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Kieft R, Yan H, Schmitz RJ, Sabatini R. Mono-allelic epigenetic regulation of bi-directional polycistronic transcription initiation by RNA Polymerase II in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600114. [PMID: 38948844 PMCID: PMC11213002 DOI: 10.1101/2024.06.21.600114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Unique for a eukaryote, protein-coding genes in trypanosomes are arranged in polycistronic units (PTUs). This genome arrangement has led to a model where Pol II transcription of PTUs is unregulated. The initial step in trypanosome lytic factor (TLF) mediated lysis of Trypanosoma brucei requires high affinity haptoglobin/hemoglobin receptor (HpHbR) binding. Here we demonstrate that by in vitro selection with TLF, resistance is obtained in a stepwise process correlating with loss of HpHbR expression at an allelic level. RNA-seq, Pol II ChIP and run-on analysis indicate HpHbR silencing is at the transcriptional level, where loss of Pol II binding at the promoter region specifically shuts down transcription of the HpHbR containing gene cluster and the adjacent opposing gene cluster. Reversible transcriptional silencing of the divergent PTUs correlates with DNA base J modification of the shared promoter region. Therefore, epigenetic mechanisms exist to regulate gene expression via Pol II transcription initiation of gene clusters in a mono-allelic fashion. These findings suggest epigenetic chromatin-based regulation of gene expression is deeply conserved among eukaryotes, including primitive eukaryotes that rely on polycistronic transcription.
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2
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Vitarelli MDO, Franco TA, Pires DDS, Lima ARJ, Viala VL, Kraus AJ, de Azevedo IDLMJ, da Cunha JPC, Elias MC. Integrating high-throughput analysis to create an atlas of replication origins in Trypanosoma cruzi in the context of genome structure and variability. mBio 2024; 15:e0031924. [PMID: 38441981 PMCID: PMC11005370 DOI: 10.1128/mbio.00319-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Trypanosoma cruzi is the etiologic agent of the most prevalent human parasitic disease in Latin America, Chagas disease. Its genome is rich in multigenic families that code for virulent antigens and are present in the rapidly evolving genomic compartment named Disruptive. DNA replication is a meticulous biological process in which flaws can generate mutations and changes in chromosomal and gene copy numbers. Here, integrating high-throughput and single-molecule analyses, we were able to identify Predominant, Flexible, and Dormant Orc1Cdc6-dependent origins as well as Orc1Cdc6-independent origins. Orc1Cdc6-dependent origins were found in multigenic family loci, while independent origins were found in the Core compartment that contains conserved and hypothetical protein-coding genes, in addition to multigenic families. In addition, we found that Orc1Cdc6 density is related to the firing of origins and that Orc1Cdc6-binding sites within fired origins are depleted of a specific class of nucleosomes that we previously categorized as dynamic. Together, these data suggest that Orc1Cdc6-dependent origins may contribute to the rapid evolution of the Disruptive compartment and, therefore, to the success of T. cruzi infection and that the local epigenome landscape is also involved in this process.IMPORTANCETrypanosoma cruzi, responsible for Chagas disease, affects millions globally, particularly in Latin America. Lack of vaccine or treatment underscores the need for research. Parasite's genome, with virulent antigen-coding multigenic families, resides in the rapidly evolving Disruptive compartment. Study sheds light on the parasite's dynamic DNA replication, discussing the evolution of the Disruptive compartment. Therefore, the findings represent a significant stride in comprehending T. cruzi's biology and the molecular bases that contribute to the success of infection caused by this parasite.
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Affiliation(s)
- Marcela de Oliveira Vitarelli
- Cell Cycle Laboratory, Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
| | | | | | | | - Vincent Louis Viala
- Biochemistry Laboratory, Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
| | - Amelie Johanna Kraus
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | | | - Julia Pinheiro Chagas da Cunha
- Cell Cycle Laboratory, Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
| | - Maria Carolina Elias
- Cell Cycle Laboratory, Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, Av. Vital Brazil, São Paulo, Brazil
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Silvester E, Szoor B, Ivens A, Awuah-Mensah G, Gadelha C, Wickstead B, Matthews KR. A conserved trypanosomatid differentiation regulator controls substrate attachment and morphological development in Trypanosoma congolense. PLoS Pathog 2024; 20:e1011889. [PMID: 38408115 PMCID: PMC10919850 DOI: 10.1371/journal.ppat.1011889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/07/2024] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Trypanosomatid parasites undergo developmental regulation to adapt to the different environments encountered during their life cycle. In Trypanosoma brucei, a genome wide selectional screen previously identified a regulator of the protein family ESAG9, which is highly expressed in stumpy forms, a morphologically distinct bloodstream stage adapted for tsetse transmission. This regulator, TbREG9.1, has an orthologue in Trypanosoma congolense, despite the absence of a stumpy morphotype in that parasite species, which is an important cause of livestock trypanosomosis. RNAi mediated gene silencing of TcREG9.1 in Trypanosoma congolense caused a loss of attachment of the parasites to a surface substrate in vitro, a key feature of the biology of these parasites that is distinct from T. brucei. This detachment was phenocopied by treatment of the parasites with a phosphodiesterase inhibitor, which also promotes detachment in the insect trypanosomatid Crithidia fasciculata. RNAseq analysis revealed that TcREG9.1 silencing caused the upregulation of mRNAs for several classes of surface molecules, including transferrin receptor-like molecules, immunoreactive proteins in experimental bovine infections, and molecules related to those associated with stumpy development in T. brucei. Depletion of TcREG9.1 in vivo also generated an enhanced level of parasites in the blood circulation consistent with reduced parasite attachment to the microvasculature. The morphological progression to insect forms of the parasite was also perturbed. We propose a model whereby TcREG9.1 acts as a regulator of attachment and development, with detached parasites being adapted for transmission.
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Affiliation(s)
- Eleanor Silvester
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Balazs Szoor
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Alasdair Ivens
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
| | - Georgina Awuah-Mensah
- Medical School, Centre for Genetics and Genomics, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Catarina Gadelha
- Medical School, Centre for Genetics and Genomics, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Bill Wickstead
- Medical School, Centre for Genetics and Genomics, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Keith R. Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Ashworth laboratories, Charlotte Auerbach Road, Edinburgh, United Kingdom
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Penteado RF, da Silva RS, Moura DMN, de Lima GB, Malvezzi AM, Monteiro TTDS, Xavier CC, Vichier-Guerre S, Dugué L, Pochet S, Zanchin NIT, Reis CRDS, de Melo Neto OP, Guimarães BG. Structural analysis of the Trypanosoma brucei EIF4E6/EIF4G5 complex reveals details of the interaction between unusual eIF4F subunits. Sci Rep 2024; 14:2178. [PMID: 38272944 PMCID: PMC10810786 DOI: 10.1038/s41598-024-52364-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Recognition of the mRNA 5' end is a critical step needed for translation initiation. This step is performed by the cap binding protein eIF4E, which joins the larger eIF4G subunit to form the eIF4F complex. Trypanosomatids have a minimum of five different eIF4F-like complexes formed through specific but not well-defined interactions between four different eIF4E and five eIF4G homologues. The EIF4E6/EIF4G5 complex has been linked with the stage-specific translation of mRNAs encoding the major Trypanosoma brucei virulence factors. Here, to better define the molecular basis for the TbEIF4E6/TbEIF4G5 interaction, we describe the identification of the peptide interacting with TbEIF4E6 in the region comprising residues 79-166 of TbEIF4G5. The TbEIF4E6-TbEIF4G5_79-116 complex reconstituted with recombinant proteins is highly stable even in the absence of cap-4. The crystal structure of the complex was subsequently solved, revealing extensive interacting surfaces. Comparative analyses highlight the conservation of the overall structural arrangement of different eIF4E/eIF4G complexes. However, highly different interacting surfaces are formed with distinct binding contacts occurring both in the canonical and noncanonical elements within eIF4G and the respective eIF4E counterpart. These specific pairs of complementary interacting surfaces are likely responsible for the selective association needed for the formation of distinct eIF4F complexes in trypanosomatids.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Laurence Dugué
- Epigenetic Chemical Biology, Institut Pasteur, Paris, France
| | - Sylvie Pochet
- Epigenetic Chemical Biology, Institut Pasteur, Paris, France
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5
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Baron N, Purushotham R, Pullaiahgari D, Bose P, Zarivach R, Shapira M. LeishIF4E2 is a cap-binding protein that plays a role in Leishmania cell cycle progression. FASEB J 2024; 38:e23367. [PMID: 38095329 DOI: 10.1096/fj.202301665r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023]
Abstract
Leishmania encode six paralogs of the cap-binding protein eIF4E and five eIF4G candidates, forming unique complexes. Two cap-binding proteins, LeishIF4E1 and LeishIF4E2, do not bind any identified LeishIF4Gs, thus their roles are intriguing. Here, we combine structural prediction, proteomic analysis, and interaction assays to shed light on LeishIF4E2 function. A nonconserved C-terminal extension was identified through structure prediction and sequence alignment. m7 GTP-binding assays involving both recombinant and transgenic LeishIF4E2 with and without the C-terminal extension revealed that this extension functions as a regulatory gate, modulating the cap-binding activity of LeishIF4E2. The interactomes of the two LeishIF4E2 versions were investigated, highlighting the role of the C-terminal extension in binding to SLBP2. SLBP2 is known to interact with a stem-loop structure in the 3' UTRs of histone mRNAs. Consistent with the predicted inhibitory effect of SLBP2 on histone expression in Xenopus laevis, a hemizygous deletion mutant of LeishIF4E2, exhibited an upregulation of several histones. We therefore propose that LeishIF4E2 is involved in histone expression, possibly through its interaction between SLBP2 and LeishIF4E2, thus affecting cell cycle progression. In addition, cell synchronization showed that LeishIF4E2 expression decreased during the S-phase, when histones are known to be synthesized. Previous studies in T. brucei also highlighted an association between TbEIF4E2 and SLBP2, and further reported on an interaction between TbIF4E2 and S-phase-abundant mRNAs. Our results show that overexpression of LeishIF4E2 correlates with upregulation of cell cycle and chromosome maintenance proteins. Along with its effect on histone expression, we propose that LeishIF4E2 is involved in cell cycle progression.
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Affiliation(s)
- Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Rajaram Purushotham
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | | | - Priyanka Bose
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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6
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Díaz-Viraqué F, Chiribao ML, Libisch MG, Robello C. Genome-wide chromatin interaction map for Trypanosoma cruzi. Nat Microbiol 2023; 8:2103-2114. [PMID: 37828247 PMCID: PMC10627812 DOI: 10.1038/s41564-023-01483-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/25/2023] [Indexed: 10/14/2023]
Abstract
Trypanosomes are eukaryotic, unicellular parasites, such as Trypanosoma brucei, which causes sleeping sickness, and Trypanosoma cruzi, which causes Chagas disease. Genomes of these parasites comprise core regions and species-specific disruptive regions that encode multigene families of surface glycoproteins. Few transcriptional regulators have been identified in these parasites, and the role of spatial organization of the genome in gene expression is unclear. Here we mapped genome-wide chromatin interactions in T. cruzi using chromosome conformation capture (Hi-C), and we show that the core and disruptive regions form three-dimensional chromatin compartments named C and D. These chromatin compartments differ in levels of DNA methylation, nucleosome positioning and chromatin interactions, affecting genome expression dynamics. Our data reveal that the trypanosome genome is organized into chromatin-folding domains and transcription is affected by the local chromatin structure. We propose a model in which epigenetic mechanisms affect gene expression in trypanosomes.
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Affiliation(s)
- Florencia Díaz-Viraqué
- Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María Laura Chiribao
- Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - María Gabriela Libisch
- Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Carlos Robello
- Laboratorio de Interacciones Hospedero-Patógeno-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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7
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Camacho E, González-de la Fuente S, Solana JC, Tabera L, Carrasco-Ramiro F, Aguado B, Requena JM. Leishmania infantum (JPCM5) Transcriptome, Gene Models and Resources for an Active Curation of Gene Annotations. Genes (Basel) 2023; 14:genes14040866. [PMID: 37107624 PMCID: PMC10137940 DOI: 10.3390/genes14040866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023] Open
Abstract
Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5′- and 3′-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteins.
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Affiliation(s)
- Esther Camacho
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | - Jose Carlos Solana
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Laura Tabera
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Fernando Carrasco-Ramiro
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain
| | - Jose M. Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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8
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Kruse E, Göringer HU. Nanopore-Based Direct RNA Sequencing of the Trypanosoma brucei Transcriptome Identifies Novel lncRNAs. Genes (Basel) 2023; 14:genes14030610. [PMID: 36980882 PMCID: PMC10048164 DOI: 10.3390/genes14030610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/23/2023] [Accepted: 02/26/2023] [Indexed: 03/04/2023] Open
Abstract
Trypanosomatids are single-cell eukaryotic parasites. Unlike higher eukaryotes, they control gene expression post-transcriptionally and not at the level of transcription initiation. This involves all known cellular RNA circuits, from mRNA processing to mRNA decay, to translation, in addition to a large panel of RNA-interacting proteins that modulate mRNA abundance. However, other forms of gene regulation, for example by lncRNAs, cannot be excluded. LncRNAs are poorly studied in trypanosomatids, with only a single lncRNA characterized to date. Furthermore, it is not clear whether the complete inventory of trypanosomatid lncRNAs is known, because of the inherent cDNA-recoding and DNA-amplification limitations of short-read RNA sequencing. Here, we overcome these limitations by using long-read direct RNA sequencing (DRS) on nanopore arrays. We analyze the native RNA pool of the two main lifecycle stages of the African trypanosome Trypanosoma brucei, with a special emphasis on the inventory of lncRNAs. We identify 207 previously unknown lncRNAs, 32 of which are stage-specifically expressed. We also present insights into the complexity of the T. brucei transcriptome, including alternative transcriptional start and stop sites and potential transcript isoforms, to provide a bias-free understanding of the intricate RNA landscape in T. brucei.
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Kamran M, Bhattacharjee R, Das S, Mukherjee S, Ali N. The paradigm of intracellular parasite survival and drug resistance in leishmanial parasite through genome plasticity and epigenetics: Perception and future perspective. Front Cell Infect Microbiol 2023; 13:1001973. [PMID: 36814446 PMCID: PMC9939536 DOI: 10.3389/fcimb.2023.1001973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Leishmania is an intracellular, zoonotic, kinetoplastid eukaryote with more than 1.2 million cases all over the world. The leishmanial chromosomes are divided into polymorphic chromosomal ends, conserved central domains, and antigen-encoding genes found in telomere-proximal regions. The genome flexibility of chromosomal ends of the leishmanial parasite is known to cause drug resistance and intracellular survival through the evasion of host defense mechanisms. Therefore, in this review, we discuss the plasticity of Leishmania genome organization which is the primary cause of drug resistance and parasite survival. Moreover, we have not only elucidated the causes of such genome plasticity which includes aneuploidy, epigenetic factors, copy number variation (CNV), and post-translation modification (PTM) but also highlighted their impact on drug resistance and parasite survival.
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Affiliation(s)
| | | | - Sonali Das
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Sohitri Mukherjee
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
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10
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Singh SS, Mansuri MS, Naiyer S, Kaur D, Agrahari M, Srinivasan S, Jhingan GD, Bhattacharya A, Bhattacharya S. Multi-omics analysis to characterize molecular adaptation of Entamoeba histolytica during serum stress. Proteomics 2022; 22:e2200148. [PMID: 36066285 DOI: 10.1002/pmic.202200148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 12/29/2022]
Abstract
Entamoeba histolytica is responsible for dysentery and extraintestinal disease in humans. To establish successful infection, it must generate adaptive response against stress due to host defense mechanisms. We have developed a robust proteomics workflow by combining miniaturized sample preparation, low flow-rate chromatography, and ultra-high sensitivity mass spectrometry, achieving increased proteome coverage, and further integrated proteomics and RNA-seq data to decipher regulation at translational and transcriptional levels. Label-free quantitative proteomics led to identification of 2344 proteins, an improvement over the maximum number identified in E. histolytica proteomic studies. In serum-starved cells, 127 proteins were differentially abundant and were associated with functions including antioxidant activity, cytoskeleton, translation, catalysis, and transport. The virulence factor, Gal/GalNAc-inhibitable lectin subunits, was significantly altered. Integration of transcriptomic and proteomic data revealed that only 30% genes were coordinately regulated at both transcriptional and translational levels. Some highly expressed transcripts did not change in protein abundance. Conversely, genes with no transcriptional change showed enhanced protein abundance, indicating post-transcriptional regulation. This multi-omics approach enables more refined gene expression analysis to understand the adaptive response of E. histolytica during growth stress.
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Affiliation(s)
- Shashi Shekhar Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Center for RNA Science and Therapeutics, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mohammad Shahid Mansuri
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Department of Immunology and Microbiology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Central University of Punjab, Bathinda, Punjab, India
| | - Mridula Agrahari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Vproteomics, Valerian Chem Private Limited, New Delhi, India
| | | | | | - Alok Bhattacharya
- Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
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11
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Jamabo M, Bentley SJ, Macucule-Tinga P, Tembo P, Edkins AL, Boshoff A. In silico analysis of the HSP90 chaperone system from the African trypanosome, Trypanosoma brucei. Front Mol Biosci 2022; 9:947078. [PMID: 36213128 PMCID: PMC9538636 DOI: 10.3389/fmolb.2022.947078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
African trypanosomiasis is a neglected tropical disease caused by Trypanosoma brucei (T. brucei) and spread by the tsetse fly in sub-Saharan Africa. The trypanosome relies on heat shock proteins for survival in the insect vector and mammalian host. Heat shock protein 90 (HSP90) plays a crucial role in the stress response at the cellular level. Inhibition of its interactions with chaperones and co-chaperones is being explored as a potential therapeutic target for numerous diseases. This study provides an in silico overview of HSP90 and its co-chaperones in both T. brucei brucei and T. brucei gambiense in relation to human and other trypanosomal species, including non-parasitic Bodo saltans and the insect infecting Crithidia fasciculata. A structural analysis of T. brucei HSP90 revealed differences in the orientation of the linker and C-terminal domain in comparison to human HSP90. Phylogenetic analysis displayed the T. brucei HSP90 proteins clustering into three distinct groups based on subcellular localizations, namely, cytosol, mitochondria, and endoplasmic reticulum. Syntenic analysis of cytosolic HSP90 genes revealed that T. b. brucei encoded for 10 tandem copies, while T. b. gambiense encoded for three tandem copies; Leishmania major (L. major) had the highest gene copy number with 17 tandem copies. The updated information on HSP90 from recently published proteomics on T. brucei was examined for different life cycle stages and subcellular localizations. The results show a difference between T. b. brucei and T. b. gambiense with T. b. brucei encoding a total of twelve putative HSP90 genes, while T. b. gambiense encodes five HSP90 genes. Eighteen putative co-chaperones were identified with one notable absence being cell division cycle 37 (Cdc37). These results provide an updated framework on approaching HSP90 and its interactions as drug targets in the African trypanosome.
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Affiliation(s)
- Miebaka Jamabo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | | | | | - Praise Tembo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | - Adrienne Lesley Edkins
- Department of Biochemistry and Microbiology, Biomedical Biotechnology Research Unit (BioBRU), Rhodes University, Grahamstown, South Africa
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
- *Correspondence: Aileen Boshoff,
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Cortazzo da Silva L, Aoki JI, Floeter-Winter LM. Finding Correlations Between mRNA and Protein Levels in Leishmania Development: Is There a Discrepancy? Front Cell Infect Microbiol 2022; 12:852902. [PMID: 35903202 PMCID: PMC9318571 DOI: 10.3389/fcimb.2022.852902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple genes and proteins have been identified as differentially expressed in the stages of the Leishmania life cycle. The differentiation processes are implicated in specific transcriptional and proteomic adjustments driven by gene expression regulation mechanisms. Leishmania parasites lack gene-specific transcriptional control, and gene expression regulation mostly depends on posttranscriptional mechanisms. Due to the lack of transcriptional regulation, criticism regarding the relevance of transcript quantification as a possible and efficient prediction of protein levels is recurrent in studies that use transcriptomic information. The advent of high-throughput technologies has improved the analysis of genomes, transcriptomes and proteomes for different organisms under several conditions. Nevertheless, defining the correlation between transcriptional and proteomic profiles requires arduous and expensive work and remains a challenge in Leishmania. In this review, we analyze transcriptomic and proteomic data for several Leishmania species in two different stages of the parasite life cycle: metacyclogenesis and amastigogenesis (amastigote differentiation). We found a correlation between mRNA and protein levels of 60.9% and 69.8% for metacyclogenesis and amastigogenesis, respectively; showing that majority mRNA and protein levels increase or decrease concomitantly. Among the analyzed genes that did not present correlation indicate that transcriptomic data should be carefully interpreted as protein expression. We also discuss possible explanations and mechanisms involved for this lack of correlation.
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Alonso A, Larraga J, Loayza FJ, Martínez E, Valladares B, Larraga V, Alcolea PJ. Stable Episomal Transfectant Leishmania infantum Promastigotes Over-Expressing the DEVH1 RNA Helicase Gene Down-Regulate Parasite Survival Genes. Pathogens 2022; 11:pathogens11070761. [PMID: 35890006 PMCID: PMC9323391 DOI: 10.3390/pathogens11070761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 12/10/2022] Open
Abstract
The compartmentalization of untranslated mRNA molecules in granules occurring in many eukaryotic organisms including trypanosomatids involves the formation of complexes between mRNA molecules and RNA-binding proteins (RBPs). The putative ATP-dependent DEAD/H RNA helicase (DEVH1) from Leishmania infantum (Kinetoplastida: Trypanosomatidae) is one such proteins. The objective of this research is finding differentially expressed genes in a stable episomal transfectant L. infantum promastigote line over-expressing DEVH1 in the stationary phase of growth in axenic culture to get insight into the biological roles of this RNA helicase in the parasite. Interestingly, genes related to parasite survival and virulence factors, such as the hydrophilic surface protein/small hydrophilic endoplasmic reticulum protein (HASP/SHERP) gene cluster, an amastin, and genes related to reactive oxygen species detoxification are down-regulated in DEVH1 transfectant promastigotes.
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Affiliation(s)
- Ana Alonso
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Jaime Larraga
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Francisco Javier Loayza
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Enrique Martínez
- Department of Obstetrics and Gynecology, Pediatrics, Preventive Medicine and Public Health, Toxicology, Legal and Forensic Medicine and Parasitology, Faculty of Pharmacy, University Institute of Public Health of the Canary Islands (IUETSPC), University of La Laguna (ULL), Avda, Astrofísico Francisco, Sánchez s/n, Campus de Anchieta, 38207 La Laguna, Spain; (E.M.); (B.V.)
| | - Basilio Valladares
- Department of Obstetrics and Gynecology, Pediatrics, Preventive Medicine and Public Health, Toxicology, Legal and Forensic Medicine and Parasitology, Faculty of Pharmacy, University Institute of Public Health of the Canary Islands (IUETSPC), University of La Laguna (ULL), Avda, Astrofísico Francisco, Sánchez s/n, Campus de Anchieta, 38207 La Laguna, Spain; (E.M.); (B.V.)
| | - Vicente Larraga
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
| | - Pedro José Alcolea
- Laboratory of Molecular Parasitology and Vaccines, Biological, Immunological, and Chemical Drug Development for Global Health Unit (BICS), Department of Cellular and Molecular Biology, Center for Biological Research Margarita Salas, Spanish Research Council (CIBMS-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.A.); (J.L.); (F.J.L.); (V.L.)
- Correspondence: ; Tel.: +34-9-1837-3112; Fax: +34-9-1536-0432
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14
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Ali V, Behera S, Nawaz A, Equbal A, Pandey K. Unique thiol metabolism in trypanosomatids: Redox homeostasis and drug resistance. ADVANCES IN PARASITOLOGY 2022; 117:75-155. [PMID: 35878950 DOI: 10.1016/bs.apar.2022.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Trypanosomatids are mainly responsible for heterogeneous parasitic diseases: Leishmaniasis, Sleeping sickness, and Chagas disease and control of these diseases implicates serious challenges due to the emergence of drug resistance. Redox-active biomolecules are the endogenous substances in organisms, which play important role in the regulation of redox homeostasis. The redox-active substances like glutathione, trypanothione, cysteine, cysteine persulfides, etc., and other inorganic intermediates (hydrogen peroxide, nitric oxide) are very useful as defence mechanism. In the present review, the suitability of trypanothione and other essential thiol molecules of trypanosomatids as drug targets are described in Leishmania and Trypanosoma. We have explored the role of tryparedoxin, tryparedoxin peroxidase, ascorbate peroxidase, superoxide dismutase, and glutaredoxins in the anti-oxidant mechanism and drug resistance. Up-regulation of some proteins in trypanothione metabolism helps the parasites in survival against drug pressure (sodium stibogluconate, Amphotericin B, etc.) and oxidative stress. These molecules accept electrons from the reduced trypanothione and donate their electrons to other proteins, and these proteins reduce toxic molecules, neutralize reactive oxygen, or nitrogen species; and help parasites to cope with oxidative stress. Thus, a better understanding of the role of these molecules in drug resistance and redox homeostasis will help to target metabolic pathway proteins to combat Leishmaniasis and trypanosomiases.
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Affiliation(s)
- Vahab Ali
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar, India.
| | - Sachidananda Behera
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar, India
| | - Afreen Nawaz
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar, India
| | - Asif Equbal
- Laboratory of Molecular Biochemistry and Cell Biology, Department of Biochemistry, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar, India; Department of Botany, Araria College, Purnea University, Purnia, Bihar, India
| | - Krishna Pandey
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences (RMRIMS), Patna, Bihar, India
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15
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Kangethe RT, Winger EM, Settypalli TBK, Datta S, Wijewardana V, Lamien CE, Unger H, Coetzer TH, Cattoli G, Diallo A. Low Dose Gamma Irradiation of Trypanosoma evansi Parasites Identifies Molecular Changes That Occur to Repair Radiation Damage and Gene Transcripts That May Be Involved in Establishing Disease in Mice Post-Irradiation. Front Immunol 2022; 13:852091. [PMID: 35634275 PMCID: PMC9136415 DOI: 10.3389/fimmu.2022.852091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
The protozoan parasite Trypanosoma evansi is responsible for causing surra in a variety of mammalian hosts and is spread by many vectors over a wide geographical area making it an ideal target for irradiation as a tool to study the initial events that occur during infection. Parasites irradiated at the representative doses 100Gy, 140Gy, and 200Gy were used to inoculate BALB/c mice revealing that parasites irradiated at 200Gy were unable to establish disease in all mice. Cytokine analysis of mice inoculated with 200Gy of irradiated parasites showed significantly lower levels of interleukins when compared to mice inoculated with non-irradiated and 100Gy irradiated parasites. Irradiation also differentially affected the abundance of gene transcripts in a dose-dependent trend measured at 6- and 20-hours post-irradiation with 234, 325, and 484 gene transcripts affected 6 hours post-irradiation for 100Gy-, 140Gy- and 200Gy-irradiated parasites, respectively. At 20 hours post-irradiation, 422, 381, and 457 gene transcripts were affected by irradiation at 100Gy, 140Gy, and 200Gy, respectively. A gene ontology (GO) term analysis was carried out for the three representative doses at 6 hours and 20 hours post-irradiation revealing different processes occurring at 20 hours when compared to 6 hours for 100Gy irradiation. The top ten most significant processes had a negative Z score. These processes fall in significance at 140Gy and even further at 200Gy, revealing that they were least likely to occur at 200Gy, and thus may have been responsible for infection in mice by 100Gy and 140Gy irradiated parasites. When looking at 100Gy irradiated parasites 20 hours post-irradiation processes with a positive Z score, we identified genes that were involved in multiple processes and compared their fold change values at 6 hours and 20 hours. We present these genes as possibly necessary for repair from irradiation damage at 6 hours and suggestive of being involved in the establishment of disease in mice at 20 hours post-irradiation. A potential strategy using this information to develop a whole parasite vaccine is also postulated.
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Affiliation(s)
- Richard T. Kangethe
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
- *Correspondence: Richard T. Kangethe,
| | - Eva M. Winger
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Tirumala Bharani K. Settypalli
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Sneha Datta
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Viskam Wijewardana
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Charles E. Lamien
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Hermann Unger
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Theresa H.T. Coetzer
- Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Adama Diallo
- Animal Production and Health Laboratory, FAO/IAEA Agriculture and Biotechnology Laboratory, IAEA Laboratories Seibersdorf, International Atomic Energy Agency (IAEA), Vienna, Austria
- UMR CIRAD INRA, Animal, Santé, Territoires, Risques et Ecosystèmes (ASTRE), Montpellier, France
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16
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Piel L, Rajan KS, Bussotti G, Varet H, Legendre R, Proux C, Douché T, Giai-Gianetto Q, Chaze T, Cokelaer T, Vojtkova B, Gordon-Bar N, Doniger T, Cohen-Chalamish S, Rengaraj P, Besse C, Boland A, Sadlova J, Deleuze JF, Matondo M, Unger R, Volf P, Michaeli S, Pescher P, Späth GF. Experimental evolution links post-transcriptional regulation to Leishmania fitness gain. PLoS Pathog 2022; 18:e1010375. [PMID: 35294501 PMCID: PMC8959184 DOI: 10.1371/journal.ppat.1010375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/28/2022] [Accepted: 02/15/2022] [Indexed: 12/30/2022] Open
Abstract
The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network associated with parasite fitness gain, with genome instability causing highly reproducible, gene dosage-independent and -dependent changes. Reduction of flagellar transcripts and increase in coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation were not correlated to dosage changes of the corresponding genes, revealing a gene dosage-independent, post-transcriptional mechanism of regulation. In contrast, abundance of gene products implicated in post-transcriptional regulation itself correlated to corresponding gene dosage changes. Thus, RNA abundance during parasite adaptation is controled by direct and indirect gene dosage changes. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification, providing first evidence that Leishmania fitness gain in culture may be controlled by post-transcriptional and epitranscriptomic regulation. Our findings propose a novel model for Leishmania fitness gain in culture, where differential regulation of mRNA stability and the generation of modified ribosomes may potentially filter deleterious from beneficial gene dosage effects and provide proteomic robustness to genetically heterogenous, adapting parasite populations. This model challenges the current, genome-centric approach to Leishmania epidemiology and identifies the Leishmania transcriptome and non-coding small RNome as potential novel sources for the discovery of biomarkers that may be associated with parasite phenotypic adaptation in clinical settings. Genome instability plays a central yet poorly understood role in human disease. Gene amplifications and deletions drive cancer development, microbial infection and therapeutic failure. The molecular mechanisms that harness the deleterious effects of genome instability to generate beneficial phenotypes in pathogenic systems are unknown. Here we study this important open question in the protozoan parasite Leishmania that causes devastating human diseases termed leishmaniases. Leishmania parasites lack transcriptional control and instead exploit genome instability to adapt to their host environment. Analyzing in vitro adaptation of hamster-derived parasites via gene copy number (genomic level) and gene expression changes (transcriptomic and proteomic levels), we show that these parasites likely exploit small nucleolar RNAs (snoRNAs) to mitigate toxic effects of genome instability by post-transcriptional regulation and the establishment of modified ribosomes. Our findings propose non-coding RNAs as potential novel biomarkers with diagnostic and prognostic value that may be linked to changes in parasite tissue tropism or drug susceptibility. This novel insight into Leishmania adaptation will be likely applicable to other fast evolving eukaryotic systems with unstable genomes, such as fungi or cancer cells.
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Affiliation(s)
- Laura Piel
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Giovanni Bussotti
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Caroline Proux
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Quentin Giai-Gianetto
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Thibault Chaze
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Barbora Vojtkova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nadav Gordon-Bar
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Praveenkumar Rengaraj
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Céline Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Jovana Sadlova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Mariette Matondo
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Pascale Pescher
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- * E-mail: (PP); (GS)
| | - Gerald F. Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- * E-mail: (PP); (GS)
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17
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Borg Y, Alsford S, Pavlika V, Zaikin A, Nesbeth DN. Synthetic biology tools for engineering Goodwin oscillation in Trypanosoma brucei brucei. Heliyon 2022; 8:e08891. [PMID: 35198764 PMCID: PMC8844716 DOI: 10.1016/j.heliyon.2022.e08891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/10/2021] [Accepted: 01/30/2022] [Indexed: 11/30/2022] Open
Abstract
Kinetoplastid protozoa possess properties that are highly divergent from the mammalian, yeast and bacterial cells more commonly used in synthetic biology and represent a tantalisingly untapped source of bioengineering potential. Trypanosoma brucei brucei (T. b. brucei), an established model organism for studying the Kinetoplastida, is non-pathogenic to humans and provides an interesting test case for establishing synthetic biology in this phylogenetic class. To demonstrate further the tractability of Kinetoplastida to synthetic biology, we sought to construct and demonstrate a Goodwin oscillator, the simplest oscillatory gene network, in T. b. brucei for the first time. We report one completed iteration of the archetypal synthetic biology Design-Build-Test-Learn (DBTL) cycle; firstly, using Ab initio mathematical modelling of the behaviour a theoretical, oscillatory, trypanosomal synthetic gene network (SGN) to inform the design of a plasmid encoding that network. Once assembled, the plasmid was then used to generate a stable transfectant T. b. brucei cell line. To test the performance of the oscillatory SGN, a novel experimental setup was established to capture images of the fluorescent signal from motion-restricted live cells. Data captured were consistent with oscillatory behaviour of the SGN, with cellular fluorescence observed to oscillate with a period of 50 min, with varying amplitude and linear growth trend. This first DBTL cycle establishes a foundation for future cycles in which the SGN design and experimental monitoring setup can be further refined.
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Affiliation(s)
- Yanika Borg
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, Bernard Katz Building, Gordon Street, University College London, London, WC1E 6BT, UK.,Department of Mathematics and Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sam Alsford
- Faculty of Infectious and Tropical Diseases & Department of Infection Biology, The London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Vasos Pavlika
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, Bernard Katz Building, Gordon Street, University College London, London, WC1E 6BT, UK
| | - Alexei Zaikin
- Department of Mathematics and Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK.,World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, Russia.,Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Darren N Nesbeth
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, Bernard Katz Building, Gordon Street, University College London, London, WC1E 6BT, UK
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18
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Glockzin K, Meek TD, Katzfuss A. Characterization of adenine phosphoribosyltransferase (APRT) activity in Trypanosoma brucei brucei: Only one of the two isoforms is kinetically active. PLoS Negl Trop Dis 2022; 16:e0009926. [PMID: 35104286 PMCID: PMC8836349 DOI: 10.1371/journal.pntd.0009926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/11/2022] [Accepted: 01/22/2022] [Indexed: 11/17/2022] Open
Abstract
Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a Neglected Tropical Disease endemic to 36 African countries, with approximately 70 million people currently at risk for infection. Current therapeutics are suboptimal due to toxicity, adverse side effects, and emerging resistance. Thus, both effective and affordable treatments are urgently needed. The causative agent of HAT is the protozoan Trypanosoma brucei ssp. Annotation of its genome confirms previous observations that T. brucei is a purine auxotroph. Incapable of de novo purine synthesis, these protozoan parasites rely on purine phosphoribosyltransferases to salvage purines from their hosts for the synthesis of purine monophosphates. Complete and accurate genome annotations in combination with the identification and characterization of the catalytic activity of purine salvage enzymes enables the development of target-specific therapies in addition to providing a deeper understanding of purine metabolism in T. brucei. In trypanosomes, purine phosphoribosyltransferases represent promising drug targets due to their essential and central role in purine salvage. Enzymes involved in adenine and adenosine salvage, such as adenine phosphoribosyltransferases (APRTs, EC 2.4.2.7), are of particular interest for their potential role in the activation of adenine and adenosine-based pro-drugs. Analysis of the T. brucei genome shows two putative aprt genes: APRT1 (Tb927.7.1780) and APRT2 (Tb927.7.1790). Here we report studies of the catalytic activity of each putative APRT, revealing that of the two T. brucei putative APRTs, only APRT1 is kinetically active, thereby signifying a genomic misannotation of Tb927.7.1790 (putative APRT2). Reliable genome annotation is necessary to establish potential drug targets and identify enzymes involved in adenine and adenosine-based pro-drug activation.
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Affiliation(s)
- Kayla Glockzin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Thomas D. Meek
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (TDM); (AK)
| | - Ardala Katzfuss
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (TDM); (AK)
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19
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Santi AMM, Murta SMF. Impact of Genetic Diversity and Genome Plasticity of Leishmania spp. in Treatment and the Search for Novel Chemotherapeutic Targets. Front Cell Infect Microbiol 2022; 12:826287. [PMID: 35141175 PMCID: PMC8819175 DOI: 10.3389/fcimb.2022.826287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 11/21/2022] Open
Abstract
Leishmaniasis is one of the major public health concerns in Latin America, Africa, Asia, and Europe. The absence of vaccines for human use and the lack of effective vector control programs make chemotherapy the main strategy to control all forms of the disease. However, the high toxicity of available drugs, limited choice of therapeutic agents, and occurrence of drug-resistant parasite strains are the main challenges related to chemotherapy. Currently, only a small number of drugs are available for leishmaniasis treatment, including pentavalent antimonials (SbV), amphotericin B and its formulations, miltefosine, paromomycin sulphate, and pentamidine isethionate. In addition to drug toxicity, therapeutic failure of leishmaniasis is a serious concern. The occurrence of drug-resistant parasites is one of the causes of therapeutic failure and is closely related to the diversity of parasites in this genus. Owing to the enormous plasticity of the genome, resistance can occur by altering different metabolic pathways, demonstrating that resistance mechanisms are multifactorial and extremely complex. Genetic variability and genome plasticity cause not only the available drugs to have limitations, but also make the search for new drugs challenging. Here, we examined the biological characteristics of parasites that hinder drug discovery.
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Glans H, Lind Karlberg M, Advani R, Bradley M, Alm E, Andersson B, Downing T. High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria. PLoS Negl Trop Dis 2021; 15:e0010110. [PMID: 34968388 PMCID: PMC8754299 DOI: 10.1371/journal.pntd.0010110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/12/2022] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
Background The kinetoplastid protozoan Leishmania tropica mainly causes cutaneous leishmaniasis in humans in the Middle East, and relapse or treatment failure after treatment are common in this area. L. tropica’s digenic life cycle includes distinct stages in the vector sandfly and the mammalian host. Sexual reproduction and genetic exchange appear to occur more frequently than in other Leishmania species. Understanding these processes is complicated by chromosome instability during cell division that yields aneuploidy, recombination and heterozygosity. This combination of rare recombination and aneuploid permits may reveal signs of hypothetical parasexual mating, where diploid cells fuse to form a transient tetraploid that undergoes chromosomal recombination and gradual chromosomal loss. Methodology/principal findings The genome-wide SNP diversity from 22 L. tropica isolates showed chromosome-specific runs of patchy heterozygosity and extensive chromosome copy number variation. All these isolates were collected during 2007–2017 in Sweden from patients infected in the Middle East and included isolates from a patient possessing two genetically distinct leishmaniasis infections three years apart with no evidence of re-infection. We found differing ancestries on the same chromosome (chr36) across multiple samples: matching the reference genome with few derived alleles, followed by blocks of heterozygous SNPs, and then by clusters of homozygous SNPs with specific recombination breakpoints at an inferred origin of replication. Other chromosomes had similar marked changes in heterozygosity at strand-switch regions separating polycistronic transcriptional units. Conclusion/significance These large-scale intra- and inter-chromosomal changes in diversity driven by recombination and aneuploidy suggest multiple mechanisms of cell reproduction and diversification in L. tropica, including mitotic, meiotic and parasexual processes. It underpins the need for more genomic surveillance of Leishmania, to detect emerging hybrids that could spread more widely and to better understand the association between genetic variation and treatment outcome. Furthering our understanding of Leishmania genome evolution and ancestry will aid better diagnostics and treatment for cutaneous leishmaniasis caused by L.tropica in the Middle East. Cutaneous leishmaniasis is mainly caused by Leishmania tropica in the Middle East, where it is known for treatment failure and a need for prolonged and/or multiple treatments. Several factors affect the clinical presentation and treatment outcome, such as host genetic variability and specific immune response, as well as environmental factors and the vector species. Little is known about the parasite genome and its influence on treatment response. By analysing the genome of 22 isolates of L. tropica, we have revealed extensive genomic variation and a complex population structure with evidence of genetic exchange within and among the isolates, indicating a possible presence of sexual or parasexual mechanisms. Understanding the Leishmania genome better may improve future treatment and better understanding of treatment failure and relapse.
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Affiliation(s)
- Hedvig Glans
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Maria Lind Karlberg
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Reza Advani
- Department of Microbiology, The Public Health Agency of Sweden, Stockholm, Sweden
| | - Maria Bradley
- Division of Dermatology & Venerology, Dept of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venerology, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Alm
- The European Center for Disease Prevention and Control, Stockholm, Sweden
| | - Björn Andersson
- Department of Cell & Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
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Characterization of an Atypical eIF4E Ortholog in Leishmania, LeishIF4E-6. Int J Mol Sci 2021; 22:ijms222312720. [PMID: 34884522 PMCID: PMC8657474 DOI: 10.3390/ijms222312720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 01/11/2023] Open
Abstract
Leishmania parasites are digenetic protists that shuffle between sand fly vectors and mammalian hosts, transforming from flagellated extracellular promastigotes that reside within the intestinal tract of female sand flies to the obligatory intracellular and non-motile amastigotes within mammalian macrophages. Stage differentiation is regulated mainly by post-transcriptional mechanisms, including translation regulation. Leishmania parasites encode six different cap-binding proteins, LeishIF4E1-6, that show poor conservation with their counterparts from higher eukaryotes and among themselves. In view of the changing host milieu encountered throughout their life cycle, we propose that each LeishIF4E has a unique role, although these functions may be difficult to determine. Here we characterize LeishIF4E-6, a unique eIF4E ortholog that does not readily associate with m7GTP cap in either of the tested life forms of the parasite. We discuss the potential effect of substituting two essential tryptophan residues in the cap-binding pocket, expected to be involved in the cap-binding activity, as judged from structural studies in the mammalian eIF4E. LeishIF4E-6 binds to LeishIF4G-5, one of the five eIF4G candidates in Leishmania. However, despite this binding, LeishIF4E-6 does not appear to function as a translation factor. Its episomal overexpression causes a general reduction in the global activity of protein synthesis, which was not observed in the hemizygous deletion mutant generated by CRISPR-Cas9. This genetic profile suggests that LeishIF4E-6 has a repressive role. The interactome of LeishIF4E-6 highlights proteins involved in RNA metabolism such as the P-body marker DHH1, PUF1 and an mRNA-decapping enzyme that is homologous to the TbALPH1.
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22
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Abstract
Leishmania donovani is a parasitic protist that causes the lethal Kala-azar fever in India and East Africa. Gene expression in Leishmania is regulated by gene copy number variation and inducible translation while RNA synthesis initiates at a small number of sites per chromosome and proceeds through polycistronic transcription units, precluding a gene-specific regulation (C. Clayton and M. Shapira, Mol Biochem Parasitol 156:93–101, 2007, https://doi.org/10.1016/j.molbiopara.2007.07.007). Here, we analyze the dynamics of chromatin structure in both life cycle stages of the parasite and find evidence for an additional, epigenetic gene regulation pathway in this early branching eukaryote. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis (J. D. Buenrostro, P. G. Giresi, L. C. Zaba, H. Y. Chang, and W. J. Greenleaf, Nat Methods 10:1213–1218, 2013, https://doi.org/10.1038/nmeth.2688) predominantly shows euchromatin at transcription start regions in fast-growing promastigotes, but mostly heterochromatin in the slowly proliferating amastigotes, the mammalian stage, reflecting a previously shown increase of histone synthesis in the latter stage. IMPORTANCELeishmania parasites are important pathogens with a global impact and cause poverty-related illness and death. They are devoid of classic cis- and trans-acting transcription regulators but use regulated translation and gene copy number variations to adapt to hosts and environments. In this work, we show that transcription start regions present as open euchromatin in fast-growing insect stages but as less-accessible heterochromatin in the slowly proliferating amastigote stage, indicating an epigenetic control of gene accessibility in this early branching eukaryotic pathogen. This finding should stimulate renewed interest in the control of RNA synthesis in Leishmania and related parasites.
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Characterization of the RNA-Binding Protein TcSgn1 in Trypanosoma cruzi. Microorganisms 2021; 9:microorganisms9050986. [PMID: 34063193 PMCID: PMC8147501 DOI: 10.3390/microorganisms9050986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022] Open
Abstract
RNA-binding proteins (RBPs) participate in several steps of post-transcriptional regulation of gene expression, such as splicing, messenger RNA transport, mRNA localization, and translation. Gene-expression regulation in trypanosomatids occurs primarily at the post-transcriptional level, and RBPs play important roles in the process. Here, we characterized the RBP TcSgn1, which contains one RNA recognition motif (RRM). TcSgn1 is a close ortholog of yeast Saccharomyces cerevisiae protein ScSgn1, which plays a role in translational regulation in the cytoplasm. We found that TcSgn1 in Trypanosoma cruzi is localized in the nucleus in exponentially growing epimastigotes. By performing immunoprecipitation assays of TcSgn1, we identified hundreds of mRNAs associated with the protein, a significant fraction of them coding for nucleic acids binding, transcription, and endocytosis proteins. In addition, we show that TcSgn1 is capable of interacting directly with the poly(A) tail of the mRNAs. The study of parasites under nutritional stress showed that TcSgn1 was localized in cytoplasmic granules in addition to localizing in the nucleus. Similar to ScSgn1, we observed that TcSgn1 also interacts with the PABP1 protein, suggesting that this protein may play a role in regulating gene expression in T. cruzi. Taken together, our results show that RNA-binding protein TcSgn1 is part of ribonucleoprotein complexes associated with nuclear functions, stress response, and RNA metabolism.
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Hernández-Alvarez L, Oliveira AB, Hernández-González JE, Chahine J, Pascutti PG, de Araujo AS, de Souza FP. Computational study on the allosteric mechanism of Leishmania major IF4E-1 by 4E-interacting protein-1: Unravelling the determinants of m 7GTP cap recognition. Comput Struct Biotechnol J 2021; 19:2027-2044. [PMID: 33995900 PMCID: PMC8085901 DOI: 10.1016/j.csbj.2021.03.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Atomistic details on perturbations induced by Lm4E-IP1 binding are described. The modulation of LmIF4E-1 affinity for the cap is confirmed by energetic analyses. Signaling paths between the allosteric and othosteric sites of LmIF4E-1 are predicted. Lm4E-IP1 binding increases the side-chain entropy of W83 and R172 of LmIF4E-1. A mechanism of dynamic allostery is proposed for the regulation mediated by Lm4E-IP1.
During their life cycle, Leishmania parasites display a fine-tuned regulation of the mRNA translation through the differential expression of isoforms of eukaryotic translation initiation factor 4E (LeishIF4Es). The interaction between allosteric modulators such as 4E-interacting proteins (4E-IPs) and LeishIF4E affects the affinity of this initiation factor for the mRNA cap. Here, several computational approaches were employed to elucidate the molecular bases of the previously-reported allosteric modulation in L. major exerted by 4E-IP1 (Lm4E-IP1) on eukaryotic translation initiation factor 4E 1 (LmIF4E-1). Molecular dynamics (MD) simulations and accurate binding free energy calculations (ΔGbind) were combined with network-based modeling of residue-residue correlations. We also describe the differences in internal motions of LmIF4E-1 apo form, cap-bound, and Lm4E-IP1-bound systems. Through community network calculations, the differences in the allosteric pathways of allosterically-inhibited and active forms of LmIF4E-1 were revealed. The ΔGbind values show significant differences between the active and inhibited systems, which are in agreement with the available experimental data. Our study thoroughly describes the dynamical perturbations of LmIF4E-1 cap-binding site triggered by Lm4E-IP1. These findings are not only essential for the understanding of a critical process of trypanosomatids’ gene expression but also for gaining insight into the allostery of eukaryotic IF4Es, which could be useful for structure-based design of drugs against this protein family.
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Affiliation(s)
- Lilian Hernández-Alvarez
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Antonio B Oliveira
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Center for Theoretical Biological Physics, Rice University, Huston, TX, United States
| | - Jorge Enrique Hernández-González
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jorge Chahine
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Pedro Geraldo Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Suman de Araujo
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Julio de Mesquita Filho, São José do Rio Preto, São Paulo, Brazil
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Comparative phosphoproteomic analysis unravels MAPK1 regulated phosphoproteins in Leishmania donovani. J Proteomics 2021; 240:104189. [PMID: 33757882 DOI: 10.1016/j.jprot.2021.104189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/05/2021] [Accepted: 03/09/2021] [Indexed: 12/18/2022]
Abstract
Mitogen Activated Protein Kinase1 (MAPK1) of Leishmania donovani functions as key regulators of various cellular activities, which seem to be imperative for parasite survival, infectivity, drug resistance and post-translational modification of chaperones/co-chaperones. However, very less is known about LdMAPK1 target proteins. With recent advancements in proteomics, we aimed to identify phosphoproteins which were differentially expressed in LdMAPK1 overexpressing (Dd8++/++) and single replacement mutants (Dd8+/) as compared to wild type (Dd8+/+) parasites, utilizing LC-MS/MS approach. An in-depth label-free phospoproteomic analysis revealed that modulation of LdMAPK1 expression significantly modulates expression levels of miscellaneous phosphoproteins which may act as its targets/substrates. Out of 1974 quantified phosphoproteins in parasite, 140 were significantly differentially expressed in MAPK1 overexpressing and single replacement mutants. These differentially expressed phosphoproteins are majorly associated with metabolism, signal transduction, replication, transcription, translation, transporters and cytoskeleton/motor proteins, hence suggested that MAPK1 may act in concert to modulate global biological processes. The study further implicated possible role of LdMAPK1 in regulation and management of stress machinery in parasite through post translational modifications. Precisely, comparative phosphoproteomics study has elucidated significant role of LdMAPK1 in regulating various pathways contributing in parasite biology with relevance to future drug development. SIGNIFICANCE: MAPKinase1, the downstream kinase of MAPK signal transduction pathway, has drawn much attention as potential therapeutic drug target due to their indispensable role in survival and infectivity of Leishmania donovani. However, limited information is available about its downstream effector proteins/signaling networks. Utilizing label free LC-MS/MS analysis, phosphoproteome of LdMAPK1 over-expressing (Dd8++/++) and LdMAPK1 single replacement mutants (Dd8+/-) with wild type (Dd8+/+) parasites was compared and identified 140 LdMAPK1 modulated phosphoproteins, mainly involved in pathways like signal transduction, metabolism, transcriptional, translational, post-translational modification and regulation of heat shock proteins. Interestingly, LdMAPK1 interacts directly with only six phosphoproteins i.e. casein kinase, casein kinase II, HSP83/HSP90, LACK, protein kinase and serine/threonine protein kinase. Thus, the study elucidates significant role of LdMAPK1 in Leishmania biology which may drive drug-discovery efforts against visceral leishmaniasis.
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26
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Mwangi KW, Macharia RW, Bargul JL. Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector. Parasit Vectors 2021; 14:74. [PMID: 33482903 PMCID: PMC7821691 DOI: 10.1186/s13071-021-04597-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/13/2021] [Indexed: 01/14/2023] Open
Abstract
Background Trypanosoma brucei species are motile protozoan parasites that are cyclically transmitted by tsetse fly (genus Glossina) causing human sleeping sickness and nagana in livestock in sub-Saharan Africa. African trypanosomes display digenetic life cycle stages in the tsetse fly vector and in their mammalian host. Experimental work on insect-stage trypanosomes is challenging because of the difficulty in setting up successful in vitro cultures. Therefore, there is limited knowledge on the trypanosome biology during its development in the tsetse fly. Consequently, this limits the development of new strategies for blocking parasite transmission in the tsetse fly. Methods In this study, RNA-Seq data of insect-stage trypanosomes were used to construct a T. brucei gene co-expression network using the weighted gene co-expression analysis (WGCNA) method. The study identified significant enriched modules for genes that play key roles during the parasite’s development in tsetse fly. Furthermore, potential 3′ untranslated region (UTR) regulatory elements for genes that clustered in the same module were identified using the Finding Informative Regulatory Elements (FIRE) tool. Results A fraction of gene modules (12 out of 27 modules) in the constructed network were found to be enriched in functional roles associated with the cell division, protein biosynthesis, mitochondrion, and cell surface. Additionally, 12 hub genes encoding proteins such as RNA-binding protein 6 (RBP6), arginine kinase 1 (AK1), brucei alanine-rich protein (BARP), among others, were identified for the 12 significantly enriched gene modules. In addition, the potential regulatory elements located in the 3′ untranslated regions of genes within the same module were predicted. Conclusions The constructed gene co-expression network provides a useful resource for network-based data mining to identify candidate genes for functional studies. This will enhance understanding of the molecular mechanisms that underlie important biological processes during parasite’s development in tsetse fly. Ultimately, these findings will be key in the identification of potential molecular targets for disease control.![]()
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Affiliation(s)
- Kennedy W Mwangi
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya. .,Jomo Kenyatta University of Agriculture and Technology, P.O. BOX 62000-00200, Nairobi, Kenya.
| | | | - Joel L Bargul
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772-00100, Nairobi, Kenya.,Jomo Kenyatta University of Agriculture and Technology, P.O. BOX 62000-00200, Nairobi, Kenya
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27
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Grünebast J, Clos J. Leishmania: Responding to environmental signals and challenges without regulated transcription. Comput Struct Biotechnol J 2020; 18:4016-4023. [PMID: 33363698 PMCID: PMC7744640 DOI: 10.1016/j.csbj.2020.11.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Here we describe the non-canonical control of gene expression in Leishmania, a single-cell parasite that is responsible for one of the major neglected tropical diseases. We discuss the lack of regulated RNA synthesis, the post-transcriptional gene regulation including RNA stability and regulated translation. We also show that genetic adaptations such as mosaic aneuploidy, gene copy number variations and DNA sequence polymorphisms are important means for overcoming drug challenge and environmental diversity. These mechanisms are discussed in the context of the unique flow of genetic information found in Leishmania and related protists.
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Affiliation(s)
- Janne Grünebast
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Joachim Clos
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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28
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Nocua PA, Requena JM, Puerta CJ. Identification of the interactomes associated with SCD6 and RBP42 proteins in Leishmania braziliensis. J Proteomics 2020; 233:104066. [PMID: 33296709 DOI: 10.1016/j.jprot.2020.104066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/16/2020] [Accepted: 11/29/2020] [Indexed: 02/04/2023]
Abstract
Leishmania are protozoan parasites responsible for leishmaniasis. These parasites present a precise gene regulation that allows them to survive different environmental conditions during their digenetic life cycle. This adaptation depends on the regulation of the expression of a wide variety of genes, which occurs, mainly at the post-transcriptional level. This differential gene expression is achieved by mechanisms based mainly in RNA binding proteins that regulate the translation and/or stability of mRNA targets by interaction with cis elements principally located in the untranslated regions (UTR). In recent studies, our group identified and characterized two proteins, SCD6 and RBP42, as RNA binding proteins in Leishmania braziliensis. To find clues about the cellular processes in which these proteins are involved, this work was aimed to determine the SCD6- and RBP42-interacting proteins (interactome) in L. braziliensis promastigotes. For this purpose, after an in vivo UV cross-linking, cellular extracts were used to immunoprecipitated, by specific antibodies, protein complexes in which SCD6 or RBP42 were present. Protein mass spectrometry analysis of the immunoprecipitated proteins identified 96 proteins presumably associated with SCD6 and 173 proteins associated with RBP42. Notably, a significant proportion of the identified proteins were shared in both interactomes, indicating a possible functional relationship between SCD6 and RBP42. Remarkably, many of the proteins identified in the SCD6 and RBP42 interactomes are related to RNA metabolism and translation processes, and many of them have been described as components of ribonucleoprotein (RNP) granules in Leishmania and related trypanosomatids. Thus, these results support a role of SCD6 and RBP42 in the assembly and/or function of mRNA-protein complexes, participating in the fate (decay/accumulation/translation) of L. braziliensis transcripts. SIGNIFICANCE: Parasites of the Leishmania genus present a particular regulation of gene expression, operating mainly at the post-transcriptional level, surely aimed to modulate quickly both mRNA and protein levels to survive the sudden environmental changes that occur during a parasite's life cycle as it moves from one host to another. This regulation of gene expression processes would be governed by the interaction of mRNA with RNA binding proteins. Nevertheless, the entirety of protein networks involved in these regulatory processes is far from being understood. In this regard, our work is contributing to stablish protein networks in which the L. braziliensis SCD6 and RBP42 proteins are involved; these proteins, in previous works, have been described as RNA binding proteins and found to participate in gene regulation in different cells and organisms. Additionally, our data point out a possible functional relationship between SCD6 and RBP42 proteins as constituents of mRNA granules, like processing bodies or stress granules, which are essential structures in the regulation of gene expression. This knowledge could provide a new approach for the development of therapeutic targets to control Leishmania infections.
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Affiliation(s)
- Paola A Nocua
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia; Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - José M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Concepción J Puerta
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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De Souza W, Barrias ES. May the epimastigote form of Trypanosoma cruzi be infective? Acta Trop 2020; 212:105688. [PMID: 32888934 DOI: 10.1016/j.actatropica.2020.105688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/24/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022]
Abstract
For many years it has been considered that there are three basic developmental stages of Trypanosoma cruzi: Epimastigote (Epi), Amastigote (Ama) and Trypomastigote (Typo). Epi and Ama are able to divide while Trypo does not divide. Epi are not infective while Ama and Trypo are able to infect host cells. Here we review the available data for the epimastigote form. Taken together the data show that (a) there are intermediate forms between epimastigotes and trypomastigotes in axenic cultures as well as between amastigote and trypomastigote forms within the cells (both in vitro and in vivo), and (c) that the intermediate forms, here designated as "Transitional Epimastigote", most of the time considered as epimastigotes, are able to infect cells. The recognition of the existence of this stage is of practical importance for those work with T. cruzi. Many laboratories working only with T. cruzi in axenic cultures usually consider to work with nonpathogenic cultures. This attitude needs to be changed requiring special care by those working with this protozoan to avoid accidental infections in the laboratory. In view of these observation a new scheme for the life cycle of T. cruzi is proposed.
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30
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Andrade JM, Gonçalves LO, Liarte DB, Lima DA, Guimarães FG, de Melo Resende D, Santi AMM, de Oliveira LM, Velloso JPL, Delfino RG, Pescher P, Späth GF, Ruiz JC, Murta SMF. Comparative transcriptomic analysis of antimony resistant and susceptible Leishmania infantum lines. Parasit Vectors 2020; 13:600. [PMID: 33256787 PMCID: PMC7706067 DOI: 10.1186/s13071-020-04486-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022] Open
Abstract
Background One of the major challenges to leishmaniasis treatment is the emergence of parasites resistant to antimony. To study differentially expressed genes associated with drug resistance, we performed a comparative transcriptomic analysis between wild-type and potassium antimonyl tartrate (SbIII)-resistant Leishmania infantum lines using high-throughput RNA sequencing. Methods All the cDNA libraries were constructed from promastigote forms of each line, sequenced and analyzed using STAR for mapping the reads against the reference genome (L. infantum JPCM5) and DESeq2 for differential expression statistical analyses. All the genes were functionally annotated using sequence similarity search. Results The analytical pipeline considering an adjusted p-value < 0.05 and fold change > 2.0 identified 933 transcripts differentially expressed (DE) between wild-type and SbIII-resistant L. infantum lines. Out of 933 DE transcripts, 504 presented functional annotation and 429 were assigned as hypothetical proteins. A total of 837 transcripts were upregulated and 96 were downregulated in the SbIII-resistant L. infantum line. Using this DE dataset, the proteins were further grouped in functional classes according to the gene ontology database. The functional enrichment analysis for biological processes showed that the upregulated transcripts in the SbIII-resistant line are associated with protein phosphorylation, microtubule-based movement, ubiquitination, host–parasite interaction, cellular process and other categories. The downregulated transcripts in the SbIII-resistant line are assigned in the GO categories: ribonucleoprotein complex, ribosome biogenesis, rRNA processing, nucleosome assembly and translation. Conclusions The transcriptomic profile of L. infantum showed a robust set of genes from different metabolic pathways associated with the antimony resistance phenotype in this parasite. Our results address the complex and multifactorial antimony resistance mechanisms in Leishmania, identifying several candidate genes that may be further evaluated as molecular targets for chemotherapy of leishmaniasis.![]()
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Affiliation(s)
- Juvana Moreira Andrade
- Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Leilane Oliveira Gonçalves
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil.,Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Davi Alvarenga Lima
- Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil.,Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | | | - Daniela de Melo Resende
- Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil.,Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Ana Maria Murta Santi
- Genômica Funcional de Parasitos, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Luciana Marcia de Oliveira
- Unité Biologie des ARN des Pathogènes Fongiques, Département de Mycologie, Institut Pasteur, Paris, France
| | | | - Renato Guimarães Delfino
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Pascale Pescher
- Unité de Parasitologie moléculaire et Signalisation, Département de Parasitologie et Mycologie, Institut Pasteur, Paris, France
| | - Gerald F Späth
- Unité de Parasitologie moléculaire et Signalisation, Département de Parasitologie et Mycologie, Institut Pasteur, Paris, France
| | - Jeronimo Conceição Ruiz
- Grupo Informática de Biossistemas, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, MG, Brazil. .,Programa de Pós-graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil.
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Identification of Novel Interspersed DNA Repetitive Elements in the Trypanosoma cruzi Genome Associated with the 3'UTRs of Surface Multigenic Families. Genes (Basel) 2020; 11:genes11101235. [PMID: 33096822 PMCID: PMC7593948 DOI: 10.3390/genes11101235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 11/23/2022] Open
Abstract
Trypanosoma cruzi is the etiological agent of Chagas disease, which affects millions of people in Latin America. No transcriptional control of gene expression has been demonstrated in this organism, and 50% of its genome consists of repetitive elements and members of multigenic families. In this study, we applied a novel bioinformatics approach to predict new repetitive elements in the genome sequence of T. cruzi. A new repetitive sequence measuring 241 nt was identified and found to be interspersed along the genome sequence from strains of different DTUs. This new repeat was mostly on intergenic regions, and upstream and downstream regions of the 241 nt repeat were enriched in surface protein genes. RNAseq analysis revealed that the repeat was part of processed mRNAs and was predominantly found in the 3′ untranslated regions (UTRs) of genes of multigenic families encoding surface proteins. Moreover, we detected a correlation between the presence of the repeat in the 3′UTR of multigenic family genes and the level of differential expression of these genes when comparing epimastigote and trypomastigote transcriptomes. These data suggest that this sequence plays a role in the posttranscriptional regulation of the expression of multigenic families.
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Bea A, Kröber-Boncardo C, Sandhu M, Brinker C, Clos J. The Leishmania donovani SENP Protease Is Required for SUMO Processing but Not for Viability. Genes (Basel) 2020; 11:E1198. [PMID: 33066659 PMCID: PMC7602377 DOI: 10.3390/genes11101198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Accepted: 10/10/2020] [Indexed: 01/13/2023] Open
Abstract
The protozoan parasite Leishmania donovani is part of an early eukaryotic branch and depends on post-transcriptional mechanisms for gene expression regulation. This includes post-transcriptional protein modifications, such as protein phosphorylation. The presence of genes for protein SUMOylation, i.e., the covalent attachment of small ubiquitin-like modifier (SUMO) polypeptides, in the Leishmania genomes prompted us to investigate the importance of the sentrin-specific protease (SENP) and its putative client, SUMO, for the vitality and infectivity of Leishmania donovani. While SENP null mutants are viable with reduced vitality, viable SUMO null mutant lines could not be obtained. SUMO C-terminal processing is disrupted in SENP null mutants, preventing SUMO from covalent attachment to proteins and nuclear translocation. Infectivity in vitro is not affected by the loss of SENP-dependent SUMO processing. We conclude that SENP is required for SUMO processing, but that functions of unprocessed SUMO are critical for Leishmania viability.
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Affiliation(s)
- Annika Bea
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany; (A.B.); (C.K.-B.); (M.S.); (C.B.)
| | - Constanze Kröber-Boncardo
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany; (A.B.); (C.K.-B.); (M.S.); (C.B.)
| | - Manpreet Sandhu
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany; (A.B.); (C.K.-B.); (M.S.); (C.B.)
- Boehringer Ingelheim RCV, A-1121 Vienna, Austria
| | - Christine Brinker
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany; (A.B.); (C.K.-B.); (M.S.); (C.B.)
| | - Joachim Clos
- Leishmaniasis Group, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany; (A.B.); (C.K.-B.); (M.S.); (C.B.)
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Karpiyevich M, Artavanis-Tsakonas K. Ubiquitin-Like Modifiers: Emerging Regulators of Protozoan Parasites. Biomolecules 2020; 10:E1403. [PMID: 33022940 PMCID: PMC7600729 DOI: 10.3390/biom10101403] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
Post-translational protein regulation allows for fine-tuning of cellular functions and involves a wide range of modifications, including ubiquitin and ubiquitin-like modifiers (Ubls). The dynamic balance of Ubl conjugation and removal shapes the fates of target substrates, in turn modulating various cellular processes. The mechanistic aspects of Ubl pathways and their biological roles have been largely established in yeast, plants, and mammalian cells. However, these modifiers may be utilised differently in highly specialised and divergent organisms, such as parasitic protozoa. In this review, we explore how these parasites employ Ubls, in particular SUMO, NEDD8, ATG8, ATG12, URM1, and UFM1, to regulate their unconventional cellular physiology. We discuss emerging data that provide evidence of Ubl-mediated regulation of unique parasite-specific processes, as well as the distinctive features of Ubl pathways in parasitic protozoa. We also highlight the potential to leverage these essential regulators and their cognate enzymatic machinery for development of therapeutics to protect against the diseases caused by protozoan parasites.
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Kröber-Boncardo C, Lorenzen S, Brinker C, Clos J. Casein kinase 1.2 over expression restores stress resistance to Leishmania donovani HSP23 null mutants. Sci Rep 2020; 10:15969. [PMID: 32994468 PMCID: PMC7525241 DOI: 10.1038/s41598-020-72724-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/04/2020] [Indexed: 01/25/2023] Open
Abstract
Leishmania donovani is a trypanosomatidic parasite and causes the lethal kala-azar fever, a neglected tropical disease. The Trypanosomatida are devoid of transcriptional gene regulation and rely on gene copy number variations and translational control for their adaption to changing conditions. To survive at mammalian tissue temperatures, L. donovani relies on the small heat shock protein HSP23, the loss of which renders the parasites stress sensitive and impairs their proliferation. Here, we analysed a spontaneous escape mutant with wild type-like in vitro growth. Further selection of this escape strains resulted in a complete reversion of the phenotype. Whole genome sequencing revealed a correlation between stress tolerance and the massive amplification of a six-gene cluster on chromosome 35, with further analysis showing over expression of the casein kinase 1.2 gene as responsible. In vitro phosphorylation experiments established both HSP23 and the related P23 co-chaperone as substrates and modulators of casein kinase 1.2, providing evidence for another crucial link between chaperones and signal transduction protein kinases in this early branching eukaryote.
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Affiliation(s)
- Constanze Kröber-Boncardo
- Leishmania Group, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany
| | - Stephan Lorenzen
- Department of Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christine Brinker
- Leishmania Group, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany
| | - Joachim Clos
- Leishmania Group, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht St 74, 20359, Hamburg, Germany.
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Rashidi S, Kalantar K, Fernandez-Rubio C, Anvari E, Nguewa P, Hatam G. Chitin binding protein as a possible RNA binding protein in Leishmania parasites. Pathog Dis 2020; 78:5735439. [PMID: 32053190 DOI: 10.1093/femspd/ftaa007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/12/2020] [Indexed: 12/17/2022] Open
Abstract
Leishmaniasis includes a broad spectrum of pathological outcomes in humans caused by protozoan parasites from the genus Leishmania. In recent years, proteomic techniques have introduced novel proteins with critical functions in Leishmania parasites. Based on our report of a Chitin binding protein (CBP) in our previous immunoproteomic study, this article suggests that CBP might be an RNA binding protein (RBP) in Leishmania parasites. RBPs, as key regulatory factors, have a role in post-transcriptional gene regulation. The presence of RBPs in Leishmania parasites has not been considered so far; however, this study aims to open a new venue regarding RBPs in Leishmania parasites. Confirming CBP as an RBP in Leishmania parasites, exploring other RBPs and their functions might lead to interesting issues in leishmaniasis. In fact, due to the regulatory role of RBPs in different diseases including cancers and their further classification as therapeutic targets, the emerging evaluation of CBP and RBPs from Leishmania parasites may allow the discovery of novel and effective drugs against leishmaniasis.
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Affiliation(s)
- Sajad Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kurosh Kalantar
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Celia Fernandez-Rubio
- University of Navarra, ISTUN Instituto de Salud Tropical, IdiSNa, Department of Microbiology and Parasitology. c/ Irunlarrea 1, 31008 Pamplona, Spain
| | - Enayat Anvari
- Department of Physiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Paul Nguewa
- University of Navarra, ISTUN Instituto de Salud Tropical, IdiSNa, Department of Microbiology and Parasitology. c/ Irunlarrea 1, 31008 Pamplona, Spain
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Sanchiz Á, Morato E, Rastrojo A, Camacho E, González-de la Fuente S, Marina A, Aguado B, Requena JM. The Experimental Proteome of Leishmania infantum Promastigote and Its Usefulness for Improving Gene Annotations. Genes (Basel) 2020; 11:E1036. [PMID: 32887454 PMCID: PMC7563732 DOI: 10.3390/genes11091036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/02/2022] Open
Abstract
Leishmania infantum causes visceral leishmaniasis (kala-azar), the most severe form of leishmaniasis, which is lethal if untreated. A few years ago, the re-sequencing and de novo assembling of the L. infantum (JPCM5 strain) genome was accomplished, and now we aimed to describe and characterize the experimental proteome of this species. In this work, we performed a proteomic analysis from axenic cultured promastigotes and carried out a detailed comparison with other Leishmania experimental proteomes published to date. We identified 2352 proteins based on a search of mass spectrometry data against a database built from the six-frame translated genome sequence of L. infantum. We detected many proteins belonging to organelles such as glycosomes, mitochondria, or flagellum, as well as many metabolic enzymes and many putative RNA binding proteins and molecular chaperones. Moreover, we listed some proteins presenting post-translational modifications, such as phosphorylations, acetylations, and methylations. On the other hand, the identification of peptides mapping to genomic regions previously annotated as non-coding allowed for the correction of annotations, leading to the N-terminal extension of protein sequences and the uncovering of eight novel protein-coding genes. The alliance of proteomics, genomics, and transcriptomics has resulted in a powerful combination for improving the annotation of the L. infantum reference genome.
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Affiliation(s)
| | | | | | | | | | | | | | - Jose M. Requena
- Centro de Biología Molecular “Severo Ochoa” (CBMSO, CSIC-UAM) Campus de Excelencia Internacional (CEI) UAM+CSIC, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (Á.S.); (E.M.); (A.R.); (E.C.); (S.G.-d.l.F.); (A.M.); (B.A.)
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de Lima LP, Poubel SB, Yuan ZF, Rosón JN, Vitorino FNDL, Holetz FB, Garcia BA, da Cunha JPC. Improvements on the quantitative analysis of Trypanosoma cruzi histone post translational modifications: Study of changes in epigenetic marks through the parasite's metacyclogenesis and life cycle. J Proteomics 2020; 225:103847. [PMID: 32480077 DOI: 10.1016/j.jprot.2020.103847] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/26/2020] [Accepted: 05/24/2020] [Indexed: 02/06/2023]
Abstract
Trypanosome histone N-terminal sequences are very divergent from the other eukaryotes, although they are still decorated by post-translational modifications (PTMs). Here, we used a highly robust workflow to analyze histone PTMs in the parasite Trypanosoma cruzi using mass spectrometry-based (MS-based) data-independent acquisition (DIA). We adapted the workflow for the analysis of the parasite's histone sequences by modifying the software EpiProfile 2.0, improving peptide and PTM quantification accuracy. This workflow could now be applied to the study of 141 T. cruzi modified histone peptides, which we used to investigate the dynamics of histone PTMs along the metacyclogenesis and the life cycle of T. cruzi. Global levels of histone acetylation and methylation fluctuates along metacyclogenesis, however most critical differences were observed between parasite life forms. More than 66 histone PTM changes were detected. Strikingly, the histone PTM pattern of metacyclic trypomastigotes is more similar to epimastigotes than to cellular trypomastigotes. Finally, we highlighted changes at the H4 N-terminus and at H3K76 discussing their impact on the trypanosome biology. Altogether, we have optimized a workflow easily applicable to the analysis of histone PTMs in T. cruzi and generated a dataset that may shed lights on the role of chromatin modifications in this parasite. SIGNIFICANCE: Trypanosomes are unicellular parasites that have divergent histone sequences, no chromosome condensation and a peculiar genome/gene regulation. Genes are transcribed from divergent polycistronic regions and post-transcriptional gene regulation play major role on the establishment of transcripts and protein levels. In this regard, the fact that their histones are decorated with multiple PTMs raises interesting questions about their role. Besides, this digenetic organism must adapt to different environments changing its metabolism accordingly. As metabolism and epigenetics are closely related, the study of histone PTMs in trypanosomes may enlighten this strikingly, and not yet fully understood, interplay. From a biomedical perspective, the comprehensive study of molecular mechanisms associated to the metacyclogenesis process is essential to create better strategies for controlling Chagas disease.
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Affiliation(s)
- Loyze P de Lima
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil
| | - Saloe Bispo Poubel
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil; Instituto Carlos Chagas, FIOCRUZ, Rua Algacyr Munhoz Mader, 3775. CIC, Curitiba, PR 81350-010, Brazil
| | - Zuo-Fei Yuan
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Juliana Nunes Rosón
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil
| | - Francisca Nathalia de Luna Vitorino
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil
| | - Fabiola Barbieri Holetz
- Instituto Carlos Chagas, FIOCRUZ, Rua Algacyr Munhoz Mader, 3775. CIC, Curitiba, PR 81350-010, Brazil
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil; Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil.
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38
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Tupperwar N, Meleppattu S, Shrivastava R, Baron N, Gilad A, Wagner G, Léger-Abraham M, Shapira M. A newly identified Leishmania IF4E-interacting protein, Leish4E-IP2, modulates the activity of cap-binding protein paralogs. Nucleic Acids Res 2020; 48:4405-4417. [PMID: 32232353 PMCID: PMC7192595 DOI: 10.1093/nar/gkaa173] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/04/2020] [Accepted: 03/16/2020] [Indexed: 01/06/2023] Open
Abstract
Translation of most cellular mRNAs in eukaryotes proceeds through a cap-dependent pathway, whereby the cap-binding complex, eIF4F, anchors the preinitiation complex at the 5′ end of mRNAs and regulates translation initiation. The requirement of Leishmania to survive in changing environments can explain why they encode multiple eIF4E (LeishIF4Es) and eIF4G (LeishIF4Gs) paralogs, as each could be assigned a discrete role during their life cycle. Here we show that the expression and activity of different LeishIF4Es change during the growth of cultured promastigotes, urging a search for regulatory proteins. We describe a novel LeishIF4E-interacting protein, Leish4E-IP2, which contains a conserved Y(X)4LΦ IF4E-binding-motif. Despite its capacity to bind several LeishIF4Es, Leish4E-IP2 was not detected in m7GTP-eluted cap-binding complexes, suggesting that it could inhibit the cap-binding activity of LeishIF4Es. Using a functional assay, we show that a recombinant form of Leish4E-IP2 inhibits the cap-binding activity of LeishIF4E-1 and LeishIF4E-3. Furthermore, we show that transgenic parasites expressing a tagged version of Leish4E-IP2 also display reduced cap-binding activities of tested LeishIF4Es, and decreased global translation. Given its ability to bind more than a single LeishIF4E, we suggest that Leish4E-IP2 could serve as a broad-range repressor of Leishmania protein synthesis.
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Affiliation(s)
- Nitin Tupperwar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Shimi Meleppattu
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02138, USA
| | - Rohit Shrivastava
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Nofar Baron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Ayelet Gilad
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02138, USA
| | - Mélissa Léger-Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Michal Shapira
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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Barbosa RL, da Cunha JPC, Menezes AT, Melo RDFP, Elias MC, Silber AM, Coltri PP. Proteomic analysis of Trypanosoma cruzi spliceosome complex. J Proteomics 2020; 223:103822. [PMID: 32422275 DOI: 10.1016/j.jprot.2020.103822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 05/01/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022]
Abstract
The unicellular protists of the group Kinetoplastida include the genera Leishmania and Trypanosoma, which are pathogens of invertebrate and vertebrate animals. Despite their medical and economical importance, critical aspects of their biology such as specific molecular characteristics of gene expression regulation are just beginning to be deciphered. Gene expression regulation also depends on post-transcriptional processing steps, such as the trans-splicing process. Despite being widely used in trypanosomes, trans-splicing is a rare event in other eukaryotes. We sought to describe the protein composition of spliceosomes in epimastigotes of T. cruzi, the etiological agent of Chagas disease. We used two TAP-tagged proteins to affinity purify spliceosomes and analyzed their composition by mass spectrometry. Among the 115 identified proteins we detected conserved spliceosome components, as Sm and LSm proteins, RNA helicases, U2- and U5-snRNP specific proteins. Importantly, by comparing our data with proteomic data of human and T. brucei spliceosome complexes, we observed a core group of proteins common to all spliceosomes. By using amino acid sequence comparisons, we identified RNA-associated proteins that might be involved with splicing regulation in T. cruzi, namely the orthologous of WDR33, PABPCL1 and three different HNRNPs. Data are available via ProteomeXchange with identifier PXD018776.
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Affiliation(s)
- Rosicler L Barbosa
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Arthur T Menezes
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Raíssa de F P Melo
- Laboratory of Biochemistry of Tryps - LaBTryps. Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Maria Carolina Elias
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Butantan Institute, São Paulo 05503-900, Brazil
| | - Ariel M Silber
- Laboratory of Biochemistry of Tryps - LaBTryps. Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil
| | - Patricia P Coltri
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil.
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Van den Kerkhof M, Sterckx YGJ, Leprohon P, Maes L, Caljon G. Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites. Microorganisms 2020; 8:E950. [PMID: 32599761 PMCID: PMC7356981 DOI: 10.3390/microorganisms8060950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of treatment failure and drug resistance. Therefore, there is an urgency for the development of new drugs. Phenotypic screening already allowed the identification of promising new chemical entities with anti-kinetoplastid activity potential, but knowledge on their mode-of-action (MoA) is lacking due to the generally applied whole-cell based approach. However, identification of the drug target is essential to steer further drug discovery and development. Multiple complementary techniques have indeed been used for MoA elucidation. In this review, the different 'omics' approaches employed to define the MoA or mode-of-resistance of current reference drugs and some new anti-kinetoplastid compounds are discussed.
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Affiliation(s)
- Magali Van den Kerkhof
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB), University of Antwerp, 2610 Wilrijk, Belgium;
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du Centre Hospitalier Universitaire de Québec, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, 2610 Wilrijk, Belgium; (M.V.d.K.); (L.M.)
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41
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Parthasarathy A, Kalesh K. Defeating the trypanosomatid trio: proteomics of the protozoan parasites causing neglected tropical diseases. RSC Med Chem 2020; 11:625-645. [PMID: 33479664 PMCID: PMC7549140 DOI: 10.1039/d0md00122h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/12/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry-based proteomics enables accurate measurement of the modulations of proteins on a large scale upon perturbation and facilitates the understanding of the functional roles of proteins in biological systems. It is a particularly relevant methodology for studying Leishmania spp., Trypanosoma cruzi and Trypanosoma brucei, as the gene expression in these parasites is primarily regulated by posttranscriptional mechanisms. Large-scale proteomics studies have revealed a plethora of information regarding modulated proteins and their molecular interactions during various life processes of the protozoans, including stress adaptation, life cycle changes and interactions with the host. Important molecular processes within the parasite that regulate the activity and subcellular localisation of its proteins, including several co- and post-translational modifications, are also accurately captured by modern proteomics mass spectrometry techniques. Finally, in combination with synthetic chemistry, proteomic techniques facilitate unbiased profiling of targets and off-targets of pharmacologically active compounds in the parasites. This provides important data sets for their mechanism of action studies, thereby aiding drug development programmes.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology , Thomas H. Gosnell School of Life Sciences , 85 Lomb Memorial Dr , Rochester , NY 14623 , USA
| | - Karunakaran Kalesh
- Department of Chemistry , Durham University , Lower Mount Joy, South Road , Durham DH1 3LE , UK .
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Cruz-Saavedra L, Vallejo GA, Guhl F, Ramírez JD. Transcriptomic changes across the life cycle of Trypanosoma cruzi II. PeerJ 2020; 8:e8947. [PMID: 32461822 PMCID: PMC7231504 DOI: 10.7717/peerj.8947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Trypanosoma cruzi is a flagellated protozoan that causes Chagas disease; it presents a complex life cycle comprising four morphological stages: epimastigote (EP), metacyclic trypomastigote (MT), cell-derived trypomastigote (CDT) and amastigote (AM). Previous transcriptomic studies on three stages (EPs, CDTs and AMs) have demonstrated differences in gene expressions among them; however, to the best of our knowledge, no studies have reported on gene expressions in MTs. Therefore, the present study compared differentially expressed genes (DEGs), and signaling pathway reconstruction in EPs, MTs, AMs and CDTs. The results revealed differences in gene expressions in the stages evaluated; these differences were greater between MTs and AMs-PTs. The signaling pathway that presented the highest number of DEGs in all the stages was associated with ribosomes protein profiles, whereas the other related pathways activated were processes related to energy metabolism from glucose, amino acid metabolism, or RNA regulation. However, the role of autophagy in the entire life cycle of T. cruzi and the presence of processes such as meiosis and homologous recombination in MTs (where the expressions of SPO11 and Rad51 plays a role) are crucial. These findings represent an important step towards the full understanding of the molecular basis during the life cycle of T. cruzi.
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Affiliation(s)
- Lissa Cruz-Saavedra
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
| | - Gustavo A Vallejo
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Felipe Guhl
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Facultad de Ciencias, Universidad de Los Andes, Bogota, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogota, Colombia
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Bracamonte ME, Álvarez AM, Sosa AM, Hoyos CL, Lauthier JJ, Cajal SP, Juarez M, Uncos RE, Sánchez-Valdéz FJ, Acuña L, Diosque P, Basombrío MA, Nasser JR, Hashiguchi Y, Korenaga M, Barroso PA, Marco JD. High performance of an enzyme linked immunosorbent assay for American tegumentary leishmaniasis diagnosis with Leishmania (Viannia) braziliensis amastigotes membrane crude antigens. PLoS One 2020; 15:e0232829. [PMID: 32379842 PMCID: PMC7205302 DOI: 10.1371/journal.pone.0232829] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/22/2020] [Indexed: 11/26/2022] Open
Abstract
The diagnosis of American tegumentary leishmaniasis (ATL) still requires the design of more effective tools. Leishmania (Viannia) braziliensis is the causal agent of the 90% of Argentinean ATL cases. Considering the current knowledge, an ELISA based crude antigen (CA) for the diagnosis was designed. Ninety-nine subjects diagnosed as ATL, 27 as no-ATL, and 84 donors from non-ATL-endemic areas were included in this study. The current ATL diagnosis was based four techniques, dermal smear microscopic examination (parasitological test), PCR, Leishmanin skin test, and clinical records. We obtained CA extracts from promastigotes and amastigotes from macrophage cultures of different zymodemes of endemic Leishmania species circulating in the study area. Crude antigens from the ‘local’ main zymodeme of L. (V.) braziliensis showed the highest reactivity against anti-Leishmania antibodies compared to the other included species. The CA of amastigotes of this zymodeme was 3.4 fold more reactive than promastigotes one. Moreover, amastigote-membrane CA (MCA) were 3.6 fold more reactive than the soluble antigens. The MCA-ELISA reached a sensitivity and specificity of 98% (CI = 94.7%-100%) and 63.6% (53.9–73.1), respectively. When anti-Trypanosoma cruzi reactive sera were excluded, the specificity reached 98.4% (94.4–100), while the sensitivity was similar, with a positive predictive value (PV) of 98.6% (94.6–100) and negative PV of 96.3% (91.6–100). The performance of the MCA-ELISA results strongly contribute to the final diagnostic decision, since a non-reactive serological result almost discards the suspected ATL, because of its high negative PV. The developed MCA-ELISA showed a high diagnostic performance, which makes it a good candidate for ATL diagnosis, for seroprevalence studies, or for monitoring treatments efficacy.
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Affiliation(s)
- María E. Bracamonte
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Agustín Moya Álvarez
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Andrea M. Sosa
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Carlos L. Hoyos
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Juan J. Lauthier
- Department of Parasitology, Kochi Medical School, Kochi University, Nankoku, Kochi, Japan
| | - Silvana P. Cajal
- Instituto de Investigaciones en Enfermedades Tropicales (IIET), Sede Regional Orán, San Ramón de la Nueva Orán, Salta, Argentina
| | - Marisa Juarez
- Instituto de Investigaciones en Enfermedades Tropicales (IIET), Sede Regional Orán, San Ramón de la Nueva Orán, Salta, Argentina
| | - Renato E. Uncos
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Fernando J. Sánchez-Valdéz
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Leonardo Acuña
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Patricio Diosque
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Miguel A. Basombrío
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Julio R. Nasser
- Laboratorio de Química Biológica y Biología Molecular (LQByBM), Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Yoshihisa Hashiguchi
- Department of Parasitology, Kochi Medical School, Kochi University, Nankoku, Kochi, Japan
| | - Masataka Korenaga
- Department of Parasitology, Kochi Medical School, Kochi University, Nankoku, Kochi, Japan
- Faculty of Health Sciences, Kochi Gakuen University, Kochi, Kochi, Japan
| | - Paola A. Barroso
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
| | - Jorge D. Marco
- Facultad de Ciencias de la Salud, Instituto de Patología Experimental, Universidad Nacional de Salta / Consejo Nacional de Investigaciones Científicas y Técnicas, Salta, Argentina
- * E-mail:
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Regulation of Translation in the Protozoan Parasite Leishmania. Int J Mol Sci 2020; 21:ijms21082981. [PMID: 32340274 PMCID: PMC7215931 DOI: 10.3390/ijms21082981] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/31/2023] Open
Abstract
Leishmaniasis represents a serious health problem worldwide and drug resistance is a growing concern. Leishmania parasites use unusual mechanisms to control their gene expression. In contrast to many other species, they do not have transcriptional regulation. The lack of transcriptional control is mainly compensated by post-transcriptional mechanisms, including tight translational control and regulation of mRNA stability/translatability by RNA-binding proteins. Modulation of translation plays a major role in parasite survival and adaptation to dramatically different environments during change of host; however, our knowledge of fine molecular mechanisms of translation in Leishmania remains limited. Here, we review the current progress in our understanding of how changes in the translational machinery promote parasite differentiation during transmission from a sand fly to a mammalian host, and discuss how translational reprogramming can contribute to the development of drug resistance.
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Kieft R, Zhang Y, Marand AP, Moran JD, Bridger R, Wells L, Schmitz RJ, Sabatini R. Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. PLoS Genet 2020; 16:e1008390. [PMID: 32084124 PMCID: PMC7055916 DOI: 10.1371/journal.pgen.1008390] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/04/2020] [Accepted: 01/08/2020] [Indexed: 11/18/2022] Open
Abstract
Base J, β-D-glucosyl-hydroxymethyluracil, is a modification of thymine DNA base involved in RNA Polymerase (Pol) II transcription termination in kinetoplastid protozoa. Little is understood regarding how specific thymine residues are targeted for J-modification or the mechanism of J regulated transcription termination. To identify proteins involved in J-synthesis, we expressed a tagged version of the J-glucosyltransferase (JGT) in Leishmania tarentolae, and identified four co-purified proteins by mass spectrometry: protein phosphatase (PP1), a homolog of Wdr82, a potential PP1 regulatory protein (PNUTS) and a protein containing a J-DNA binding domain (named JBP3). Gel shift studies indicate JBP3 is a J-DNA binding protein. Reciprocal tagging, co-IP and sucrose gradient analyses indicate PP1, JGT, JBP3, Wdr82 and PNUTS form a multimeric complex in kinetoplastids, similar to the mammalian PTW/PP1 complex involved in transcription termination via PP1 mediated dephosphorylation of Pol II. Using RNAi and analysis of Pol II termination by RNA-seq and RT-PCR, we demonstrate that ablation of PNUTS, JBP3 and Wdr82 lead to defects in Pol II termination at the 3'-end of polycistronic gene arrays in Trypanosoma brucei. Mutants also contain increased antisense RNA levels upstream of transcription start sites, suggesting an additional role of the complex in regulating termination of bi-directional transcription. In addition, PNUTS loss causes derepression of silent Variant Surface Glycoprotein genes involved in host immune evasion. Our results suggest a novel mechanistic link between base J and Pol II polycistronic transcription termination in kinetoplastids.
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Affiliation(s)
- Rudo Kieft
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Yang Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Alexandre P. Marand
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Jose Dagoberto Moran
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Robert Bridger
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Yagoubat A, Crobu L, Berry L, Kuk N, Lefebvre M, Sarrazin A, Bastien P, Sterkers Y. Universal highly efficient conditional knockout system in
Leishmania
, with a focus on untranscribed region preservation. Cell Microbiol 2020; 22:e13159. [DOI: 10.1111/cmi.13159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Akila Yagoubat
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Lucien Crobu
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Laurence Berry
- Laboratory of Pathogen Host Interactions, Microscopie Electronique et Analytique, CNRSUniversity of Montpellier Montpellier France
| | - Nada Kuk
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Michèle Lefebvre
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Amélie Sarrazin
- Montpellier RIO Imaging Facility, Montpellier BIOCAMPUSUniversity of Montpellier, Arnaud de Villeneuve Campus Imaging Facility‐Institut de Génétique Humaine‐CNRS Montpellier France
| | - Patrick Bastien
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
| | - Yvon Sterkers
- MiVEGECUniversity of Montpellier, CNRS, IRD, CHU Montpellier France
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Bombaça ACS, Brunoro GVF, Dias-Lopes G, Ennes-Vidal V, Carvalho PC, Perales J, d'Avila-Levy CM, Valente RH, Menna-Barreto RFS. Glycolytic profile shift and antioxidant triggering in symbiont-free and H 2O 2-resistant Strigomonas culicis. Free Radic Biol Med 2020; 146:392-401. [PMID: 31760093 DOI: 10.1016/j.freeradbiomed.2019.11.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/16/2019] [Accepted: 11/18/2019] [Indexed: 02/07/2023]
Abstract
During their life cycle, trypanosomatids are exposed to stress conditions and adapt their energy and antioxidant metabolism to colonize their hosts. Strigomonas culicis is a monoxenous protist found in invertebrates with an endosymbiotic bacterium that completes essential biosynthetic pathways for the trypanosomatid. Our research group previously generated a wild-type H2O2-resistant (WTR) strain that showed improved mitochondrial metabolism and antioxidant defenses, which led to higher rates of Aedes aegypti infection. Here, we assess the biological contribution of the S. culicis endosymbiont and reactive oxygen species (ROS) resistance to oxidative and energy metabolism processes. Using high-throughput proteomics, several proteins involved in glycolysis and gluconeogenesis, the pentose phosphate pathway and glutathione metabolism were identified. The results suggest that ROS resistance decreases glucose consumption and indicate that the metabolic products from gluconeogenesis are key to supplying the protist with high-energy and reducing intermediates. Our hypothesis was confirmed by biochemical assays showing opposite profiles for glucose uptake and hexokinase and pyruvate kinase activity levels in the WTR and aposymbiotic strains, while the enzyme glucose-6P 1-dehydrogenase was more active in both strains. Regarding the antioxidant system, ascorbate peroxidase has an important role in H2O2 resistance and may be responsible for the high infection rates previously described for A. aegypti. In conclusion, our data indicate that the energy-related and antioxidant metabolic processes of S. culicis are modulated in response to oxidative stress conditions, providing new perspectives on the biology of the trypanosomatid-insect interaction as well as on the possible impact of resistant parasites in accidental human infection.
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Affiliation(s)
| | | | - Geovane Dias-Lopes
- Laboratory of Molecular Biology and Endemic Diseases, IOC, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Vitor Ennes-Vidal
- Laboratory of Integrated Studies in Protozoology, IOC, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Paulo Costa Carvalho
- Laboratory for Structural and Computational Proteomics, ICC, Oswaldo Cruz Foundation (FIOCRUZ), Curitiba, PR, Brazil
| | - Jonas Perales
- Laboratory of Toxinology, IOC, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Claudia Masini d'Avila-Levy
- Laboratory of Integrated Studies in Protozoology, IOC, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Richard Hemmi Valente
- Laboratory of Toxinology, IOC, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil
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Kalesh K, Denny PW. A BONCAT-iTRAQ method enables temporally resolved quantitative profiling of newly synthesised proteins in Leishmania mexicana parasites during starvation. PLoS Negl Trop Dis 2019; 13:e0007651. [PMID: 31856154 PMCID: PMC6939940 DOI: 10.1371/journal.pntd.0007651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/02/2020] [Accepted: 11/20/2019] [Indexed: 11/19/2022] Open
Abstract
Adaptation to starvation is integral to the Leishmania life cycle. The parasite can survive prolonged periods of nutrient deprivation both in vitro and in vivo. The identification of parasite proteins synthesised during starvation is key to unravelling the underlying molecular mechanisms facilitating adaptation to these conditions. Additionally, as stress adaptation mechanisms in Leishmania are linked to virulence as well as infectivity, profiling of the complete repertoire of Newly Synthesised Proteins (NSPs) under starvation is important for drug target discovery. However, differential identification and quantitation of low abundance, starvation-specific NSPs from the larger background of the pre-existing parasite proteome has proven difficult, as this demands a highly selective and sensitive methodology. Herein we introduce an integrated chemical proteomics method in L. mexicana promastigotes that involves a powerful combination of the BONCAT technique and iTRAQ quantitative proteomics Mass Spectrometry (MS), which enabled temporally resolved quantitative profiling of de novo protein synthesis in the starving parasite. Uniquely, this approach integrates the high specificity of the BONCAT technique for the NSPs, with the high sensitivity and multiplexed quantitation capability of the iTRAQ proteomics MS. Proof-of-concept experiments identified over 250 starvation-responsive NSPs in the parasite. Our results show a starvation-specific increased relative abundance of several translation regulating and stress-responsive proteins in the parasite. GO analysis of the identified NSPs for Biological Process revealed translation (enrichment P value 2.47e-35) and peptide biosynthetic process (enrichment P value 4.84e-35) as extremely significantly enriched terms indicating the high specificity of the NSP towards regulation of protein synthesis. We believe that this approach will find widespread use in the study of the developmental stages of Leishmania species and in the broader field of protozoan biology. Periodic nutrient scarcity plays crucial roles in the life cycle of the protozoan parasite Leishmania spp. Although adaptation to nutrient stress has a pivotal role in Leishmania biology, the underlying mechanisms remain poorly understood. In a period of nutrient starvation, the parasite responds by decreasing its protein production to conserve nutrient resources and to prevent formation of toxic proteins. However, even during severe starvation, the parasite generates certain essential quality control and rescue proteins. Differential identification of the complete repertoire of these proteins synthesised during starvation from the pre-existing proteins in the parasite holds the key to understanding the starvation adaptation mechanisms. This has been challenging to accomplish due to technical limitations. Using a combination of chemical labelling techniques and protein mass-spectrometry, we selectively identified and measured the proteins generated in the starving Leishmania parasite. Our results show a starvation time-dependent differential expression of important protein synthesis regulators in the parasite. This will serve as an important dataset for a holistic understanding of the starvation adaptation mechanisms in Leishmania. We also believe that this method will find widespread applications in the field of protozoa and other parasites causing Neglected Tropical Diseases.
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Affiliation(s)
- Karunakaran Kalesh
- Department of Chemistry, Durham University, Durham, United Kingdom
- * E-mail:
| | - Paul W. Denny
- Department of Biosciences, Durham University, Durham, United Kingdom
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Alonso VL, Tavernelli LE, Pezza A, Cribb P, Ritagliati C, Serra E. Aim for the Readers! Bromodomains As New Targets Against Chagas’ Disease. Curr Med Chem 2019; 26:6544-6563. [DOI: 10.2174/0929867325666181031132007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022]
Abstract
Bromodomains recognize and bind acetyl-lysine residues present in histone and non-histone
proteins in a specific manner. In the last decade they have raised as attractive targets for drug discovery
because the miss-regulation of human bromodomains was discovered to be involved in the development
of a large spectrum of diseases. However, targeting eukaryotic pathogens bromodomains
continues to be almost unexplored. We and others have reported the essentiality of diverse bromodomain-
containing proteins in protozoa, offering a new opportunity for the development of antiparasitic
drugs, especially for Trypansoma cruzi, the causative agent of Chagas’ disease. Mammalian bromodomains
were classified in eight groups based on sequence similarity but parasitic bromodomains are very
divergent proteins and are hard to assign them to any of these groups, suggesting that selective inhibitors
can be obtained. In this review, we describe the importance of lysine acetylation and bromodomains
in T. cruzi as well as the current knowledge on mammalian bromodomains. Also, we summarize
the myriad of small-molecules under study to treat different pathologies and which of them have been
tested in trypanosomatids and other protozoa. All the information available led us to propose that
T. cruzi bromodomains should be considered as important potential targets and the search for smallmolecules
to inhibit them should be empowered.
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Affiliation(s)
- Victoria Lucia Alonso
- Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Alejandro Pezza
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Pamela Cribb
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Carla Ritagliati
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Esteban Serra
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
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50
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de Oliveira TA, Silva WD, da Rocha Torres N, Badaró de Moraes JV, Senra RL, de Oliveira Mendes TA, Júnior AS, Bressan GC, Fietto JLR. Application of the LEXSY Leishmania tarentolae system as a recombinant protein expression platform: A review. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.08.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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