1
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Li B. Telomere maintenance in African trypanosomes. Front Mol Biosci 2023; 10:1302557. [PMID: 38074093 PMCID: PMC10704157 DOI: 10.3389/fmolb.2023.1302557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024] Open
Abstract
Telomere maintenance is essential for genome integrity and chromosome stability in eukaryotic cells harboring linear chromosomes, as telomere forms a specialized structure to mask the natural chromosome ends from DNA damage repair machineries and to prevent nucleolytic degradation of the telomeric DNA. In Trypanosoma brucei and several other microbial pathogens, virulence genes involved in antigenic variation, a key pathogenesis mechanism essential for host immune evasion and long-term infections, are located at subtelomeres, and expression and switching of these major surface antigens are regulated by telomere proteins and the telomere structure. Therefore, understanding telomere maintenance mechanisms and how these pathogens achieve a balance between stability and plasticity at telomere/subtelomere will help develop better means to eradicate human diseases caused by these pathogens. Telomere replication faces several challenges, and the "end replication problem" is a key obstacle that can cause progressive telomere shortening in proliferating cells. To overcome this challenge, most eukaryotes use telomerase to extend the G-rich telomere strand. In addition, a number of telomere proteins use sophisticated mechanisms to coordinate the telomerase-mediated de novo telomere G-strand synthesis and the telomere C-strand fill-in, which has been extensively studied in mammalian cells. However, we recently discovered that trypanosomes lack many telomere proteins identified in its mammalian host that are critical for telomere end processing. Rather, T. brucei uses a unique DNA polymerase, PolIE that belongs to the DNA polymerase A family (E. coli DNA PolI family), to coordinate the telomere G- and C-strand syntheses. In this review, I will first briefly summarize current understanding of telomere end processing in mammals. Subsequently, I will describe PolIE-mediated coordination of telomere G- and C-strand synthesis in T. brucei and implication of this recent discovery.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, United States
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2
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Mukherjee A, Hossain Z, Erben E, Ma S, Choi JY, Kim HS. Identification of a small-molecule inhibitor that selectively blocks DNA-binding by Trypanosoma brucei replication protein A1. Nat Commun 2023; 14:4390. [PMID: 37474515 PMCID: PMC10359466 DOI: 10.1038/s41467-023-39839-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 06/30/2023] [Indexed: 07/22/2023] Open
Abstract
Replication Protein A (RPA) is a broadly conserved complex comprised of the RPA1, 2 and 3 subunits. RPA protects the exposed single-stranded DNA (ssDNA) during DNA replication and repair. Using structural modeling, we discover an inhibitor, JC-229, that targets RPA1 in Trypanosoma brucei, the causative parasite of African trypanosomiasis. The inhibitor is highly toxic to T. brucei cells, while mildly toxic to human cells. JC-229 treatment mimics the effects of TbRPA1 depletion, including DNA replication inhibition and DNA damage accumulation. In-vitro ssDNA-binding assays demonstrate that JC-229 inhibits the activity of TbRPA1, but not the human ortholog. Indeed, despite the high sequence identity with T. cruzi and Leishmania RPA1, JC-229 only impacts the ssDNA-binding activity of TbRPA1. Site-directed mutagenesis confirms that the DNA-Binding Domain A (DBD-A) in TbRPA1 contains a JC-229 binding pocket. Residue Serine 105 determines specific binding and inhibition of TbRPA1 but not T. cruzi and Leishmania RPA1. Our data suggest a path toward developing and testing highly specific inhibitors for the treatment of African trypanosomiasis.
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Affiliation(s)
- Aditi Mukherjee
- Public Health Research Institute, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA
| | - Zakir Hossain
- Department of Chemistry and Biochemistry, Queens College, New York, NY, 11367, USA
| | - Esteban Erben
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Provincia de Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, San Martín, Provincia de Buenos Aires, Argentina
| | - Shuai Ma
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Jun Yong Choi
- Department of Chemistry and Biochemistry, Queens College, New York, NY, 11367, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Hee-Sook Kim
- Public Health Research Institute, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.
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3
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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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da Silva MS. DNA Double-Strand Breaks: A Double-Edged Sword for Trypanosomatids. Front Cell Dev Biol 2021; 9:669041. [PMID: 33937271 PMCID: PMC8085331 DOI: 10.3389/fcell.2021.669041] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/29/2021] [Indexed: 01/09/2023] Open
Abstract
For nearly all eukaryotic cells, stochastic DNA double-strand breaks (DSBs) are one of the most deleterious types of DNA lesions. DSB processing and repair can cause sequence deletions, loss of heterozygosity, and chromosome rearrangements resulting in cell death or carcinogenesis. However, trypanosomatids (single-celled eukaryotes parasites) do not seem to follow this premise strictly. Several studies have shown that trypanosomatids depend on DSBs to perform several events of paramount importance during their life cycle. For Trypanosoma brucei, DSBs formation is associated with host immune evasion via antigenic variation. In Trypanosoma cruzi, DSBs play a crucial role in the genetic exchange, a mechanism that is still little explored but appear to be of fundamental importance for generating variability. In Leishmania spp., DSBs are necessary to generate genomic changes by gene copy number variation (CNVs), events that are essential for these organisms to overcome inhospitable conditions. As DSB repair in trypanosomatids is primarily conducted via homologous recombination (HR), most of the events associated with DSBs are HR-dependent. This review will discuss the latest findings on how trypanosomatids balance the benefits and inexorable challenges caused by DSBs.
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Affiliation(s)
- Marcelo Santos da Silva
- DNA Replication and Repair Laboratory (DRRL), Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
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Morea EGO, Vasconcelos EJR, Alves CDS, Giorgio S, Myler PJ, Langoni H, Azzalin CM, Cano MIN. Exploring TERRA during Leishmania major developmental cycle and continuous in vitro passages. Int J Biol Macromol 2021; 174:573-586. [PMID: 33548324 DOI: 10.1016/j.ijbiomac.2021.01.192] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 12/22/2022]
Abstract
Telomeres from different eukaryotes, including trypanosomatids, are transcribed into TERRA noncoding RNAs, crucial in regulating chromatin deposition and telomere length. TERRA is transcribed from the C-rich subtelomeric strand towards the 3'-ends of the telomeric array. Using bioinformatics, we confirmed the presence of subtelomeric splice acceptor sites at all L. major chromosome ends. Splice leader sequences positioned 5' upstream of L. major chromosomes subtelomeres were then mapped using SL-RNA-Seq libraries constructed from three independent parasite life stages and helped confirm TERRA expression from several chromosomes ends. Northern blots and RT-qPCR validated the results showing that L. major TERRA is processed by trans-splicing and polyadenylation coupled reactions. The number of transcripts varied with the parasite's life stage and continuous passages, being more abundant in the infective forms. However, no putative subtelomeric promoters involved in TERRA's transcriptional regulation were detected. In contrast, the observed changes in parasite's telomere length during development, suggest that differences in telomeric base J levels may control TERRA transcription in L. major. Also, TERRA-R loops' detection, mainly in the infective forms, was suggestive of TERRA's involvement in telomere protection. Therefore, Leishmania TERRA shares conserved features with other eukaryotes and advances new telomere specific functions in a Public Health-impacting parasite.
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Affiliation(s)
- Edna Gicela Ortiz Morea
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil
| | | | - Cristiane de Santis Alves
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil
| | - Selma Giorgio
- Department of Animal Biology, Biology Institute, State University of Campinas, UNICAMP, Brazil
| | - Peter J Myler
- Department of Global Health and Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, WA, United States of America
| | - Helio Langoni
- Department of Public Health, Veterinary Medical School, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil
| | | | - Maria Isabel Nogueira Cano
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University, UNESP, Botucatu, São Paulo, Brazil.
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Fernandes CAH, Morea EGO, Cano MIN. RPA-1 from Leishmania sp.: Recombinant Protein Expression and Purification, Molecular Modeling, and Molecular Dynamics Simulations Protocols. Methods Mol Biol 2021; 2281:169-191. [PMID: 33847958 DOI: 10.1007/978-1-0716-1290-3_10] [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] [Indexed: 06/12/2023]
Abstract
RPA is a conserved heterotrimeric complex and the major single-stranded DNA (ssDNA)-binding protein heterotrimeric complex, which in eukaryotes is formed by the RPA-1, RPA-2, and RPA-3 subunits. The main structural feature of RPA is the presence of the oligonucleotide/oligosaccharide-binding fold (OB-fold) domains, responsible for ssDNA binding and protein:protein interactions. Among the RPA subunits, RPA-1 bears three of the four OB folds involved with RPA-ssDNA binding, although in some organisms RPA-2 can also bind ssDNA. The OB-fold domains are also present in telomere end-binding proteins (TEBP), essential for chromosome end protection. RPA-1 from Leishmania sp., as well as RPA-1 from trypanosomatids, a group of early-divergent protozoa, shows some structural differences compared to higher eukaryote RPA-1. Also, RPA-1 from Leishmania sp., similar to TEBPs, may exert telomeric protective functions. Remarkably, different pieces of evidence have pointed out that trypanosomatids may not have OB fold-containing TEBPs. Moreover, recent data indicate that trypanosomatid RPA-1 may be considered a TEBP since it shares with TEBPs conserved functional and structural features. However, it is still unknown whether the RPA-1 protective telomeric role is exclusive to trypanosomatids or is also present in other primitive eukaryotes. Here, we describe a protocol to obtain highly purified and biologically active Leishmania amazonensis recombinant RPA-1, and to perform molecular modeling and molecular dynamics simulations methods which could be probably applied to functional and structural studies of homologous proteins in other primitive eukaryotes.
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Affiliation(s)
- Carlos A H Fernandes
- Department of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Edna G O Morea
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Maria Isabel N Cano
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil.
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Fernandes CAH, Morea EGO, Dos Santos GA, da Silva VL, Vieira MR, Viviescas MA, Chatain J, Vadel A, Saintomé C, Fontes MRM, Cano MIN. A multi-approach analysis highlights the relevance of RPA-1 as a telomere end-binding protein (TEBP) in Leishmania amazonensis. Biochim Biophys Acta Gen Subj 2020; 1864:129607. [PMID: 32222548 DOI: 10.1016/j.bbagen.2020.129607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/21/2020] [Accepted: 03/24/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Telomeres are chromosome end structures important in the maintenance of genome homeostasis. They are replenished by the action of telomerase and associated proteins, such as the OB (oligonucleotide/oligosaccharide-binding)-fold containing telomere-end binding proteins (TEBP) which plays an essential role in telomere maintenance and protection. The nature of TEBPs is well known in higher and some primitive eukaryotes, but it remains undetermined in trypanosomatids. Previous in silico searches have shown that there are no homologs of the classical TEPBs in trypanosomatids, including Leishmania sp. However, Replication Protein A subunit 1 (RPA-1), an OB-fold containing DNA-binding protein, was found co-localized with trypanosomatids telomeres and showed a high preference for the telomeric G-rich strand. METHODS AND RESULTS We predicted the absence of structural homologs of OB-fold containing TEBPs in the Leishmania sp. genome using structural comparisons. We demonstrated by molecular docking that the ssDNA binding mode of LaRPA-1 shares features with the higher eukaryotes POT1 and RPA-1 crystal structures ssDNA binding mode. Using fluorescence spectroscopy, protein-DNA interaction assays, and FRET, we respectively show that LaRPA-1 shares some telomeric functions with the classical TEBPs since it can bind at least one telomeric repeat, protect the telomeric G-rich DNA from 3'-5' Exonuclease I digestion, and unfold telomeric G-quadruplex. CONCLUSIONS Our results suggest that RPA-1 emerges as a TEBP in trypanosomatids, and in this context, we present two possible evolutionary landscapes of trypanosomatids RPA-1 that could reflect upon the evolution of OB-fold containing TEBPs from all eukaryotes.
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Affiliation(s)
- Carlos A H Fernandes
- Department of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP) - Botucatu, SP, Brazil; Laboratoire de Biologie et Pharmacologie Appliquée, École Normale Supérieure Paris-Saclay, Cachan, France
| | - Edna Gicela O Morea
- Department of Chemical and Biological Sciences, São Paulo State University (UNESP) - Botucatu, SP, Brazil
| | - Gabriel A Dos Santos
- Department of Chemical and Biological Sciences, São Paulo State University (UNESP) - Botucatu, SP, Brazil
| | - Vitor L da Silva
- Department of Chemical and Biological Sciences, São Paulo State University (UNESP) - Botucatu, SP, Brazil
| | - Marina Roveri Vieira
- Department of Chemical and Biological Sciences, São Paulo State University (UNESP) - Botucatu, SP, Brazil
| | - Maria Alejandra Viviescas
- Department of Chemical and Biological Sciences, São Paulo State University (UNESP) - Botucatu, SP, Brazil
| | - Jean Chatain
- MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005 Paris, France
| | - Aurélie Vadel
- MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005 Paris, France
| | - Carole Saintomé
- MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005 Paris, France; Sorbonne Université, UFR927, 4 place Jussieu, 75005 Paris, France
| | - Marcos Roberto M Fontes
- Department of Biophysics and Pharmacology, Biosciences Institute, São Paulo State University (UNESP) - Botucatu, SP, Brazil
| | - Maria Isabel Nogueira Cano
- Department of Chemical and Biological Sciences, São Paulo State University (UNESP) - Botucatu, SP, Brazil.
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Pavani RS, Lima LP, Lima AA, Fernandes CAH, Fragoso SP, Calderano SG, Elias MC. Nuclear export of replication protein A in the nonreplicative infective forms of
Trypanosoma cruzi. FEBS Lett 2020; 594:1596-1607. [DOI: 10.1002/1873-3468.13755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Raphael S. Pavani
- Laboratório de Ciclo Celular Instituto Butantan São Paulo Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
| | - Loyze P. Lima
- Laboratório de Ciclo Celular Instituto Butantan São Paulo Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
| | - André A. Lima
- Laboratório de Ciclo Celular Instituto Butantan São Paulo Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
| | - Carlos A. H. Fernandes
- Departamento de Física e Biofísica Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP) Botucatu Brazil
- Laboratorie de Biologie et Pharmacologie Appliquée Ecole Normale Supérieure Paris‐Saclay Cachan France
| | | | - Simone G. Calderano
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
- Laboratório de Parasitologia Instituto Butantan São Paulo Brazil
| | - Maria Carolina Elias
- Laboratório de Ciclo Celular Instituto Butantan São Paulo Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS) Instituto Butantan São Paulo Brazil
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Marin PA, da Silva MS, Pavani RS, Machado CR, Elias MC. Recruitment kinetics of the homologous recombination pathway in procyclic forms of Trypanosoma brucei after ionizing radiation treatment. Sci Rep 2018; 8:5405. [PMID: 29599445 PMCID: PMC5876374 DOI: 10.1038/s41598-018-23731-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/13/2018] [Indexed: 12/31/2022] Open
Abstract
One of the most important mechanisms for repairing double-strand breaks (DSBs) in model eukaryotes is homologous recombination (HR). Although the genes involved in HR have been found in Trypanosoma brucei and studies have identified some of the proteins that participate in this HR pathway, the recruitment kinetics of the HR machinery onto DNA during DSB repair have not been clearly elucidated in this organism. Using immunofluorescence, protein DNA-bound assays, and DNA content analysis, we established the recruitment kinetics of the HR pathway in response to the DSBs generated by ionizing radiation (IR) in procyclic forms of T. brucei. These kinetics involved the phosphorylation of histone H2A and the sequential recruitment of the essential HR players Exo1, RPA, and Rad51. The process of DSB repair took approximately 5.5 hours. We found that DSBs led to a decline in the G2/M phase after IR treatment, concomitant with cell cycle arrest in the G1/S phase. This finding suggests that HR repairs DSBs faster than the other possible DSB repair processes that act during the G1/S transition. Taken together, these data suggest that the interplay between DNA damage detection and HR machinery recruitment is finely coordinated, allowing these parasites to repair DNA rapidly after DSBs during the late S/G2 proficient phases.
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Affiliation(s)
- Paula Andrea Marin
- Cell Cycle Laboratory (LECC) - Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, 05503-900, Brazil
| | - Marcelo Santos da Silva
- Cell Cycle Laboratory (LECC) - Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, 05503-900, Brazil
| | - Raphael Souza Pavani
- Cell Cycle Laboratory (LECC) - Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, 05503-900, Brazil
| | - Carlos Renato Machado
- Biochemical and Immunology Department, Institute of Biomedical Science, ICB, Federal University of Minas Gerais (UFMG), Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Maria Carolina Elias
- Cell Cycle Laboratory (LECC) - Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, 05503-900, Brazil.
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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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da Silva MS, Muñoz PAM, Armelin HA, Elias MC. Differences in the Detection of BrdU/EdU Incorporation Assays Alter the Calculation for G1, S, and G2 Phases of the Cell Cycle in Trypanosomatids. J Eukaryot Microbiol 2017; 64:756-770. [PMID: 28258618 DOI: 10.1111/jeu.12408] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/17/2017] [Accepted: 02/23/2017] [Indexed: 01/22/2023]
Abstract
Trypanosomatids are the etiologic agents of various infectious diseases in humans. They diverged early during eukaryotic evolution and have attracted attention as peculiar models for evolutionary and comparative studies. Here, we show a meticulous study comparing the incorporation and detection of the thymidine analogs BrdU and EdU in Leishmania amazonensis, Trypanosoma brucei, and Trypanosoma cruzi to monitor their DNA replication. We used BrdU- and EdU-incorporated parasites with the respective standard detection approaches: indirect immunofluorescence to detect BrdU after standard denaturation (2 M HCl) and "click" chemistry to detect EdU. We found a discrepancy between these two thymidine analogs due to the poor detection of BrdU, which is reflected on the estimative of the duration of the cell cycle phases G1, S, and G2. To solve this discrepancy, we increase the exposure of incorporated BrdU using different concentrations of HCl. Using a new value for HCl concentration, we re-estimated the phases G1, S, G2 + M, and cytokinesis durations, confirming the values found by this approach using EdU. In conclusion, we suggest that the studies using BrdU with standard detection approach, not only in trypanosomatids but also in others cell types, should be reviewed to ensure an accurate estimation of DNA replication monitoring.
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Affiliation(s)
- Marcelo Santos da Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, 1500, Vital Brasil Avenue, 05503-900, São Paulo, Brazil
| | - Paula Andrea Marin Muñoz
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, 1500, Vital Brasil Avenue, 05503-900, São Paulo, Brazil
| | - Hugo Aguirre Armelin
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, 1500, Vital Brasil Avenue, 05503-900, São Paulo, Brazil
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, 1500, Vital Brasil Avenue, 05503-900, São Paulo, Brazil
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12
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da Silva MS, Segatto M, Pavani RS, Gutierrez-Rodrigues F, Bispo VDS, de Medeiros MHG, Calado RT, Elias MC, Cano MIN. Consequences of acute oxidative stress in Leishmania amazonensis : From telomere shortening to the selection of the fittest parasites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:138-150. [DOI: 10.1016/j.bbamcr.2016.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/17/2016] [Accepted: 11/01/2016] [Indexed: 01/08/2023]
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Nocua PA, Ramirez CA, Barreto GE, González J, Requena JM, Puerta CJ. Leishmania braziliensis replication protein A subunit 1: molecular modelling, protein expression and analysis of its affinity for both DNA and RNA. Parasit Vectors 2014; 7:573. [PMID: 25498946 PMCID: PMC4269926 DOI: 10.1186/s13071-014-0573-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 11/26/2014] [Indexed: 11/28/2022] Open
Abstract
Background Replication factor A (RPA) is a single-strand DNA binding protein involved in DNA replication, recombination and repair processes. It is composed by the subunits RPA-1, RPA-2 and RPA-3; the major DNA-binding activity resides in the subunit 1 of the heterotrimeric RPA complex. In yeast and higher eukaryotes, besides the three basic structural DNA-binding domains, the RPA-1 subunit contains an N-terminal region involved in protein-protein interactions with a fourth DNA-binding domain. Remarkably, the N-terminal extension is absent in the RPA-1 of the pathogenic protozoan Leishmania (Leishmania) amazonensis; however, the protein maintains its ability to bind ssDNA. In a recent work, we identify Leishmania (Viannia) braziliensis RPA-1 by its specific binding to the untranslated regions of the HSP70 mRNAs, suggesting that this protein might be also an RNA-binding protein. Methods Both rLbRPA-1 purified by His-tag affinity chromatography as well as the in vitro transcribed L. braziliensis 3′ HSP70-II UTR were used to perform pull down assays to asses nucleic acid binding properties. Also, homology modeling was carried out to construct the LbRPA-1 tridimensional structure to search relevant amino acid residues to bind nucleic acids. Results In this work, after obtaining the recombinant L. braziliensis RPA-1 protein under native conditions, competitive and non-competitive pull-down assays confirmed the single-stranded DNA binding activity of this protein and demonstrated its interaction with the 3′ UTR from the HSP70-II mRNA. As expected, this protein exhibits a high affinity for ssDNA, but we have found that RPA-1 interacts also with RNA. Additionally, we carried out a structural analysis of L. braziliensis RPA-1 protein using the X-ray diffraction structure of Ustilago maydis homologous protein as a template. Our results indicate that, in spite of the evolutionary divergence between both organisms, the structure of these two RPA-1 proteins seems to be highly conserved. Conclusion The LbRPA-1 protein is a ssDNA binding protein, but also it shows affinity in vitro for the HSP70 mRNA; this finding supports a possible in vivo role in the HSP70 mRNA metabolism. On the other hand, the three dimensional model of Leishmania RPA-1 serves as a starting point for both functional analysis and its exploration as a chemotherapeutic target to combat leishmaniasis.
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Affiliation(s)
- Paola A Nocua
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 No 43-82, Edificio 50, Laboratorio 113, Bogotá, Colombia.
| | - Cesar A Ramirez
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 No 43-82, Edificio 50, Laboratorio 113, Bogotá, Colombia.
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
| | - 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, Carrera 7 No 43-82, Edificio 50, Laboratorio 113, Bogotá, Colombia.
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RPA-1 from Leishmania amazonensis (LaRPA-1) structurally differs from other eukaryote RPA-1 and interacts with telomeric DNA via its N-terminal OB-fold domain. FEBS Lett 2014; 588:4740-8. [PMID: 25451229 DOI: 10.1016/j.febslet.2014.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/25/2014] [Accepted: 11/06/2014] [Indexed: 12/18/2022]
Abstract
Replication protein A-1 (RPA-1) is a single-stranded DNA-binding protein involved in DNA metabolism. We previously demonstrated the interaction between LaRPA-1 and telomeric DNA. Here, we expressed and purified truncated mutants of LaRPA-1 and used circular dichroism measurements and molecular dynamics simulations to demonstrate that the tertiary structure of LaRPA-1 differs from human and yeast RPA-1. LaRPA-1 interacts with telomeric ssDNA via its N-terminal OB-fold domain, whereas RPA from higher eukaryotes show different binding modes to ssDNA. Our results show that LaRPA-1 is evolutionary distinct from other RPA-1 proteins and can potentially be used for targeting trypanosomatid telomeres.
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DNA repair pathways in trypanosomatids: from DNA repair to drug resistance. Microbiol Mol Biol Rev 2014; 78:40-73. [PMID: 24600040 DOI: 10.1128/mmbr.00045-13] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
All living organisms are continuously faced with endogenous or exogenous stress conditions affecting genome stability. DNA repair pathways act as a defense mechanism, which is essential to maintain DNA integrity. There is much to learn about the regulation and functions of these mechanisms, not only in human cells but also equally in divergent organisms. In trypanosomatids, DNA repair pathways protect the genome against mutations but also act as an adaptive mechanism to promote drug resistance. In this review, we scrutinize the molecular mechanisms and DNA repair pathways which are conserved in trypanosomatids. The recent advances made by the genome consortiums reveal the complete genomic sequences of several pathogens. Therefore, using bioinformatics and genomic sequences, we analyze the conservation of DNA repair proteins and their key protein motifs in trypanosomatids. We thus present a comprehensive view of DNA repair processes in trypanosomatids at the crossroads of DNA repair and drug resistance.
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Abstract
Telomeres are the physical ends of eukaryotic linear chromosomes. Telomeres form special structures that cap chromosome ends to prevent degradation by nucleolytic attack and to distinguish chromosome termini from DNA double-strand breaks. With few exceptions, telomeres are composed primarily of repetitive DNA associated with proteins that interact specifically with double- or single-stranded telomeric DNA or with each other, forming highly ordered and dynamic complexes involved in telomere maintenance and length regulation. In proliferative cells and unicellular organisms, telomeric DNA is replicated by the actions of telomerase, a specialized reverse transcriptase. In the absence of telomerase, some cells employ a recombination-based DNA replication pathway known as alternative lengthening of telomeres. However, mammalian somatic cells that naturally lack telomerase activity show telomere shortening with increasing age leading to cell cycle arrest and senescence. In another way, mutations or deletions of telomerase components can lead to inherited genetic disorders, and the depletion of telomeric proteins can elicit the action of distinct kinases-dependent DNA damage response, culminating in chromosomal abnormalities that are incompatible with life. In addition to the intricate network formed by the interrelationships among telomeric proteins, long noncoding RNAs that arise from subtelomeric regions, named telomeric repeat-containing RNA, are also implicated in telomerase regulation and telomere maintenance. The goal for the next years is to increase our knowledge about the mechanisms that regulate telomere homeostasis and the means by which their absence or defect can elicit telomere dysfunction, which generally results in gross genomic instability and genetic diseases.
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da Silva MS, Monteiro JP, Nunes VS, Vasconcelos EJ, Perez AM, Freitas-Júnior LDH, Elias MC, Cano MIN. Leishmania amazonensis promastigotes present two distinct modes of nucleus and kinetoplast segregation during cell cycle. PLoS One 2013; 8:e81397. [PMID: 24278433 PMCID: PMC3836779 DOI: 10.1371/journal.pone.0081397] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 10/11/2013] [Indexed: 11/18/2022] Open
Abstract
Here, we show the morphological events associated with organelle segregation and their timing in the cell cycle of a reference strain of Leishmania (L.) amazonensis promastigotes, the main causative agent of Tegumentary leishmaniasis in the Americas. We show evidences that during the cell cycle, L. amazonensis promastigotes present two distinct modes of nucleus and kinetoplast segregation, which occur in different temporal order in different proportions of cells. We used DAPI-staining and EdU-labeling to monitor the segregation of DNA-containing organelles and DNA replication in wild-type parasites. The emergence of a new flagellum was observed using a specific monoclonal antibody. The results show that L. amazonensis cell cycle division is peculiar, with 65% of the dividing cells duplicating the kinetoplast before the nucleus, and the remaining 35% doing the opposite or duplicating both organelles concomitantly. In both cases, the new flagellum appeared during S to G2 phase in 1N1K cells and thus before the segregation of both DNA-containing organelles; however, we could not determine the exact timing of flagellar synthesis. Most of these results were confirmed by the synchronization of parasites using hydroxyurea. Altogether, our data show that during the cell cycle of L. amazonensis promastigotes, similarly to L. donovani, the segregation of nucleus and kinetoplast do not follow a specific order, especially when compared to other trypanosomatids, reinforcing the idea that this characteristic seems to be species-specific and may represent differences in cellular biology among members of the Leishmania genus.
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Affiliation(s)
- Marcelo Santos da Silva
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
- Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Jomar Patrício Monteiro
- Empresa Brasileira de Pesquisa Agropecuária (Embrapa) Caprinos e Ovinos, Sobral, Ceará, Brazil
| | - Vinícius Santana Nunes
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | | | - Arina Marina Perez
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | - Lúcio de Holanda Freitas-Júnior
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Maria Carolina Elias
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Maria Isabel Nogueira Cano
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
- * E-mail:
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