, five were glycosomal enzymes belonging to glucose metabolism, four to the mitochondrial TCA (tricarboxylic acid) cycle and seven participate in cell redox homoeostasis. These unpublished results are in agreement with those obtained for T. gondii  and P. falciparum , and confirm that acetylation is a conserved post-translation modification in protozoans. In addition, the two Sir2-related deacetylases recently characterized in our laboratory, are cytoplasmic (TcSIR2RP1) and mitochondrial (TcSIR2RP3), and their overexpression has an impact on the different stages of T. cruzi’s life cycle . All of these observations support the idea that acetylation is a ubiquitous and dynamic post-translational modification in T. cruzi, and that acetylomes from different parasite life cycle stages may differ. Taking into account the results already observed in mammals, yeast and bacteria, it seems very plausible that acetylation could also play a role in the metabolic regulation of T. cruzi.
It is well established that the different developmental stages of the parasite change their energetic metabolism in response to the available nutrients. The energy source of epimastigotes comes from the oxidation of amino acids, because the concentration of glucose is very low in the gut of the insect. However, in the presence of glucose, epimastigotes rapidly switch to aerobic glucose fermentation. Metacyclic trypomastigotes obtain their energy from proteins and amino acids, whereas bloodstream trypomastigotes catabolize glucose. Amastigotes consume mostly amino and fatty acids. The glycosome confines most of the glycolytic/gluconeogenic pathway together with enzymes belonging to other metabolic pathways. Turnover of glycosomes by autophagy of redundant ones and biogenesis of a new population of organelles with a different set of metabolic enzymes plays a pivotal role in the efficient adaptation of the glycosomal repertoire to the sudden major nutritional changes encountered during the transitions in the life cycle . A relevant feature of these glycosomal metabolic enzymes is that they lack the regulatory inhibition. For example, HK and PFK (phosphofructokinase) lack the allosteric regulation present in most cells. Under these conditions, the antagonistic enzymes PFK and FBPase (fructose-1,6-biphosphatase) coexist in the organelle, but FBPase is kept silent under glycolytic conditions due to an unknown mechanism. It has been proposed that a post-translational modification could be responsible for this phenomenon. The differential phosphorylation status of the glycolytic enzymes from procyclic and bloodstream forms of T. brucei has been studied, but these data cannot completely explain so far the regulation of the whole activity within the glycosome . It has been already demonstrated in other organisms that changes in the nutrients available to cells altered the total profile of acetylated metabolic enzymes, and that acetylation/deacetylation of proteins has multiple effects, increasing the activity of some metabolic enzymes while inhibiting the activity of others. For example, aldolase is switched off when acetylated in mammals and plants [14,16]. Phosphoglycerate kinase and glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis and glycerol-3-phosphate dehydrogenase and PEPCK1 (phosphoenolpyruvate carboxykinase) from mammals, are also inhibited by acetylation [14,16,18,49]. However, lysine acetylation does not always lead to enzyme inhibition, in mammals malate dehydrogenase acetylation increases its enzyme activity . Furthermore, the effects of acetylation appear to be co-ordinated to simultaneously shunt metabolic flux down specific pathways and away from others. We consider that acetylation has to be seriously taken into account as an important post-translational modification responsible for the regulation of the metabolic enzymes in the glycosome. Even though the data available about acetylation in glycolytic enzymes from trypanosomatids are too limited to build a hypothesis, it is clear that, in most other cells, acetylation leads to down-regulation of glycolysis.
Currently, it is hard to define how bromodomains partake in this puzzle. In fact, even though plenty of research has been carried out on bromodomains of yeast and mammals over the last few years, their real role remains elusive in most cases. In the nucleus, the association of bromodomains with acetyltransferases led to the proposition of a role in the hyperacetylation of some regions of the chromatin. In this model, the bromodomain-containing proteins or complexes recognize acetylated histones and promote intensive acetylation. Apart from this, no additional function has been yet proposed. TcBDF1 has no other functional domain apart from the bromodomain, but it probably interacts with other proteins through its low complexity C-terminus. It is possible that TcBDF1 could have several roles depending on the different proteins with which it interacts in each developmental stage. It is a reader domain, and its function will vary with its interactors and the requirements of the cell. Although the role and targets of TcBDF1 remain to be determined, we now know that its expression is tightly regulated throughout the parasite's life cycle and that overexpression in epimastigotes, where it exhibits low expression levels, is detrimental and triggers cell death. On the other hand, it enhances the infectivity of trypomastigotes and the duplication rate of amastigotes. As reported for other trypanosomatids, the glycosomal function, glycolysis in the bloodstream form and gluconeogenesis in intracellular amastigotes, is essential for viability and virulence. This is in agreement with our results. In this context, TcBDF1 could be part of a global regulatory mechanism of the glycosomal activity either by being part of the acetylation/deacetylation complexes, by protecting acetylated lysine residues from deacetylases, by participating in the biogenesis of the organelle or acting as a chaperone, localizing acetylated proteins to the glycosome. Considering the overexpressing phenotypes obtained, TcBDF1 could be involved in the up-regulation of gluconeogenesis in the replicative forms, which would be detrimental for epimastigotes grown in the presence of glucose, but favourable for amastigotes. On the other hand, in the infective form, it probably enhances glycolysis and ether-lipid synthesis, which depends on glycosomal enzymes. It has been already described that Leishmania and T. brucei have high levels of ether-lipids, mainly found in the glycosylphosphatidylinositol-anchored glycolipids and glycoproteins present on the surface of the parasites [50,51], that are important for infection.
The search for inhibitors of KATs (lysine acetyltransferases) and KDACs (lysine deacetylases) had a strong impulse in the last few years, and the number of diseases associated with alterations in the epigenetic regulation that could be treated with these inhibitors has significantly increased . A number of sirtuin inhibitors have also been assayed against parasites . More recently, different families of drugs that target bromodomains from the BET family have shown selective activity in carcinoma models . Many other inhibitors of the bromodomain–acetyl-lysine interaction have also been developed, putting bromodomains alongside KATs and KDACs as interesting targets for drug development for diseases caused by aberrant acetylation of lysine residues . Furthermore, the metabolic disturbance resulting from mislocalization of glycosomal proteins may lead to death of the parasites and, for this reason, they are also being studied with the aim of developing new drugs against parasitic diseases . The results of the present study show that TcBDF1 is essential for host invasion and progression of the infection, and strongly support the idea that bromodomains can be considered as potential targets for the development of new drugs against trypanosomiasis.
Gabriela Vanina Villanova cloned and purified recombinant TcBDF1 and raised the anti-TcBDF1 antibodies in rabbit and mouse. Carla Ritagliati constructed the pTREX and pTcINDEX-GW plasmids and transfected the parasites. Carla Ritagliati, Victoria Lucia Alonso and Pamela Cribb performed the Western blot assays, immunofluorescence microscopies, growth curves and infection experiments. Carla Ritagliati and Gabriela Vanina Villanova performed the sequence alignments. Aline Araujo Zuma and María Cristina Machado Motta performed and interpreted the immunoelectron microscopies. Esteban Carlos Serra and Carla Ritagliati conceived and supervised the project, and wrote the paper with contributions from all other authors.
We thank Dr C. Nowiki for the gift of anti-T. cruzi TAT and anti-MDHm and anti-MDHg, and Dr W. Quiñones for anti-HK. Also special thanks go to Rodrigo Vena for the assistance in the acquisition of the confocal microscopy images and Dolores Campos and Romina Manarin for their assistance in cell culture.
This work was supported by the National Research Council (CONICET) [grant number PIP2010-0685] and National Agency of Scientific and Technological Promotion (ANPCyT) and GlaxoSmithKline joint grant [grant number PICTO2011-0046].
Dulbecco's modified Eagle's medium
liver infusion tryptose
glycosomal malate dehydrogenase
mitochondrial malate dehydrogenase
p300/CREB (cAMP-response-element-binding protein)-binding protein-associated factor
Trypanosoma cruzi bromodomain factor
TcBDF1 double mutant