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Pal J, Sharma V, Khanna A, Saha S. The SET7 protein of Leishmania donovani moderates the parasite's response to a hostile oxidative environment. J Biol Chem 2024; 300:105720. [PMID: 38311179 PMCID: PMC10907163 DOI: 10.1016/j.jbc.2024.105720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
SET domain proteins methylate specific lysines on proteins, triggering stimulation or repression of downstream processes. Twenty-nine SET domain proteins have been identified in Leishmania donovani through sequence annotations. This study initiates the first investigation into these proteins. We find LdSET7 is predominantly cytosolic. Although not essential, set7 deletion slows down promastigote growth and hypersensitizes the parasite to hydroxyurea-induced G1/S arrest. Intriguingly, set7-nulls survive more proficiently than set7+/+ parasites within host macrophages, suggesting that LdSET7 moderates parasite response to the inhospitable intracellular environment. set7-null in vitro promastigote cultures are highly tolerant to hydrogen peroxide (H2O2)-induced stress, reflected in their growth pattern, and no detectable DNA damage at H2O2 concentrations tested. This is linked to reactive oxygen species levels remaining virtually unperturbed in set7-nulls in response to H2O2 exposure, contrasting to increased reactive oxygen species in set7+/+ cells under similar conditions. In analyzing the cell's ability to scavenge hydroperoxides, we find peroxidase activity is not upregulated in response to H2O2 exposure in set7-nulls. Rather, constitutive basal levels of peroxidase activity are significantly higher in these cells, implicating this to be a factor contributing to the parasite's high tolerance to H2O2. Higher levels of peroxidase activity in set7-nulls are coupled to upregulation of tryparedoxin peroxidase transcripts. Rescue experiments using an LdSET7 mutant suggest that LdSET7 methylation activity is critical to the modulation of the cell's response to oxidative environment. Thus, LdSET7 tunes the parasite's behavior within host cells, enabling the establishment and persistence of infection without eradicating the host cell population it needs for survival.
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Affiliation(s)
- Jyoti Pal
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Varshni Sharma
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Arushi Khanna
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Swati Saha
- Department of Microbiology, University of Delhi South Campus, New Delhi, India.
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2
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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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3
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Gupta D, Singh PK, Yadav PK, Narender T, Patil UK, Jain SK, Chourasia MK. Emerging strategies and challenges of molecular therapeutics in antileishmanial drug development. Int Immunopharmacol 2023; 115:109649. [PMID: 36603357 DOI: 10.1016/j.intimp.2022.109649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/16/2022] [Accepted: 12/24/2022] [Indexed: 01/05/2023]
Abstract
Molecular therapy refers to targeted therapies based on molecules which have been intelligently directed towards specific biomolecular structures and include small molecule drugs, monoclonal antibodies, proteins and peptides, DNA or RNA-based strategies, targeted chemotherapy and nanomedicines. Molecular therapy is emerging as the most effective strategy to combat the present challenges of life-threatening visceral leishmaniasis, where the successful human vaccine is currently unavailable. Moreover, current chemotherapy-based strategies are associated with the issues of ineffective targeting, unavoidable toxicities, invasive therapies, prolonged treatment, high treatment costs and the development of drug-resistant strains. Thus, the rational approach to antileishmanial drug development primarily demands critical exploration and exploitation of biochemical differences between host and parasite biology, immunocharacteristics of parasite homing, and host-parasite interactions at the molecular/cellular level. Following this, the novel technology-based designing and development of host and/or parasite-targeted therapeutics having leishmanicidal and immunomodulatory activity is utmost essential to improve treatment efficacy. Thus, the present review is focused on immunological and molecular checkpoint targets in host-pathogen interaction, and molecular therapeutic prospects for Leishmania intervention, and the challenges ahead.
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Affiliation(s)
- Deepak Gupta
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, M.P., India; Division of Pharmaceutics and Pharmacokinetics, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India
| | - Pankaj K Singh
- Division of Pharmaceutics and Pharmacokinetics, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India; Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, Telangana, India
| | - Pavan K Yadav
- Division of Pharmaceutics and Pharmacokinetics, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India
| | - Tadigoppula Narender
- Division of Medicinal and Process Chemistry, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India
| | - Umesh K Patil
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, M.P., India
| | - Sanjay K Jain
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar 470003, M.P., India
| | - Manish K Chourasia
- Division of Pharmaceutics and Pharmacokinetics, CSIR-Central Drug Research Institute, Lucknow 226031, U.P., India.
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4
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Bromodomain factor 5 is an essential regulator of transcription in Leishmania. Nat Commun 2022; 13:4071. [PMID: 35831302 PMCID: PMC9279504 DOI: 10.1038/s41467-022-31742-1] [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: 11/01/2021] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmania are unicellular parasites that cause human and animal diseases. Like other kinetoplastids, they possess large transcriptional start regions (TSRs) which are defined by histone variants and histone lysine acetylation. Cellular interpretation of these chromatin marks is not well understood. Eight bromodomain factors, the reader modules for acetyl-lysine, are found across Leishmania genomes. Using L. mexicana, Cas9-driven gene deletions indicate that BDF1–5 are essential for promastigotes. Dimerisable, split Cre recombinase (DiCre)-inducible gene deletion of BDF5 show it is essential for both promastigotes and murine infection. ChIP-seq identifies BDF5 as enriched at TSRs. XL-BioID proximity proteomics shows the BDF5 landscape is enriched for BDFs, HAT2, proteins involved in transcriptional activity, and RNA processing; revealing a Conserved Regulators of Kinetoplastid Transcription (CRKT) Complex. Inducible deletion of BDF5 causes global reduction in RNA polymerase II transcription. Our results indicate the requirement of Leishmania to interpret histone acetylation marks through the bromodomain-enriched CRKT complex for normal gene expression and cellular viability. Leishmania use large (5–10 kb) transcriptional start regions, where the chromatin is highly enriched for acetylated histones, to drive the expression of polycistronic gene arrays. Here the authors show bromodomain-containing protein BDF5 is enriched at transcriptional start sites and its depletion leads to cell death in vitro and in murine infections, and they identify its interactors.
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Tallant C, Bamborough P, Chung CW, Gamo FJ, Kirkpatrick R, Larminie C, Martín J, Prinjha R, Rioja I, Simola DF, Gabarró R, Calderón F. Expanding Bromodomain Targeting into Neglected Parasitic Diseases. ACS Infect Dis 2021; 7:2953-2958. [PMID: 34612618 DOI: 10.1021/acsinfecdis.1c00387] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This Perspective discusses the published data and recent developments in the research area of bromodomains in parasitic protozoa. Further work is needed to evaluate the tractability of this target class in the context of infectious diseases and launch drug discovery campaigns to identify and develop antiparasite drugs that can offer differentiated mechanisms of action.
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Affiliation(s)
- Cynthia Tallant
- Global Health R&D, GlaxoSmithKline, c/ Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Paul Bamborough
- Molecular Design, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Chun-wa Chung
- Protein, Cellular and Structural Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | | | - Robert Kirkpatrick
- GlaxoSmithKline R&D, 1250 S. Collegeville Rd., Collegeville, Pennsylvania 19426, United States
| | - Chris Larminie
- Human Genetics, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Julio Martín
- Global Health R&D, GlaxoSmithKline, c/ Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Rab Prinjha
- Immunology Research Unit, Research, R&D GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Inmaculada Rioja
- Immunology Research Unit, Research, R&D GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Daniel F. Simola
- Human Genetics and Computational Biology, GlaxoSmithKline, 1250 S. Collegeville Rd., Collegeville, Pennsylvania 19426, United States
| | - Raquel Gabarró
- Global Health R&D, GlaxoSmithKline, c/ Severo Ochoa 2, 28760 Tres Cantos, Spain
| | - Félix Calderón
- Global Health R&D, GlaxoSmithKline, c/ Severo Ochoa 2, 28760 Tres Cantos, Spain
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6
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Role of chromatin modulation in the establishment of protozoan parasite infection for developing targeted chemotherapeutics. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00356-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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7
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Histone Modifications and Other Facets of Epigenetic Regulation in Trypanosomatids: Leaving Their Mark. mBio 2020; 11:mBio.01079-20. [PMID: 32873754 PMCID: PMC7468196 DOI: 10.1128/mbio.01079-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Histone posttranslational modifications (PTMs) modulate several eukaryotic cellular processes, including transcription, replication, and repair. Vast arrays of modifications have been identified in conventional eukaryotes over the last 20 to 25 years. While initial studies uncovered these primarily on histone tails, multiple modifications were subsequently found on the central globular domains as well. Histones are evolutionarily conserved across eukaryotes, and a large number of their PTMs and the functional relevance of these PTMs are largely conserved. Histone posttranslational modifications (PTMs) modulate several eukaryotic cellular processes, including transcription, replication, and repair. Vast arrays of modifications have been identified in conventional eukaryotes over the last 20 to 25 years. While initial studies uncovered these primarily on histone tails, multiple modifications were subsequently found on the central globular domains as well. Histones are evolutionarily conserved across eukaryotes, and a large number of their PTMs and the functional relevance of these PTMs are largely conserved. Trypanosomatids, however, are early diverging eukaryotes. Although possessing all four canonical histones as well as several variants, their sequences diverge from those of other eukaryotes, particularly in the tails. Consequently, the modifications they carry also vary. Initial analyses almost 15 years ago suggested that trypanosomatids possessed a smaller collection of histone modifications. However, exhaustive high resolution mass spectrometry analyses in the last few years have overturned this belief, and it is now evident that the “histone code” proposed by Allis and coworkers in the early years of this century is as complex in these organisms as in other eukaryotes. Trypanosomatids cause several diseases, and the members of this group of organisms have varied lifestyles, evolving diverse mechanisms to evade the host immune system, some of which have been found to be principally controlled by epigenetic mechanisms. This minireview aims to acquaint the reader with the impact of histone PTMs on trypanosomatid cellular processes, as well as other facets of trypanosomatid epigenetic regulation, including the influence of three-dimensional (3D) genome architecture, and discusses avenues for future investigations.
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8
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Kumar A, Pandey SC, Samant M. DNA-based microarray studies in visceral leishmaniasis: identification of biomarkers for diagnostic, prognostic and drug target for treatment. Acta Trop 2020; 208:105512. [PMID: 32389452 DOI: 10.1016/j.actatropica.2020.105512] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/04/2020] [Accepted: 04/18/2020] [Indexed: 02/05/2023]
Abstract
Visceral leishmaniasis (VL) is one of the major infectious diseases affecting the poorest regions of the world. Current therapy is not very much satisfactory. The alarming rise of drug resistance and the unavailability of an effective vaccine against VL urges research towards identifying new targets or biomarkers for its effective treatment. New technology developments offer some fresh hope in its diagnosis, treatment, and control. DNA microarray approach is now broadly used in parasitology research to facilitate the thoughtful of mechanisms of disease and identification of drug targets and biomarkers for diagnostic and therapeutic development. An electronic search on "VL" and "Microarray" was conducted in Medline and Scopus and papers published in the English mentioning use of DNA microarray on VL were selected and read to write this paper review. Functional analysis and interpretation of microarray results remain very challenging due to the inherent nature of experimental workflows, access, cost, and complexity of data obtained. We have explained and emphasized the use of curate knowledge of microarray in the case of VL for the identification of therapeutic target and biomarker and their selection/implementation in clinical use.
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Affiliation(s)
- Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur (Chhattisgarh), INDIA
| | - Satish Chandra Pandey
- Cell and Molecular biology laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora (Uttarakhand), INDIA; Department of Biotechnology, Kumaun University Nainital, Bhimtal Campus, Bhimtal, Nainital (Uttarakhand), INDIA
| | - Mukesh Samant
- Cell and Molecular biology laboratory, Department of Zoology, Kumaun University, SSJ Campus, Almora (Uttarakhand), INDIA.
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9
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DNA replication protein Cdc45 directly interacts with PCNA via its PIP box in Leishmania donovani and the Cdc45 PIP box is essential for cell survival. PLoS Pathog 2020; 16:e1008190. [PMID: 32413071 PMCID: PMC7255605 DOI: 10.1371/journal.ppat.1008190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
DNA replication protein Cdc45 is an integral part of the eukaryotic replicative helicase whose other components are the Mcm2-7 core, and GINS. We identified a PIP box motif in Leishmania donovani Cdc45. This motif is typically linked to interaction with the eukaryotic clamp proliferating cell nuclear antigen (PCNA). The homotrimeric PCNA can potentially bind upto three different proteins simultaneously via a loop region present in each monomer. Multiple binding partners have been identified from among the replication machinery in other eukaryotes, and the concerted /sequential binding of these partners are central to the fidelity of the replication process. Though conserved in Cdc45 across Leishmania species and Trypanosoma cruzi, the PIP box is absent in Trypanosoma brucei Cdc45. Here we investigate the possibility of Cdc45-PCNA interaction and the role of such an interaction in the in vivo context. Having confirmed the importance of Cdc45 in Leishmania DNA replication we establish that Cdc45 and PCNA interact stably in whole cell extracts, also interacting with each other directly in vitro. The interaction is mediated via the Cdc45 PIP box. This PIP box is essential for Leishmania survival. The importance of the Cdc45 PIP box is also examined in Schizosaccharomyces pombe, and it is found to be essential for cell survival here as well. Our results implicate a role for the Leishmania Cdc45 PIP box in recruiting or stabilizing PCNA on chromatin. The Cdc45-PCNA interaction might help tether PCNA and associated replicative DNA polymerase to the DNA template, thus facilitating replication fork elongation. Though multiple replication proteins that associate with PCNA have been identified in other eukaryotes, this is the first report demonstrating a direct interaction between Cdc45 and PCNA, and while our analysis suggests the interaction may not occur in human cells, it indicates that it may not be confined to trypanosomatids.
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10
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Manzano-Román R, Fuentes M. Relevance and proteomics challenge of functional posttranslational modifications in Kinetoplastid parasites. J Proteomics 2020; 220:103762. [PMID: 32244008 DOI: 10.1016/j.jprot.2020.103762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/06/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
Abstract
Protozoan parasitic infections are health, social and economic issues impacting both humans and animals, with significant morbidity and mortality worldwide. Protozoan parasites have complicated life cycles with both intracellular and extracellular forms. As a consequence, protozoan adapt to changing environments in part through a dynamic enzyme-catalyzed process leading to reversible posttranslational modifications (PTMs). The characterization by proteomics approaches reveals the critical role of the PTMs of the proteins involved in host-pathogen interaction. The complexity of PTMs characterization is increased by the high diversity, stoichiometry, dynamic and also co-existence of several PTMs in the same moieties which crosstalk between them. Here, we review how to understand the complexity and the essential role of PTMs crosstalk in order to provide a new hallmark for vaccines developments, immunotherapies and personalized medicine. In addition, the importance of these motifs in the biology and biological cycle of kinetoplastid parasites is highlighted with key examples showing the potential to act as targets against protozoan diseases.
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Affiliation(s)
- R Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain..
| | - M Fuentes
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain.; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain
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11
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Afrin F, Khan I, Hemeg HA. Leishmania-Host Interactions-An Epigenetic Paradigm. Front Immunol 2019; 10:492. [PMID: 30967861 PMCID: PMC6438953 DOI: 10.3389/fimmu.2019.00492] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/25/2019] [Indexed: 12/17/2022] Open
Abstract
Leishmaniasis is one of the major neglected tropical diseases, for which no vaccines exist. Chemotherapy is hampered by limited efficacy coupled with development of resistance and other side effects. Leishmania parasites elude the host defensive mechanisms by modulating their surface proteins as well as dampening the host's immune responses. The parasites use the conventional RNA polymerases peculiarly under different environmental cues or pressures such as the host's milieu or the drugs. The mechanisms that restructure post-translational modifications are poorly understood but altered epigenetic histone modifications are believed to be instrumental in influencing the chromatin remodeling in the parasite. Interestingly, the parasite also modulates gene expression of the hosts, thereby hijacking or dampening the host immune response. Epigenetic factor such as DNA methylation of cytosine residues has been incriminated in silencing of macrophage-specific genes responsible for defense against these parasites. Although there is dearth of information regarding the epigenetic alterations-mediated pathogenesis in these parasites and the host, the unique epigenetic marks may represent targets for potential anti-leishmanial drug candidates. This review circumscribes the epigenetic changes during Leishmania infection, and the epigenetic modifications they enforce upon the host cells to ensure a safe haven. The non-coding micro RNAs as post-transcriptional regulators and correlates of wound healing and toll-like receptor signaling, as well as prognostic biomarkers of therapeutic failure and healing time are also explored. Finally, we highlight the recent advances on how the epigenetic perturbations may impact leishmaniasis vaccine development as biomarkers of safety and immunogenicity.
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Affiliation(s)
- Farhat Afrin
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Taibah University, Madina, Saudi Arabia
| | - Inbesat Khan
- Rajiv Gandhi Technical University, Bhopal, India
| | - Hassan A Hemeg
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Taibah University, Madina, Saudi Arabia
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12
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Sinha R, C MM, Raghwan, Das S, Das S, Shadab M, Chowdhury R, Tripathy S, Ali N. Genome Plasticity in Cultured Leishmania donovani: Comparison of Early and Late Passages. Front Microbiol 2018; 9:1279. [PMID: 30018594 PMCID: PMC6037818 DOI: 10.3389/fmicb.2018.01279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/25/2018] [Indexed: 11/13/2022] Open
Abstract
Leishmania donovani possesses a complex heteroxenic life cycle where infective metacyclic promastigotes are pre-adapted to infect their host and cope up with intracellular stress. Exploiting the similarities between cultured and sandfly derived promastigotes, we used early and late passage cultured promastigotes to show specific changes at genome level which compromise pathogen fitness reflected in gene expression and infection studies. The pathogen loses virulence mostly via transcriptional and translational regulations and long-time cultivation makes them struggle to convert to virulent metacyclics. At the genomic level very subtle plasticity was observed between the early and the late passages mostly in defense-related, nutrient acquisition and signal transduction genes. Chromosome Copy number variation is seen in the early and late passages involving several genes that may be playing a role in pathogenicity. Our study highlights the importance of ABC transporters and calpain like cysteine proteases in parasite virulence in cultured promastigotes. Interestingly, these proteins are emerging as important patho-adaptive factors in clinical isolates of Leishmania. We found that the currently available genome of Leishmania in the NCBI database are from late passages. Our early passage genome can act as a reference for future studies on virulent isolates of Leishmania. The annotated leads from this study can be used for virulence surveillance and therapeutic studies in the Indian subcontinent.
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Affiliation(s)
- Roma Sinha
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Mathu Malar C
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Raghwan
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhadeep Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Sonali Das
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Mohammad Shadab
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Rukhsana Chowdhury
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Nahid Ali
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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13
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Nayak A, Akpunarlieva S, Barrett M, Burchmore R. A defined medium for Leishmania culture allows definition of essential amino acids. Exp Parasitol 2018; 185:39-52. [PMID: 29326050 DOI: 10.1016/j.exppara.2018.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/18/2017] [Accepted: 01/05/2018] [Indexed: 10/18/2022]
Abstract
Axenic culture of Leishmania is generally performed in rich, serum-supplemented media which sustain robust growth over multiple passages. The use of such undefined media, however, obscures proteomic analyses and confounds the study of metabolism. We have established a simple, defined culture medium that supports the sustained growth of promastigotes over multiple passages and which yields parasites that have similar infectivity to macrophages to parasites grown in a conventional semi-defined medium. We have exploited this medium to investigate the amino acid requirements of promastigotes in culture and have found that phenylalanine, tryptophan, arginine, leucine, lysine and valine are essential for viability in culture. Most of the 20 proteogenic amino acids promote growth of Leishmania promastigotes, with the exception of alanine, asparagine, and glycine. This defined medium will be useful for further studies of promastigote substrate requirements, and will facilitate future proteomic and metabolomic analyses.
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Affiliation(s)
- Archana Nayak
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Snezhana Akpunarlieva
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Michael Barrett
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Richard Burchmore
- Institute of Infection, Immunity and Inflammation and Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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14
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Chandra U, Yadav A, Kumar D, Saha S. Cell cycle stage-specific transcriptional activation of cyclins mediated by HAT2-dependent H4K10 acetylation of promoters in Leishmania donovani. PLoS Pathog 2017; 13:e1006615. [PMID: 28938001 PMCID: PMC5627965 DOI: 10.1371/journal.ppat.1006615] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 10/04/2017] [Accepted: 08/29/2017] [Indexed: 11/18/2022] Open
Abstract
Chromatin modifications affect several processes. In investigating the Leishmania donovani histone acetyltransferase HAT2, using in vitro biochemical assays and HAT2-heterozygous genomic knockout we found the constitutively nuclear HAT2 acetylated histone H4K10 in vitro and in vivo. HAT2 was essential. HAT2-depleted cells displayed growth and cell cycle defects, and poor survival in host cells. Real time PCR and DNA microarray analyses, as well as rescue experiments, revealed that downregulation of cyclins CYC4 and CYC9 were responsible for S phase and G2/M defects of HAT2-depleted cells respectively. Leishmania genes are arranged in unidirectional clusters, and clustered genes are coordinately transcribed as long polycistronic units, typically from divergent strand switch regions (dSSRs) which initiate transcription bidirectionally on opposite strands. In investigating the mechanism by which CYC4 and CYC9 expression levels are reduced in HAT2-depleted cells without other genes in their polycistronic transcription units being coordinately downregulated, we found using reporter assays that CYC4 and CYC9 have their own specific promoters. Chromatin immunoprecipitation assays with H4acetylK10 antibodies and real time PCR analyses of RNA suggested these gene-specific promoters were activated in cell cycle-dependent manner. Nuclear run-on analyses confirmed that CYC4 and CYC9 were transcriptionally activated from their own promoters at specific cell cycle stages. Thus, there are two tiers of gene regulation. Transcription of polycistronic units primarily initiates at dSSRs, and this most likely occurs constitutively. A subset of genes have their own promoters, at least some of which are activated in a cell-cycle dependent manner. This second tier of regulation is more sensitive to H4K10 acetylation levels, resulting in downregulation of expression in HAT2-depleted cells. This report presents the first data pointing to cell cycle-specific activation of promoters in trypanosomatids, thus uncovering new facets of gene regulation in this parasite family.
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Affiliation(s)
- Udita Chandra
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Aarti Yadav
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Devanand Kumar
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Swati Saha
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
- * E-mail:
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