Phosphoproteomics of Aspergillus fumigatus Exposed to the Antifungal Drug Caspofungin.

Aspergillus fumigatus is an opportunistic and allergenic pathogenic fungus, responsible for fungal infections in humans. A. fumigatus infections are usually treated with polyenes, azoles, or echinocandins. Echinocandins, such as caspofungin, can inhibit the biosynthesis of the ß-1,3-glucan polysaccharide, affecting the integrity of the cell wall and leading to fungal death. In some A. fumigatus strains, caspofungin treatment at high concentrations induces an increase of fungal growth, a phenomenon called the caspofungin paradoxical effect (CPE). Here, we analyze the proteome and phosphoproteome of the A. fumigatus wild-type strain and of mitogen-activated protein kinase (MAPK) mpkA and sakA null mutant strains during CPE (2 µg/ml caspofungin for 1 h). The wild-type proteome showed 75 proteins and 814 phosphopeptides (corresponding to 520 proteins) altered in abundance in response to caspofungin treatment. The ΔmpkA (ΔmpkA caspofungin/wild-type caspofungin) and ΔsakA (ΔsakA caspofungin/wild-type caspofungin) strains displayed 626 proteins and 1,236 phosphopeptides (corresponding to 703 proteins) and 101 proteins and 1,217 phosphopeptides (corresponding to 645 proteins), respectively, altered in abundance. Functional characterization of the phosphopeptides from the wild-type strain exposed to caspofungin showed enrichment for transcription factors, protein kinases, and cytoskeleton proteins. Proteomic analysis of the ΔmpkA and ΔsakA mutants indicated that control of proteins involved in metabolism, such as in production of secondary metabolites, was highly represented in both mutants. Results of functional categorization of phosphopeptides from both mutants were very similar and showed a high number of proteins with decreased phosphorylation of proteins involved in transcriptional control, DNA/RNA binding, cell cycle control, and DNA processing. This report reveals novel transcription factors involved in caspofungin tolerance.IMPORTANCEAspergillus fumigatus is an opportunistic human-pathogenic fungus causing allergic reactions or systemic infections, such as invasive pulmonary aspergillosis in immunocompromised patients. Caspofungin is an echinocandin that impacts the construction of the fungal cell wall by inhibiting the biosynthesis of the ß-1,3-glucan polysaccharide. Caspofungin is a fungistatic drug and is recommended as a second-line therapy for treatment of aspergillosis. Treatment at high concentrations induces an increase of fungal growth, a phenomenon called the caspofungin paradoxical effect (CPE). Collaboration between the mitogen-activated protein kinases (MAPK) of the cell wall integrity (MapkA) and high-osmolarity glycerol (SakA) pathways is essential for CPE. Here, we investigate the global proteome and phosphoproteome of A. fumigatus wild-type, ΔmpkA, and ΔsakA strains upon CPE. This study showed intense cross talk between the two MAPKs for the CPE and identified novel protein kinases and transcription factors possibly important for CPE. Increased understanding of how the modulation of protein phosphorylation may affect the fungal growth in the presence of caspofungin represents an important step in the development of new strategies and methods to combat the fungus inside the host.

Global changes in nitration levels and DNA binding profile of Trypanosoma cruzi histones induced by incubation with host extracellular matrix.

Adhesion of T. cruzi trypomastigotes to components of the extracellular matrix (ECM) is an important step in mammalian host cell invasion. We have recently described a significant increase in the tyrosine nitration levels of histones H2A and H4 when trypomastigotes are incubated with components of the ECM. In this work, we used chromatin immunoprecipitation (ChIP) with an anti-nitrotyrosine antibody followed by mass spectrometry to identify nitrated DNA binding proteins in T. cruzi and to detect alterations in nitration levels induced upon parasite incubation with the ECM. Histone H1, H2B, H2A and H3 were detected among the 9 most abundant nitrated DNA binding proteins using this proteomic approach. One nitrated tyrosine residue (Y29) was identified in Histone H2B in the MS/MS spectrum. In addition, we observed a significant increase in the nitration levels of histones H1, H2B, H2A and H4 upon parasite incubation with ECM. Finally, we used ChIP-Seq to map global changes in the DNA binding profile of nitrated proteins. We observed a significant change in the binding pattern of nitrated proteins to DNA after parasite incubation with ECM. This work provides the first global profile of nitrated DNA binding proteins in T. cruzi and additional evidence for modification in the nitration profile of histones upon parasite incubation with ECM. Our data also indicate that the parasite interaction with the ECM induces alterations in chromatin structure, possibly affecting nuclear functions.

The Aspergillus fumigatus Phosphoproteome Reveals Roles of High-Osmolarity Glycerol Mitogen-Activated Protein Kinases in Promoting Cell Wall Damage and Caspofungin Tolerance.

The filamentous fungus Aspergillus fumigatus can cause a distinct set of clinical disorders in humans. Invasive aspergillosis (IA) is the most common life-threatening fungal disease of immunocompromised humans. The mitogen-activated protein kinase (MAPK) signaling pathways are essential to the adaptation to the human host. Fungal cell survival is highly dependent on the organization, composition, and function of the cell wall. Here, an evaluation of the global A. fumigatus phosphoproteome under cell wall stress caused by the cell wall-damaging agent Congo red (CR) revealed 485 proteins potentially involved in the cell wall damage response. Comparative phosphoproteome analyses with the ΔsakA, ΔmpkC, and ΔsakA ΔmpkC mutant strains from the osmotic stress MAPK cascades identify their additional roles during the cell wall stress response. Our phosphoproteomics allowed the identification of novel kinases and transcription factors (TFs) involved in osmotic stress and in the cell wall integrity (CWI) pathway. Our global phosphoproteome network analysis showed an enrichment for protein kinases, RNA recognition motif domains, and the MAPK signaling pathway. In contrast to the wild-type strain, there is an overall decrease of differentially phosphorylated kinases and phosphatases in ΔsakA, ΔmpkC, and ΔsakA ΔmpkC mutants. We constructed phosphomutants for the phosphorylation sites of several proteins differentially phosphorylated in the wild-type and mutant strains. For all the phosphomutants, there is an increase in the sensitivity to cell wall-damaging agents and a reduction in the MpkA phosphorylation upon CR stress, suggesting these phosphosites could be important for the MpkA modulation and CWI pathway regulation.IMPORTANCEAspergillus fumigatus is an opportunistic human pathogen causing allergic reactions or systemic infections, such as invasive pulmonary aspergillosis in immunocompromised patients. The mitogen-activated protein kinase (MAPK) signaling pathways are essential for fungal adaptation to the human host. Fungal cell survival, fungicide tolerance, and virulence are highly dependent on the organization, composition, and function of the cell wall. Upon cell wall stress, MAPKs phosphorylate multiple target proteins involved in the remodeling of the cell wall. Here, we investigate the global phosphoproteome of the ΔsakA and ΔmpkCA. fumigatus and high-osmolarity glycerol (HOG) pathway MAPK mutants upon cell wall damage. This showed the involvement of the HOG pathway and identified novel protein kinases and transcription factors, which were confirmed by fungal genetics to be involved in promoting tolerance of cell wall damage. Our results provide understanding of how fungal signal transduction networks modulate the cell wall. This may also lead to the discovery of new fungicide drug targets to impact fungal cell wall function, fungicide tolerance, and virulence.

Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance.

Aspergillus fumigatus causes invasive aspergillosis, the most common life-threatening fungal disease of immuno-compromised humans. The treatment of disseminated infections with antifungal drugs, including echinocandin cell wall biosynthesis inhibitors, is increasingly challenging due to the rise of drug-resistant pathogens. The fungal calcium responsive calcineurin-CrzA pathway influences cell morphology, cell wall composition, virulence, and echinocandin resistance. A screen of 395 A. fumigatus transcription factor mutants identified nine transcription factors important to calcium stress tolerance, including CrzA and ZipD. Here, comparative transcriptomics revealed CrzA and ZipD regulated the expression of shared and unique gene networks, suggesting they participate in both converged and distinct stress response mechanisms. CrzA and ZipD additively promoted calcium stress tolerance. However, ZipD also regulated cell wall organization, osmotic stress tolerance and echinocandin resistance. The absence of ZipD in A. fumigatus caused a significant virulence reduction in immunodeficient and immunocompetent mice. The ΔzipD mutant displayed altered cell wall organization and composition, while being more susceptible to macrophage killing and eliciting an increased pro-inflammatory cytokine response. A higher number of neutrophils, macrophages and activated macrophages were found in ΔzipD infected mice lungs. Collectively, this shows that ZipD-mediated regulation of the fungal cell wall contributes to the evasion of pro-inflammatory responses and tolerance of echinocandin antifungals, and in turn promoting virulence and complicating treatment options.

Aspergillus fumigatus High Osmolarity Glycerol Mitogen Activated Protein Kinases SakA and MpkC Physically Interact During Osmotic and Cell Wall Stresses.

Aspergillus fumigatus, a saprophytic filamentous fungus, is a serious opportunistic pathogen of mammals and it is the primary causal agent of invasive aspergillosis (IA). Mitogen activated protein Kinases (MAPKs) are important components involved in diverse cellular processes in eukaryotes. A. fumigatus MpkC and SakA, the homologs of the Saccharomyces cerevisiae Hog1 are important to adaptations to oxidative and osmotic stresses, heat shock, cell wall damage, macrophage recognition, and full virulence. We performed protein pull-down experiments aiming to identify interaction partners of SakA and MpkC by mass spectrometry analysis. In presence of osmotic stress with sorbitol, 118, and 213 proteins were detected as possible protein interactors of SakA and MpkC, respectively. Under cell wall stress caused by congo red, 420 and 299 proteins were detected interacting with SakA and MpkC, respectively. Interestingly, a group of 78 and 256 proteins were common to both interactome analysis. Co-immunoprecipitation (Co-IP) experiments showed that SakA::GFP is physically associated with MpkC:3xHA upon osmotic and cell wall stresses. We also validated the association between SakA:GFP and the cell wall integrity MAPK MpkA:3xHA and the phosphatase PtcB:3xHA, under cell wall stress. We further characterized A. fumigatus PakA, the homolog of the S. cerevisiae sexual developmental serine/threonine kinase Ste20, as a component of the SakA/MpkC MAPK pathway. The ΔpakA strain is more sensitive to cell wall damaging agents as congo red, calcofluor white, and caspofungin. Together, our data supporting the hypothesis that SakA and MpkC are part of an osmotic and general signal pathways involved in regulation of the response to the cell wall damage, oxidative stress, drug resistance, and establishment of infection. This manuscript describes an important biological resource to understand SakA and MpkC protein interactions. Further investigation of the biological roles played by these protein interactors will provide more opportunities to understand and combat IA.

Comprehensive glycoprofiling of the epimastigote and trypomastigote stages of Trypanosoma cruzi.

Trypanosoma cruzi, the protozoan that causes Chagas disease, has a complex life cycle involving insect and mammalian hosts and distinct developmental stages. During T. cruzi developmental stages, glycoproteins play important role in the host-parasite interaction, such as cellular recognition, host cell invasion and adhesion, and immune evasion. In this study, comprehensive glycoprofiling analysis was performed in the epimastigote and trypomastigote stages of T. cruzi using two glycopeptide enrichment strategies, lectin-based and hydrophilic interaction liquid chromatography, followed by high resolution LC-MS/MS. Following deglycosylation, a total of 1306 N-glycosylation sites in NxS/T/C motifs were identified from 690 T. cruzi glycoproteins. Among them, 170 and 334 glycoproteins were exclusively identified in epimastigotes and trypomastigotes, respectively. Besides, global site-specific characterization of the N- and O-linked glycan heterogeneity in the two life stages of T. cruzi was achieved by intact glycopeptide analysis, revealing 144/466 unique N-linked and 10/97 unique O-linked intact glycopeptides in epimastigotes/trypomastigotes, respectively. Conclusively, this study documents the significant T. cruzi stage-specific expression of glycoproteins that can help to better understand the T. cruzi phenotype and response caused by the interaction with different hosts during its complex life cycle. BIOLOGICAL SIGNIFICANCE: Chagas disease caused by the protozoan Trypanosoma cruzi is a neglected disease which affects millions of people especially in Latin America. The absence of efficient drugs and vaccines against Chagas disease stimulates the search for novel targets. Glycoproteins are very attractive therapeutic candidate targets since they mediate key processes in the host-parasite interaction, such as cellular recognition, host cell invasion and adhesion, and immune evasion. This study aimed to provide an in depth characterization of the N-linked and O-linked glycoproteome of two T. cruzi life stages: epimastigotes and trypomastigotes. Mass spectrometry-based proteomics showed interesting stage-specific glycoproteome signatures that are valuable to better understand the importance of protein glycosylation in epimastigotes and trypomastigotes and to expand the repertoire of potential therapeutic targets against Chagas disease.

Interação parasita-célula hospedeira: modificação de proteínas de Tripanosoma cruzi durante adesão à matriz extracelular / Parasite-host cell interaction: modifications of Trypanosoma cruzi proteins during the adhesion to extracelular matrix

A doença de Chagas foi incialmente descrita em 1090 e após mais de 100 anos de investigações sobre essa doença, ainda pouco se sabe sobre os mecanismos ativados no parasita durante sua adesão e invasão à célula hospedeira. Glicoproteínas de massa molecular de 85kDa localizadas na membrana do parasita foram identificadas como principais elementos responsáveis pela interação com o hospedeiro. Essas proteínas também são capazes de se ligar a elementos da matriz extracelular (ECM) da célula hospedeira e esse evento parece ser crucial para modulação da adesão e invasão do parasita e consequente avanço da infecção. Embora diferentes elementos tenham sido identificados no hospedeiro como componentes da via de resposta a adesão ao parasita, as modificações induzidas pela sua ligação ao hospedeiro é ainda pouco conhecida. Modificações pós-traducionais de proteínas, incluindo a fosforilação, têm sido utilizadas por diferentes organismos na transdução de sinais extracelulares. Dessa forma, a identificação de proteínas diferencialmente fosforiladas durante a adesão de tripomastigotas de T. cruzi a ECM, fibronectina e laminina foi o objetivo dessa tese. Tripomastigotas foram incubados com ECM, fibronectina-, laminina- ou BSA- previamente aderidos em placas de cultura de células. Em seguida, os parasitas foram coletados e suas proteínas extraídas e separadas por 2D-PAGE. Os géis de eletroforese foram corados com Pro-Q Diamond (para identifiicação de proteínas fosforiladas) e posteriormente com coomassie colloidal (identificação de proteínas totais). Os spots com diferença significativa na coloração com Pro-Q Diamond (p< 0,05) foram identificados por LC-MS/MS. 54 spots foram diferencialmente fosforilados durante a adesão dos parasitas a ECM, dos quais 39 sofreram um aumento da intensidade de fosforilação e 15 uma redução. Já dos 43 spots diferencialmente fosforilados durante incubação com laminina, 16 aumentaram a fosforilação enquanto 27 sofreram redução da intensidade de fosforilação. Por fim, após incubação com fibronectina, dos 50 spots selecionados, 15 spots sofreram aumento da intensidade de fosforilação e 35 sofreram redução. Após identificação dos spots, as modificações por fosforilação/desfosforilação de proteínas de função desconhecida (hypothetical proteins), proteínas do citoesqueleto, proteínas do choque térmico (HSPs) e proteínas componentes do proteassomo do parasita foram as mais evidentes. A validação por immonoblotting de algumas proteínas identificadas indicou que a desfosforilação de proteínas do citoesqueleto junto com a fosforilação de proteínas do choque térmico são os principais eventos durante a resposta do parasita a adesão a ECM e a seus elementos. Além disso, a desfosforilação de ERK 1/2 observada indicou uma inativação dessa proteína em parasitas aderidos a fibronectina e laminina. Os resultados obtidos nessa tese sugerem uma provável relação entre modificações de proteínas do citoesqueleto e HSPs com a capacidade de internalização dos parasitas na célula hospedeira

The Chagas disease was firstly described in 1909. After more than 100 years of investigation about this sickness much less is known about the mechanism triggered in the parasite during the adhesion and invasion to the host cell. 85kDa glycoproteins were identified as the major element responsible for the attachment to the host. In addition, these proteins are able to binding to extracellular matrix elements and host cytoskeletal proteins and it event appears to be an essential step in host cell invasion by T. cruzi. Although downstream signal modifications have been studied in host cells upon parasite binding, the molecular changes induced on the parasite by ligand binding are largely unknown. Since post-translational modification of proteins by phosphorylation is one of the most important mechanisms employed by organisms to transduce external signals, identification of proteins modified upon adhesion of T. cruzi trypomastigotes to ECM, laminin and fibronectin of the host cell was pursued. Trypomastigotes (Y strain) were incubated with ECM, laminin-, fibronectin- or BSA-coated surfaces, followed by 2D-PAGE stained with Pro-Q Diamond (phosphorylated protein detection) followed by colloidal coomassie stain (total protein identification). Proteins with significant differences in Pro-Q Diamond stain (p<0.05) were identified by LC-MS/MS. 54 spots were differentially phosphorylated during parasite adhesion to ECM, in which 39 spots have increased their phosphorylation level and 15 have decreased their phosphorylation. From the 43 spots presenting modification to the phosphorylation on incubation with laminin, 16 corresponded to cases of increase of phosphorylation and 27 to cases of dephosphorylation. After incubation with fibronectin: from the 50 spots selected, 15 corresponded to increase of phosphorylation and 35 to dephosphorylation. The results show phosphorylation/dephosphorylation modifications of unknown proteins, parasite cytoskeletal proteins (alpha and beta tubulin and paraflagellar-rod proteins), heat shock proteins and proteasome proteins. The validation by immunoblotting of proteins and their phosphorylation intensities indicates that cytoskeletal protein dephosphorylation in addition to heat shock proteins phosphorylation are the most important event during the trypomastigotes adhesion to the ECM. Looking for downstream signaling, dephosphorylation of ERK1/2 was also shown in trypomastigotes adhered to fibronectin or laminin, suggesting its inactivation. Thereby, those results suggest a possible correlation between cytoskeletal proteins and HSPs modification and the ability of parasite to internalize into host cells