1
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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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2
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Shikha K, Sriram Bharath G, Mukhopadhyay S, Chakraborty M, Ghosh S, Khatun S, De D, Gupta AN, Ganguly A. The catalytic core of Leishmania donovani RECQ helicase unwinds a wide spectrum of DNA substrates and is stimulated by replication protein A. FEBS J 2021; 289:394-416. [PMID: 34355508 DOI: 10.1111/febs.16153] [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: 11/26/2020] [Revised: 07/11/2021] [Accepted: 08/04/2021] [Indexed: 11/29/2022]
Abstract
RecQ helicases are superfamily 2 (SF2) DNA helicases that unwind a wide spectrum of complex DNA structures in a 3' to 5' direction and are involved in maintaining genome stability. RecQ helicases from protozoan parasites have gained significant interest in recent times because of their involvement in cellular DNA repair pathways, making them important targets for drug development. In this study, we report biophysical and biochemical characterization of the catalytic core of a RecQ helicase from hemoflagellate protozoan parasite Leishmania donovani. Among the two putative RecQ helicases identified in L. donovani, we cloned, overexpressed and purified the catalytic core of LdRECQb. The catalytic core was found to be very efficient in unwinding a wide variety of DNA substrates like forked duplex, 3' tailed duplex and Holliday junction DNA. Interestingly, the helicase core also unwound blunt duplex with slightly less efficiency. The enzyme exhibited high level of DNA-stimulated ATPase activity with preferential stimulation by forked duplex, Holliday junction and 3' tailed duplex. Walker A motif lysine mutation severely affected the ATPase activity and significantly affected unwinding activity. Like many other RecQ helicases, L. donovani RECQb also possesses strand annealing activity. Unwinding of longer DNA substrates by LdRECQb catalytic core was found to be stimulated in the presence of replication protein A (LdRPA-1) from L. donovani. Detailed biochemical characterization and comparison of kinetic parameters indicate that L. donovani RECQb shares considerable functional similarity with human Bloom syndrome helicase.
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Affiliation(s)
- Kumari Shikha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India.,School of Bioscience, Indian Institute of Technology Kharagpur, India
| | | | | | - Mayukh Chakraborty
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Susmita Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
| | - Suparna Khatun
- Department of Physics, Indian Institute of Technology Kharagpur, India
| | - Debajyoti De
- Department of Physics, Indian Institute of Technology Kharagpur, India
| | - Amar Nath Gupta
- Department of Physics, Indian Institute of Technology Kharagpur, India
| | - Agneyo Ganguly
- Department of Biotechnology, Indian Institute of Technology Kharagpur, India
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3
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Black JA, Crouch K, Lemgruber L, Lapsley C, Dickens N, Tosi LRO, Mottram JC, McCulloch R. Trypanosoma brucei ATR Links DNA Damage Signaling during Antigenic Variation with Regulation of RNA Polymerase I-Transcribed Surface Antigens. Cell Rep 2021; 30:836-851.e5. [PMID: 31968257 PMCID: PMC6988115 DOI: 10.1016/j.celrep.2019.12.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 08/19/2019] [Accepted: 12/13/2019] [Indexed: 11/29/2022] Open
Abstract
Trypanosoma brucei evades mammalian immunity by using recombination to switch its surface-expressed variant surface glycoprotein (VSG), while ensuring that only one of many subtelomeric multigene VSG expression sites are transcribed at a time. DNA repair activities have been implicated in the catalysis of VSG switching by recombination, not transcriptional control. How VSG switching is signaled to guide the appropriate reaction or to integrate switching into parasite growth is unknown. Here, we show that the loss of ATR, a DNA damage-signaling protein kinase, is lethal, causing nuclear genome instability and increased VSG switching through VSG-localized damage. Furthermore, ATR loss leads to the increased transcription of silent VSG expression sites and expression of mixed VSGs on the cell surface, effects that are associated with the altered localization of RNA polymerase I and VEX1. This work shows that ATR acts in antigenic variation both through DNA damage signaling and surface antigen expression control. Loss of the repair protein kinase ATR in Trypanosoma brucei is lethal Loss of T. brucei ATR alters VSG coat expression needed for immune evasion Monoallelic RNA polymerase I VSG expression is undermined by ATR loss ATR loss leads to expression of subtelomeric VSGs, indicative of recombination
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Affiliation(s)
- Jennifer Ann Black
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK; Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900 SP, Brazil
| | - Kathryn Crouch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK
| | - Leandro Lemgruber
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK
| | - Craig Lapsley
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK
| | - Nicholas Dickens
- Marine Science Lab, FAU Harbor Branch Oceanographic Institute, 5600 US 1 North, Fort Pierce, FL 34946, USA
| | - Luiz R O Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900 SP, Brazil
| | - Jeremy C Mottram
- Centre for Immunology and Infection, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity, and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow G12 8TA, UK.
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4
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Pavani RS, Elias MC. Following Trypanosoma cruzi RPA-DNA Interaction Using Fluorescent In Situ Hybridization Coupled with Immunofluorescence (FISH/IF). Methods Mol Biol 2021; 2281:209-215. [PMID: 33847960 DOI: 10.1007/978-1-0716-1290-3_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorescent in situ hybridization coupled with immunofluorescence (FISH/IF) is an assay that has been widely used to study DNA-protein interactions. The technique is based on the use of a fluorescent nucleic acid probe and fluorescent antibodies to reveal the localization of a DNA sequence and a specific protein in the cell. The interaction can be inferred by the quantification of the co-localization between the protein and the DNA. Here, we describe a detailed FISH/IF methodology that our group used to study RPA-telomere interaction in the pathogenic protozoa parasite Trypanosoma cruzi.
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Affiliation(s)
- Raphael S Pavani
- Laboratório de Ciclo Celular and Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil
| | - Maria Carolina Elias
- Laboratório de Ciclo Celular and Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil.
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5
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Damasceno JD, Marques CA, Black J, Briggs E, McCulloch R. Read, Write, Adapt: Challenges and Opportunities during Kinetoplastid Genome Replication. Trends Genet 2020; 37:21-34. [PMID: 32993968 PMCID: PMC9213392 DOI: 10.1016/j.tig.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022]
Abstract
The genomes of all organisms are read throughout their growth and development, generating new copies during cell division and encoding the cellular activities dictated by the genome’s content. However, genomes are not invariant information stores but are purposefully altered in minor and major ways, adapting cellular behaviour and driving evolution. Kinetoplastids are eukaryotic microbes that display a wide range of such read–write genome activities, in many cases affecting critical aspects of their biology, such as host adaptation. Here we discuss the range of read–write genome changes found in two well-studied kinetoplastid parasites, Trypanosoma brucei and Leishmania, focusing on recent work that suggests such adaptive genome variation is linked to novel strategies the parasites use to replicate their unconventional genomes. Polycistronic transcription dominates and shapes kinetoplastid genomes, inevitably leading to clashes with DNA replication. By harnessing the resultant DNA damage for adaptation, kinetoplastids have huge potential for dynamic read–write genome variation. Major origins of DNA replication are confined to the boundaries of polycistronic transcription units in the Trypanosoma brucei and Leishmania genomes, putatively limiting DNA damage. Subtelomeres may lack this arrangement, generating read–write hotspots. In T. brucei, early replication of the highly transcribed subtelomeric variant surface glycoprotein (VSG) expression site may ensure replication-transcription clashes within this site to trigger DNA recombination, an event critical for antigenic variation. Leishmania genomes show extensive aneuploidy and copy number variation. Notably, DNA replication requires recombination factors and relies on post-S phase replication of subtelomeres. Evolution of compartmentalised DNA replication programmes underpin important aspects of genome biology in kinetoplastids, illustrating the consolidation of genome maintenance strategies to promote genome plasticity.
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Affiliation(s)
- Jeziel D Damasceno
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK.
| | - Catarina A Marques
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Jennifer Black
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Emma Briggs
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK; Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, UK.
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6
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Damasceno JD, Marques CA, Beraldi D, Crouch K, Lapsley C, Obonaga R, Tosi LR, McCulloch R. Genome duplication in Leishmania major relies on persistent subtelomeric DNA replication. eLife 2020; 9:58030. [PMID: 32897188 PMCID: PMC7511235 DOI: 10.7554/elife.58030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022] Open
Abstract
DNA replication is needed to duplicate a cell’s genome in S phase and segregate it during cell division. Previous work in Leishmania detected DNA replication initiation at just a single region in each chromosome, an organisation predicted to be insufficient for complete genome duplication within S phase. Here, we show that acetylated histone H3 (AcH3), base J and a kinetochore factor co-localise in each chromosome at only a single locus, which corresponds with previously mapped DNA replication initiation regions and is demarcated by localised G/T skew and G4 patterns. In addition, we describe previously undetected subtelomeric DNA replication in G2/M and G1-phase-enriched cells. Finally, we show that subtelomeric DNA replication, unlike chromosome-internal DNA replication, is sensitive to hydroxyurea and dependent on 9-1-1 activity. These findings indicate that Leishmania’s genome duplication programme employs subtelomeric DNA replication initiation, possibly extending beyond S phase, to support predominantly chromosome-internal DNA replication initiation within S phase.
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Affiliation(s)
- Jeziel Dener Damasceno
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Catarina A Marques
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Dario Beraldi
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Kathryn Crouch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Craig Lapsley
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
| | - Ricardo Obonaga
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz Ro Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, University of Glasgow, Institute of Infection, Immunity and Inflammation, Glasgow, United Kingdom
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7
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Damasceno JD, Obonaga R, Silva GLA, Reis-Cunha JL, Duncan SM, Bartholomeu DC, Mottram JC, McCulloch R, Tosi LRO. Conditional genome engineering reveals canonical and divergent roles for the Hus1 component of the 9-1-1 complex in the maintenance of the plastic genome of Leishmania. Nucleic Acids Res 2019; 46:11835-11846. [PMID: 30380080 PMCID: PMC6294564 DOI: 10.1093/nar/gky1017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/11/2018] [Indexed: 12/16/2022] Open
Abstract
Leishmania species are protozoan parasites whose remarkably plastic genome limits the establishment of effective genetic manipulation and leishmaniasis treatment. The strategies used by Leishmania to maintain its genome while allowing variability are not fully understood. Here, we used DiCre-mediated conditional gene deletion to show that HUS1, a component of the 9-1-1 (RAD9-RAD1-HUS1) complex, is essential and is required for a G2/M checkpoint. By analyzing genome-wide instability in HUS1 ablated cells, HUS1 is shown to have a conserved role, by which it preserves genome stability and also a divergent role, by which it promotes genome variability. These roles of HUS1 are related to distinct patterns of formation and resolution of single-stranded DNA and γH2A, throughout the cell cycle. Our findings suggest that Leishmania 9-1-1 subunits have evolved to co-opt canonical genomic maintenance and genomic variation functions. Hence, this study reveals a pivotal function of HUS1 in balancing genome stability and transmission in Leishmania. These findings may be relevant to understanding the evolution of genome maintenance and plasticity in other pathogens and eukaryotes.
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Affiliation(s)
- Jeziel D Damasceno
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - Ricardo Obonaga
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - Gabriel L A Silva
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - João L Reis-Cunha
- Laboratório de Genômica de Parasitos, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brasil
| | - Samuel M Duncan
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Daniella C Bartholomeu
- Laboratório de Genômica de Parasitos, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brasil
| | - Jeremy C Mottram
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK.,Centre for Immunology and Infection, Department of Biology, University of York, York YO10 5DD, UK
| | - Richard McCulloch
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Luiz R O Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
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8
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Pavani RS, Vitarelli MO, Fernandes CAH, Mattioli FF, Morone M, Menezes MC, Fontes MRM, Cano MIN, Elias MC. Replication Protein A-1 Has a Preference for the Telomeric G-rich Sequence in Trypanosoma cruzi. J Eukaryot Microbiol 2017; 65:345-356. [PMID: 29044824 DOI: 10.1111/jeu.12478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 01/20/2023]
Abstract
Replication protein A (RPA), the major eukaryotic single-stranded binding protein, is a heterotrimeric complex formed by RPA-1, RPA-2, and RPA-3. RPA is a fundamental player in replication, repair, recombination, and checkpoint signaling. In addition, increasing evidences have been adding functions to RPA in telomere maintenance, such as interaction with telomerase to facilitate its activity and also involvement in telomere capping in some conditions. Trypanosoma cruzi, the etiological agent of Chagas disease is a protozoa parasite that appears early in the evolution of eukaryotes. Recently, we have showed that T. cruziRPA presents canonical functions being involved with DNA replication and DNA damage response. Here, we found by FISH/IF assays that T. cruziRPA localizes at telomeres even outside replication (S) phase. In vitro analysis showed that one telomeric repeat is sufficient to bind RPA-1. Telomeric DNA induces different secondary structural modifications on RPA-1 in comparison with other types of DNA. In addition, RPA-1 presents a higher affinity for telomeric sequence compared to randomic sequence, suggesting that RPA may play specific roles in T. cruzi telomeric region.
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Affiliation(s)
- Raphael Souza Pavani
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Marcela O Vitarelli
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Carlos A H Fernandes
- Biophysics and Physics Department, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, 18618970, Brazil
| | - Fabio F Mattioli
- Biophysics and Physics Department, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, 18618970, Brazil
| | - Mariana Morone
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Milene C Menezes
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, SP, 05503-900, Brazil
| | - Marcos R M Fontes
- Biophysics and Physics Department, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, 18618970, Brazil
| | - Maria Isabel N Cano
- Genetics Department, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, 18618970, Brazil
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, 05503-900, Brazil.,Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, 05503-900, Brazil
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9
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Kipandula W, Smith TK, MacNeill SA. Tandem affinity purification of exosome and replication factor C complexes from the non-human infectious kinetoplastid parasite Crithidia fasciculata. Mol Biochem Parasitol 2017; 217:19-22. [PMID: 28844893 DOI: 10.1016/j.molbiopara.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/17/2022]
Abstract
Kinetoplastid parasites are responsible for a range of diseases with significant global impact. Trypanosoma brucei and Trypanosoma cruzi cause human African trypanosomiasis and Chagas disease, respectively, while various Leishmania species are responsible for cutaneous, mucocutaneous and visceral leishmaniasis. Understanding the biology of these organisms is key for effective diagnosis, prophylaxis and treatment. The insect parasite Crithidia fasciculata offers a safe and low-cost alternative for studies of kinetoplastid biology. C. fasciculata does not infect humans, can be cultured to high yields in inexpensive serum-free medium in a standard laboratory, and has a completely sequenced publically available genome. Taking advantage of these features, however, requires the adaptation of existing methods of analysis to C. fasciculata. Tandem affinity purification is a widely used method that allows for the rapid purification of intact protein complexes under native conditions. Here we report the application of tandem affinity purification to C. fasciculata for the first time, demonstrating the effectiveness of the technique by purifying both the intact exosome and replication factor C complexes. Adding tandem affinity purification to the C. fasciculata toolbox significantly enhances the utility of this excellent model system.
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Affiliation(s)
- Wakisa Kipandula
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK; Department of Biomedical Sciences, College of Medicine, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Terry K Smith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Stuart A MacNeill
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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10
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Nuclear DNA Replication in Trypanosomatids: There Are No Easy Methods for Solving Difficult Problems. Trends Parasitol 2017; 33:858-874. [PMID: 28844718 PMCID: PMC5662062 DOI: 10.1016/j.pt.2017.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 01/09/2023]
Abstract
In trypanosomatids, etiological agents of devastating diseases, replication is robust and finely controlled to maintain genome stability and function in stressful environments. However, these parasites encode several replication protein components and complexes that show potentially variant composition compared with model eukaryotes. This review focuses on the advances made in recent years regarding the differences and peculiarities of the replication machinery in trypanosomatids, including how such divergence might affect DNA replication dynamics and the replication stress response. Comparing the DNA replication machinery and processes of parasites and their hosts may provide a foundation for the identification of targets that can be used in the development of chemotherapies to assist in the eradication of diseases caused by these pathogens. In trypanosomatids, DNA replication is tightly controlled by protein complexes that diverge from those of model eukaryotes. There is no consensus for the number of replication origins used by trypanosomatids; how their replication dynamics compares with that of model organisms is the subject of debate. The DNA replication rate in trypanosomatids is similar to, but slightly higher than, that of model eukaryotes, which may be related to chromatin structure and function. Recent data suggest that the origin recognition complex in trypanosomatids closely resembles the multisubunit eukaryotic model. The absence of fundamental replication-associated proteins in trypanosomatids suggests that new signaling pathways may be present in these parasites to direct DNA replication and the replicative stress response.
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11
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Santos RERS, Silva GLA, Santos EV, Duncan SM, Mottram JC, Damasceno JD, Tosi LRO. A DiCre recombinase-based system for inducible expression in Leishmania major. Mol Biochem Parasitol 2017. [PMID: 28629935 DOI: 10.1016/j.molbiopara.2017.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Here we present the establishment of an inducible system based on the dimerizable Cre recombinase (DiCre) for controlled gene expression in the protozoan parasite Leishmania. Rapamycin-induced DiCre activation promoted efficient flipping and expression of gene products in a time and dose-dependent manner. The DiCre flipping activity induced the expression of target genes from both integrated and episomal contexts broadening the applicability of the system. We validated the system by inducing the expression of both full length and truncated forms of the checkpoint protein Rad9, which revealed that the highly divergent C-terminal domain of Rad9 is necessary for proper subcellular localization. Thus, by establishing the DiCre-based inducible system we have created and validated a robust new tool for assessing gene function in Leishmania.
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Affiliation(s)
- Renato E R S Santos
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo; Ribeirão Preto, SP, Brazil
| | - Gabriel L A Silva
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo; Ribeirão Preto, SP, Brazil
| | - Elaine V Santos
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo; Ribeirão Preto, SP, Brazil
| | - Samuel M Duncan
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom
| | - Jeremy C Mottram
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom; Centre for Immunology and Infection, Department of Biology, University of York, York, United Kingdom
| | - Jeziel D Damasceno
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo; Ribeirão Preto, SP, Brazil.
| | - Luiz R O Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo; Ribeirão Preto, SP, Brazil.
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Pavani RS, da Silva MS, Fernandes CAH, Morini FS, Araujo CB, Fontes MRDM, Sant’Anna OA, Machado CR, Cano MI, Fragoso SP, Elias MC. Replication Protein A Presents Canonical Functions and Is Also Involved in the Differentiation Capacity of Trypanosoma cruzi. PLoS Negl Trop Dis 2016; 10:e0005181. [PMID: 27984589 PMCID: PMC5161316 DOI: 10.1371/journal.pntd.0005181] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/10/2016] [Indexed: 02/03/2023] Open
Abstract
Replication Protein A (RPA), the major single stranded DNA binding protein in eukaryotes, is composed of three subunits and is a fundamental player in DNA metabolism, participating in replication, transcription, repair, and the DNA damage response. In human pathogenic trypanosomatids, only limited studies have been performed on RPA-1 from Leishmania. Here, we performed in silico, in vitro and in vivo analysis of Trypanosoma cruzi RPA-1 and RPA-2 subunits. Although computational analysis suggests similarities in DNA binding and Ob-fold structures of RPA from T. cruzi compared with mammalian and fungi RPA, the predicted tridimensional structures of T. cruzi RPA-1 and RPA-2 indicated that these molecules present a more flexible tertiary structure, suggesting that T. cruzi RPA could be involved in additional responses. Here, we demonstrate experimentally that the T. cruzi RPA complex interacts with DNA via RPA-1 and is directly related to canonical functions, such as DNA replication and DNA damage response. Accordingly, a reduction of TcRPA-2 expression by generating heterozygous knockout cells impaired cell growth, slowing down S-phase progression. Moreover, heterozygous knockout cells presented a better efficiency in differentiation from epimastigote to metacyclic trypomastigote forms and metacyclic trypomastigote infection. Taken together, these findings indicate the involvement of TcRPA in the metacyclogenesis process and suggest that a delay in cell cycle progression could be linked with differentiation in T. cruzi.
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Affiliation(s)
- Raphael Souza Pavani
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Marcelo Santos da Silva
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Carlos Alexandre Henrique Fernandes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho -UNESP, Botucatu, São Paulo, Brazil
| | | | - Christiane Bezerra Araujo
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Marcos Roberto de Mattos Fontes
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho -UNESP, Botucatu, São Paulo, Brazil
| | - Osvaldo Augusto Sant’Anna
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, São Paulo, Brazil
- Laboratório de Imunoquímica, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Maria Isabel Cano
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Julio Mesquita Filho—UNESP, Botucatu, São Paulo, Brazil
| | | | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling—CeTICS, Instituto Butantan, São Paulo, São Paulo, Brazil
- * E-mail:
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13
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Uzcanga G, Lara E, Gutiérrez F, Beaty D, Beske T, Teran R, Navarro JC, Pasero P, Benítez W, Poveda A. Nuclear DNA replication and repair in parasites of the genus Leishmania: Exploiting differences to develop innovative therapeutic approaches. Crit Rev Microbiol 2016; 43:156-177. [PMID: 27960617 DOI: 10.1080/1040841x.2016.1188758] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Leishmaniasis is a common tropical disease that affects mainly poor people in underdeveloped and developing countries. This largely neglected infection is caused by Leishmania spp, a parasite from the Trypanosomatidae family. This parasitic disease has different clinical manifestations, ranging from localized cutaneous to more harmful visceral forms. The main limitations of the current treatments are their high cost, toxicity, lack of specificity, and long duration. Efforts to improve treatments are necessary to deal with this infectious disease. Many approved drugs to combat diseases as diverse as cancer, bacterial, or viral infections take advantage of specific features of the causing agent or of the disease. Recent evidence indicates that the specific characteristics of the Trypanosomatidae replication and repair machineries could be used as possible targets for the development of new treatments. Here, we review in detail the molecular mechanisms of DNA replication and repair regulation in trypanosomatids of the genus Leishmania and the drugs that could be useful against this disease.
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Affiliation(s)
- Graciela Uzcanga
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,b Programa Prometeo , SENESCYT, Whymper E7-37 y Alpallana, Quito , Ecuador.,c Facultad de Ciencias Naturales y Ambientales, Universidad Internacional SEK Calle Alberto Einstein sn y 5ta transversal , Quito , Ecuador.,d Fundación Instituto de Estudios Avanzados-IDEA , Caracas , Venezuela
| | - Eliana Lara
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,e Institute of Human Genetics , CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer , Montpellier cedex 5 , France
| | - Fernanda Gutiérrez
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Doyle Beaty
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Timo Beske
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Rommy Teran
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Juan-Carlos Navarro
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,f Universidad Central de Venezuela, Instituto de Zoología y Ecología Tropical , Caracas , Venezuela.,g Facultad de Ciencias Naturales y Ambientales, Universidad Internacional SEK, Calle Alberto Einstein sn y 5ta transversal , Quito , Ecuador
| | - Philippe Pasero
- e Institute of Human Genetics , CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer , Montpellier cedex 5 , France
| | - Washington Benítez
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Ana Poveda
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
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Damasceno JD, Obonaga R, Santos EV, Scott A, McCulloch R, Tosi LRO. Functional compartmentalization of Rad9 and Hus1 reveals diverse assembly of the 9-1-1 complex components during the DNA damage response in Leishmania. Mol Microbiol 2016; 101:1054-68. [PMID: 27301589 PMCID: PMC5453112 DOI: 10.1111/mmi.13441] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/17/2016] [Accepted: 06/11/2016] [Indexed: 01/22/2023]
Abstract
The Rad9‐Rad1‐Hus1 (9‐1‐1) complex is a key component in the coordination of DNA damage sensing, cell cycle progression and DNA repair pathways in eukaryotic cells. This PCNA‐related trimer is loaded onto RPA‐coated single stranded DNA and interacts with ATR kinase to mediate effective checkpoint signaling to halt the cell cycle and to promote DNA repair. Beyond these core activities, mounting evidence suggests that a broader range of functions can be provided by 9‐1‐1 structural diversification. The protozoan parasite Leishmania is an early‐branching eukaryote with a remarkably plastic genome, which hints at peculiar genome maintenance mechanisms. Here, we investigated the existence of homologs of the 9‐1‐1 complex subunits in L. major and found that LmRad9 and LmRad1 associate with chromatin in response to replication stress and form a complex in vivo with LmHus1. Similar to LmHus1, LmRad9 participates in telomere homeostasis and in the response to both replication stress and double strand breaks. However, LmRad9 and LmHus1‐deficient cells present markedly opposite phenotypes, which suggest their functional compartmentalization. We show that some of the cellular pool of LmRad9 forms an alternative complex and that some of LmHus1 exists as a monomer. We propose that the diverse assembly of the Leishmania 9‐1‐1 subunits mediates functional compartmentalization, which has a direct impact on the response to genotoxic stress.
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Affiliation(s)
- Jeziel D Damasceno
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Ricardo Obonaga
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Elaine V Santos
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Alan Scott
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow; 120 University Place, Glasgow, G128TA, UK
| | - Richard McCulloch
- The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow; 120 University Place, Glasgow, G128TA, UK
| | - Luiz R O Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil.
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15
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Identification of a Candidate Rad1 Subunit for the Kinetoplastid 9-1-1 (Rad9-Hus1-Rad1) Complex. BIOLOGY 2014; 3:922-7. [PMID: 25534152 PMCID: PMC4280517 DOI: 10.3390/biology3040922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/05/2014] [Accepted: 12/12/2014] [Indexed: 11/20/2022]
Abstract
The trimeric 9-1-1 (Rad9-Hus1-Rad1) complex plays an important role in the eukaryotic DNA damage response by recruiting DNA repair factors and checkpoint mediators to damaged sites. Extensively characterised in mammals and yeast, evidence is now emerging that 9-1-1 function is conserved beyond the relatively narrow evolutionary range of the Opisthokonts. Kinetoplastid Rad9 and Hus1 proteins have been identified and shown to be involved in the DNA damage response but Rad1 has remained elusive. In this study, PSI-BLAST iterative database searching, phylogenetic and structural modeling techniques are used to identify and characterise candidate Rad1 proteins in kinetoplastid organisms.
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