1
|
Anuntasomboon P, Siripattanapipong S, Unajak S, Choowongkomon K, Burchmore R, Leelayoova S, Mungthin M, E-kobon T. Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand. BIOLOGY 2022; 11:biology11091272. [PMID: 36138751 PMCID: PMC9495971 DOI: 10.3390/biology11091272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Leishmaniasis is a parasitic disease caused by flagellated protozoa of the genus Leishmania. Multiple genome sequencing platforms have been employed to complete Leishmania genomes at the expense of high cost. This study proposes an integrative bioinformatic workflow for assembling only the short-read data of Leishmania orientalis isolate PCM2 from Thailand and produce an acceptable-quality genome for further genomic analysis. This workflow gives extensive information required for identifying strain-specific markers and virulence-associated genes useful for drug and vaccine development before a more exhaustive and expensive investigation. Abstract Background: Leishmania orientalis (formerly named Leishmania siamensis) has been neglected for years in Thailand. The genomic study of L. orientalis has gained much attention recently after the release of the first high-quality reference genome of the isolate LSCM4. The integrative approach of multiple sequencing platforms for whole-genome sequencing has proven effective at the expense of considerably expensive costs. This study presents a preliminary bioinformatic workflow including the use of multi-step de novo assembly coupled with the reference-based assembly method to produce high-quality genomic drafts from the short-read Illumina sequence data of L. orientalis isolate PCM2. Results: The integrating multi-step de novo assembly by MEGAHIT and SPAdes with the reference-based method using the L. enriettii genome and salvaging the unmapped reads resulted in the 30.27 Mb genomic draft of L. orientalis isolate PCM2 with 3367 contigs and 8887 predicted genes. The results from the integrated approach showed the best integrity, coverage, and contig alignment when compared to the genome of L. orientalis isolate LSCM4 collected from the northern province of Thailand. Similar patterns of gene ratios and frequency were observed from the GO biological process annotation. Fifty GO terms were assigned to the assembled genomes, and 23 of these (accounting for 61.6% of the annotated genes) showed higher gene counts and ratios when results from our workflow were compared to those of the LSCM4 isolate. Conclusions: These results indicated that our proposed bioinformatic workflow produced an acceptable-quality genome of L. orientalis strain PCM2 for functional genomic analysis, maximising the usage of the short-read data. This workflow would give extensive information required for identifying strain-specific markers and virulence-associated genes useful for drug and vaccine development before a more exhaustive and expensive investigation.
Collapse
Affiliation(s)
- Pornchai Anuntasomboon
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | | | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Richard Burchmore
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Saovanee Leelayoova
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok 10400, Thailand
| | - Mathirut Mungthin
- Department of Parasitology, Phramongkutklao College of Medicine, Bangkok 10400, Thailand
| | - Teerasak E-kobon
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: ; Tel.: +66-812-85-4672
| |
Collapse
|
2
|
Garcia-Silva MR, Sollelis L, MacPherson CR, Stanojcic S, Kuk N, Crobu L, Bringaud F, Bastien P, Pagès M, Scherf A, Sterkers Y. Identification of the centromeres of Leishmania major: revealing the hidden pieces. EMBO Rep 2017; 18:1968-1977. [PMID: 28935715 DOI: 10.15252/embr.201744216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/15/2017] [Accepted: 08/28/2017] [Indexed: 01/16/2023] Open
Abstract
Leishmania affects millions of people worldwide. Its genome undergoes constitutive mosaic aneuploidy, a type of genomic plasticity that may serve as an adaptive strategy to survive distinct host environments. We previously found high rates of asymmetric chromosome allotments during mitosis that lead to the generation of such ploidy. However, the underlying molecular events remain elusive. Centromeres and kinetochores most likely play a key role in this process, yet their identification has failed using classical methods. Our analysis of the unconventional kinetochore complex recently discovered in Trypanosoma brucei (KKTs) leads to the identification of a Leishmania KKT gene candidate (LmKKT1). The GFP-tagged LmKKT1 displays "kinetochore-like" dynamics of intranuclear localization throughout the cell cycle. By ChIP-Seq assay, one major peak per chromosome is revealed, covering a region of 4 ±2 kb. We find two largely conserved motifs mapping to 14 of 36 chromosomes while a higher density of retroposons are observed in 27 of 36 centromeres. The identification of centromeres and of a kinetochore component of Leishmania chromosomes opens avenues to explore their role in mosaic aneuploidy.
Collapse
Affiliation(s)
- Maria-Rosa Garcia-Silva
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Lauriane Sollelis
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Cameron Ross MacPherson
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Slavica Stanojcic
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Nada Kuk
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Lucien Crobu
- CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), University of Bordeaux, Bordeaux, France.,CNRS, UMR 5234, Bordeaux, France
| | - Patrick Bastien
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France.,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France.,Department of Parasitology-Mycology, University Hospital Centre (CHU), Montpellier, France
| | - Michel Pagès
- CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France
| | - Artur Scherf
- Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France.,CNRS, ERL 9195, Paris, France.,INSERM, Unit U1201, Paris, France
| | - Yvon Sterkers
- Department of Parasitology-Mycology, Faculty of Medicine, University of Montpellier, Montpellier, France .,CNRS 5290 - IRD 224 - University of Montpellier (UMR "MiVEGEC"), Montpellier, France.,Department of Parasitology-Mycology, University Hospital Centre (CHU), Montpellier, France
| |
Collapse
|
3
|
Cloning and expression of transgenes using linear vectors in Trypanosoma cruzi. Int J Parasitol 2014; 44:447-56. [DOI: 10.1016/j.ijpara.2014.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/13/2014] [Accepted: 03/02/2014] [Indexed: 11/15/2022]
|
4
|
Tiengwe C, Marques CA, McCulloch R. Nuclear DNA replication initiation in kinetoplastid parasites: new insights into an ancient process. Trends Parasitol 2013; 30:27-36. [PMID: 24287149 DOI: 10.1016/j.pt.2013.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 12/23/2022]
Abstract
Nuclear DNA replication is, arguably, the central cellular process in eukaryotes, because it drives propagation of life and intersects with many other genome reactions. Perhaps surprisingly, our understanding of nuclear DNA replication in kinetoplastids was limited until a clutch of studies emerged recently, revealing new insight into both the machinery and genome-wide coordination of the reaction. Here, we discuss how these studies suggest that the earliest acting components of the kinetoplastid nuclear DNA replication machinery - the factors that demarcate sites of the replication initiation, termed origins - are diverged from model eukaryotes. In addition, we discuss how origin usage and replication dynamics relate to the highly unusual organisation of transcription in the genome of Trypanosoma brucei.
Collapse
Affiliation(s)
- Calvin Tiengwe
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK; The Johns Hopkins University School of Medicine, Department of Cell Biology, Baltimore, MD, USA
| | - Catarina A Marques
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Richard McCulloch
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
| |
Collapse
|
5
|
Lachaud L, Bourgeois N, Kuk N, Morelle C, Crobu L, Merlin G, Bastien P, Pagès M, Sterkers Y. Constitutive mosaic aneuploidy is a unique genetic feature widespread in the Leishmania genus. Microbes Infect 2013; 16:61-6. [PMID: 24120456 DOI: 10.1016/j.micinf.2013.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 11/29/2022]
Abstract
Using fluorescence in situ hybridization, we determined the ploidy of four species of Leishmania: Leishmania infantum, Leishmania donovani, Leishmania tropica and Leishmania amazonensis. We found that each cell in a strain possesses a combination of mono-, di- and trisomies for all chromosomes; ploidy patterns were different among all strains/species. These results extend those we previously described in Leishmania major, demonstrating that mosaic aneuploidy is a genetic feature widespread to the Leishmania genus. In addition to the genetic consequences induced by this mosaicism, the apparent absence of alternation between haploid/diploid stages questions the modality of genetic exchange in Leishmania sp.
Collapse
Affiliation(s)
- Laurence Lachaud
- University Montpellier 1, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France; CNRS 5290, IRD 224, University Montpellier 1&2 (UMR "MiVEGEC"), Montpellier, France
| | - Nathalie Bourgeois
- University Montpellier 1, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France; CNRS 5290, IRD 224, University Montpellier 1&2 (UMR "MiVEGEC"), Montpellier, France; Centre Hospitalier Universitaire (University Hospital Centre), Montpellier, France
| | - Nada Kuk
- University Montpellier 1, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France
| | - Christelle Morelle
- University Montpellier 1, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France; CNRS 5290, IRD 224, University Montpellier 1&2 (UMR "MiVEGEC"), Montpellier, France; Centre Hospitalier Universitaire (University Hospital Centre), Montpellier, France
| | - Lucien Crobu
- CNRS 5290, IRD 224, University Montpellier 1&2 (UMR "MiVEGEC"), Montpellier, France
| | - Gilles Merlin
- CNRS 5290, IRD 224, University Montpellier 1&2 (UMR "MiVEGEC"), Montpellier, France
| | - Patrick Bastien
- University Montpellier 1, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France; CNRS 5290, IRD 224, University Montpellier 1&2 (UMR "MiVEGEC"), Montpellier, France; Centre Hospitalier Universitaire (University Hospital Centre), Montpellier, France
| | - Michel Pagès
- CNRS 5290, IRD 224, University Montpellier 1&2 (UMR "MiVEGEC"), Montpellier, France
| | - Yvon Sterkers
- University Montpellier 1, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier, France; CNRS 5290, IRD 224, University Montpellier 1&2 (UMR "MiVEGEC"), Montpellier, France; Centre Hospitalier Universitaire (University Hospital Centre), Montpellier, France.
| |
Collapse
|
6
|
Sterkers Y, Lachaud L, Crobu L, Bastien P, Pagès M. FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major. Cell Microbiol 2010; 13:274-83. [PMID: 20964798 DOI: 10.1111/j.1462-5822.2010.01534.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The protozoan parasite Leishmania is generally considered to be diploid, although a few chromosomes have been described as aneuploid. Using fluorescence in situ hybridization (FISH), we determined the number of homologous chromosomes per individual cell in L. major (i) during interphase and (ii) during mitosis. We show that, in Leishmania, aneuploidy appears to be the rule, as it affects all the chromosomes that we studied. Moreover, every chromosome was observed in at least two ploidy states, among monosomic, disomic or trisomic, in the cell population. This variable chromosomal ploidy among individual cells generates intra-strain heterogeneity, here precisely chromosomal mosaicism. We also show that this mosaicism, hence chromosome ploidy distribution, is variable among clones and strains. Finally, when we examined dividing nuclei, we found a surprisingly high rate of asymmetric chromosome allotments, showing that the transmission of genetic material during mitosis is highly unstable in this 'divergent' eukaryote: this leads to continual generation of chromosomal mosaicism. Using these results, we propose a model for the occurrence and persistence of this mosaicism. We discuss the implications of this additional unique feature of Leishmania for its biology and genetics, in particular as a novel genetic mechanism to generate phenotypic variability from genomic plasticity.
Collapse
Affiliation(s)
- Yvon Sterkers
- Université Montpellier 1, UFR Médecine, Laboratoire de Parasitologie-Mycologie, Montpellier, France
| | | | | | | | | |
Collapse
|
7
|
Casanova M, Portalès P, Blaineau C, Crobu L, Bastien P, Pagès M. Inhibition of active nuclear transport is an intrinsic trigger of programmed cell death in trypanosomatids. Cell Death Differ 2008; 15:1910-20. [PMID: 19011643 DOI: 10.1038/cdd.2008.132] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The link between nucleocytoplasmic transport and apoptosis remains controversial. Nucleocytoplasmic exchange of molecules seems indeed essential for the initiation and execution of the apoptotic programme; but inhibition of nuclear transport factors may also represent a powerful apoptotic trigger. The GTPase Ran (together with its partners), first discovered to be essential in nucleocytoplasmic transport, has multiple key functions in cell biology, and particularly in spindle assembly, kinetochore function and nuclear envelope assembly. Among the Ran partners studied, NTF2 appears to be solely involved in nucleocytoplasmic transport. Here, we localised Ran and several of its partners, RanBP1, CAS and NTF2, at the nuclear membrane in the trypanosomatid Leishmania major. Remarkably, these proteins fused to GFP decorated a perinuclear 'collar' of about 15 dots, colocalising at nuclear pore complexes with the homologue of nucleoporin Sec13. In the other trypanosomatid Trypanosoma brucei, RNAi knockdown of the expression of the corresponding genes resulted in an apoptosis-like phenomenon. These phenotypes show that Ran and its partners have a key function in trypanosomatids like they have in mammals. Our data, notably those about TbNTF2 RNAi, support the idea that active nucleocytoplasmic transport is not essential for the initiation and execution of apoptosis, and, rather, the impairment of this transport constitutes an intrinsic signal for triggering PCD.
Collapse
Affiliation(s)
- M Casanova
- University Montpellier 1, Laboratoire de Parasitologie-Mycologie, Montpellier, France
| | | | | | | | | | | |
Collapse
|
8
|
Puechberty J, Blaineau C, Meghamla S, Crobu L, Pagès M, Bastien P. Compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-specific gene and conserved structural features and sequence motifs. BMC Genomics 2007; 8:57. [PMID: 17319967 PMCID: PMC1805754 DOI: 10.1186/1471-2164-8-57] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 02/24/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosomatids exhibit a unique gene organization into large directional gene clusters (DGCs) in opposite directions. The transcription "strand switch region" (SSR) separating the two large DGCs that constitute chromosome 1 of Leishmania major has been the subject of several studies and speculations. Thus, it has been suspected of being the single replication origin of the chromosome, the transcription initiation site for both DGCs or even a centromere. Here, we have used an inter-species compared genomics approach on this locus in order to try to identify conserved features or motifs indicative of a putative function. RESULTS We isolated, and compared the structure and nucleotide sequence of, this SSR in 15 widely divergent species of Leishmania and Sauroleishmania. As regards its intrachromosomal position, size and AT content, the general structure of this SSR appears extremely stable among species, which is another demonstration of the remarkable structural stability of these genomes at the evolutionary level. Sequence alignments showed several interesting features. Overall, only 30% of nucleotide positions were conserved in the SSR among the 15 species, versus 74% and 62% in the 5' parts of the adjacent XPP and PAXP genes, respectively. However, nucleotide divergences were not distributed homogeneously along this sequence. Thus, a central fragment of approximately 440 bp exhibited 54% of identity among the 15 species. This fragment actually represents a new Leishmania-specific CDS of unknown function which had been overlooked since the annotation of this chromosome. The encoded protein comprises two trans-membrane domains and is classified in the "structural protein" GO category. We cloned this novel gene and expressed it as a recombinant green fluorescent protein-fused version, which showed its localisation to the endoplasmic reticulum. The whole of these data shorten the actual SSR to an 887-bp segment as compared with the original 1.6 kb. In the rest of the SSR, the percentage of identity was much lower, around 22%. Interestingly, the 72-bp fragment where the putatively single transcription initiation site of chromosome 1 was identified is located in a low-conservation portion of the SSR and is itself highly polymorphic amongst species. Nevertheless, it is highly C-rich and presents a unique poly(C) tract in the same position in all species. CONCLUSION This inter-specific comparative study, the first of its kind, (a) allowed to reveal a novel genus-specific gene and (b) identified a conserved poly(C) tract in the otherwise highly polymorphic region containing the putative transcription initiation site. This allows hypothesising an intervention of poly(C)-binding proteins known elsewhere to be involved in transcriptional control.
Collapse
Affiliation(s)
- Jacques Puechberty
- CNRS/Université Montpellier I FRE 3013 "Biologie Moléculaire, Biologie Cellulaire et Biodiversité des Protozoaires Parasites", Laboratoire de Parasitologie-Mycologie, UFR Médecine, 163 Rue Auguste Broussonet, 34090 Montpellier, France
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Montpellier, France
| | - Christine Blaineau
- CNRS/Université Montpellier I FRE 3013 "Biologie Moléculaire, Biologie Cellulaire et Biodiversité des Protozoaires Parasites", Laboratoire de Parasitologie-Mycologie, UFR Médecine, 163 Rue Auguste Broussonet, 34090 Montpellier, France
| | - Sabrina Meghamla
- CNRS/Université Montpellier I FRE 3013 "Biologie Moléculaire, Biologie Cellulaire et Biodiversité des Protozoaires Parasites", Laboratoire de Parasitologie-Mycologie, UFR Médecine, 163 Rue Auguste Broussonet, 34090 Montpellier, France
| | - Lucien Crobu
- CNRS/Université Montpellier I FRE 3013 "Biologie Moléculaire, Biologie Cellulaire et Biodiversité des Protozoaires Parasites", Laboratoire de Parasitologie-Mycologie, UFR Médecine, 163 Rue Auguste Broussonet, 34090 Montpellier, France
| | - Michel Pagès
- CNRS/Université Montpellier I FRE 3013 "Biologie Moléculaire, Biologie Cellulaire et Biodiversité des Protozoaires Parasites", Laboratoire de Parasitologie-Mycologie, UFR Médecine, 163 Rue Auguste Broussonet, 34090 Montpellier, France
| | - Patrick Bastien
- CNRS/Université Montpellier I FRE 3013 "Biologie Moléculaire, Biologie Cellulaire et Biodiversité des Protozoaires Parasites", Laboratoire de Parasitologie-Mycologie, UFR Médecine, 163 Rue Auguste Broussonet, 34090 Montpellier, France
| |
Collapse
|
9
|
Casagrande L, Ruiz JC, Beverley SM, Cruz AK. Identification of a DNA fragment that increases mitotic stability of episomal linear DNAs in Leishmania major. Int J Parasitol 2006; 35:973-80. [PMID: 15996670 DOI: 10.1016/j.ijpara.2005.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 04/07/2005] [Accepted: 04/26/2005] [Indexed: 11/23/2022]
Abstract
The centromere is a specialized region of eukaryotic chromosomes, the site of kinetochore formation, spindle attachment and regulation of chromosome segregation during mitotic and meiotic cell divisions. To identify sequences which increase mitotic stability and/or act as potential centromeres in Leishmania major, we first generated libraries of Leishmania linear artificial chromosomes (LACs) bearing 30 kb inserts of randomly selected genomic DNAs. These were introduced into parasites, and then their stability was assessed following a period of 10 passages of growth in the absence of selective pressure. Approximately 80% of the 108 transfectants tested lost their LACs promptly and only 20% of the recombinants were retained; of these six showed strong but partial stability (maintained in 30-46% of cells). Mapping and sequencing of one clone (cSC10), which confers the highest degree of maintenance, revealed the presence of a sequence that was found within another stable episome, and which is dispersed in the genome of L. major. The implications of these data to the possible mechanisms of chromosomal maintenance are discussed.
Collapse
Affiliation(s)
- Liane Casagrande
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, 14049-900 Ribeirão Preto, SP, Brazil
| | | | | | | |
Collapse
|
10
|
Ginger ML. Trypanosomatid Biology and Euglenozoan Evolution: New Insights and Shifting Paradigms Revealed through Genome Sequencing. Protist 2005; 156:377-92. [PMID: 16310743 DOI: 10.1016/j.protis.2005.10.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Michael L Ginger
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| |
Collapse
|
11
|
Obado SO, Taylor MC, Wilkinson SR, Bromley EV, Kelly JM. Functional mapping of a trypanosome centromere by chromosome fragmentation identifies a 16-kb GC-rich transcriptional "strand-switch" domain as a major feature. Genome Res 2005; 15:36-43. [PMID: 15632088 PMCID: PMC540271 DOI: 10.1101/gr.2895105] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2004] [Accepted: 10/21/2004] [Indexed: 11/25/2022]
Abstract
Trypanosomatids are an ancient family that diverged from the main eukaryotic lineage early in evolution, which display several unique features of gene organization and expression. Although genome sequencing is now complete, the nature of centromeres in these and other parasitic protozoa has not been resolved. Here, we report the functional mapping of a centromere in the American trypanosome, Trypanosoma cruzi, a parasite with an unusual mechanism of genetic exchange that involves the generation of aneuploidy by nuclear hybridization. Using a telomere-associated chromosome fragmentation approach, we show that the region required for the mitotic stability of chromosome 3 encompasses a transcriptional "strand-switch" domain constituted by a 16-kb GC-rich island. The domain contains several degenerate retrotransposon-like insertions, but atypically, lacks the arrays of satellite repeats normally associated with centromeric regions. This unusual type of organization may represent a paradigm for centromeres in T. cruzi and other primitive eukaryotes.
Collapse
Affiliation(s)
- Samson O Obado
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | | | | | | | | |
Collapse
|
12
|
Lowell JE, Cross GAM. A variant histone H3 is enriched at telomeres in Trypanosoma brucei. J Cell Sci 2004; 117:5937-47. [PMID: 15522895 DOI: 10.1242/jcs.01515] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Variant histones play critical roles in transcriptional activation and repression, DNA repair and chromosome segregation. We have identified HTV, a single-copy gene in Trypanosoma brucei encoding a variant form of histone H3 (H3V). H3V is present at discrete nuclear foci that shift over the course of the cell cycle and associate with the mitotic spindle, a pattern of localization reminiscent of that described previously for both mini-chromosomes and telomeres. By combining fluorescence in situ hybridization with indirect immunofluorescence, we confirmed that the H3V foci overlap with a 177-bp repetitive sequence element found predominantly in mini-chromosomes, as well as with the TTAGGG repeats that compose telomeres. Chromatin immunoprecipitation studies, however, reveal that only the telomeric repeat DNA is substantially enriched with H3V. HTV is not essential for viability, mini-chromosome segregation, telomere maintenance or transcriptional silencing at the telomere-proximal expression sites from which bloodstream-form T. brucei controls antigenic variation. We propose that H3V represents a novel class of histone H3 variant, a finding that has evolutionary implications.
Collapse
Affiliation(s)
- Joanna E Lowell
- Laboratory of Molecular Parasitology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | | |
Collapse
|
13
|
Ghedin E, Bringaud F, Peterson J, Myler P, Berriman M, Ivens A, Andersson B, Bontempi E, Eisen J, Angiuoli S, Wanless D, Von Arx A, Murphy L, Lennard N, Salzberg S, Adams MD, White O, Hall N, Stuart K, Fraser CM, El-Sayed NMA. Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol 2004; 134:183-91. [PMID: 15003838 DOI: 10.1016/j.molbiopara.2003.11.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Accepted: 11/12/2003] [Indexed: 10/26/2022]
Abstract
The trypanosomatid protozoa Trypanosoma brucei, Trypanosoma cruzi and Leishmania major are related human pathogens that cause markedly distinct diseases. Using information from genome sequencing projects currently underway, we have compared the sequences of large chromosomal fragments from each species. Despite high levels of divergence at the sequence level, these three species exhibit a striking conservation of gene order, suggesting that selection has maintained gene order among the trypanosomatids over hundreds of millions of years of evolution. The few sites of genome rearrangement between these species are marked by the presence of retrotransposon-like elements, suggesting that retrotransposons may have played an important role in shaping trypanosomatid genome organization. A degenerate retroelement was identified in L. major by examining the regions near breakage points of the synteny. This is the first such element found in L. major suggesting that retroelements were found in the common ancestor of all three species.
Collapse
Affiliation(s)
- Elodie Ghedin
- Parasity Genomics, The Institute for Genomics Research, 9712 Medical Center Dr. Rockville, MD 20850, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Wickstead B, Ersfeld K, Gull K. The small chromosomes of Trypanosoma brucei involved in antigenic variation are constructed around repetitive palindromes. Genome Res 2004; 14:1014-24. [PMID: 15173109 PMCID: PMC419779 DOI: 10.1101/gr.2227704] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Accepted: 02/12/2004] [Indexed: 01/09/2023]
Abstract
Most eukaryotic genomes contain large regions of satellite DNA. These arrays are often associated with essential chromosomal functions, but remain largely absent from genome projects because of difficulties in cloning and sequence assembly. The numerous small chromosomes of the parasite Trypanosoma brucei fall into this category, yet are critical to understanding the genome because of their role in antigenic variation. Their relatively small size, however, makes them particularly amenable to physical mapping. We have produced fine-resolution maps of 17 complete minichromosomes and partial maps of two larger intermediate-sized chromosomes. This revealed a canonical structure shared by both chromosomal classes based around a large central core of 177-bp repeats. Around the core are variable-length genic regions, the lengths of which define chromosomal class. We show the core region to be a repetitive palindrome with a single inversion point common to all the chromosomes of both classes, suggesting a mechanism of genesis for these chromosomes. Moreover, palindromy appears to be a feature of (peri)centromeres in other species that can be easily overlooked. We propose that sequence inversion is one of the higher-order sequence motifs that confer chromosomal stability.
Collapse
Affiliation(s)
- Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom
| | | | | |
Collapse
|
15
|
Wickstead B, Ersfeld K, Gull K. Repetitive elements in genomes of parasitic protozoa. Microbiol Mol Biol Rev 2003; 67:360-75, table of contents. [PMID: 12966140 PMCID: PMC193867 DOI: 10.1128/mmbr.67.3.360-375.2003] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five medically important species with ongoing or completed genome sequencing projects: Plasmodium falciparum, Leishmania major, Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia. These organisms are used to illustrate five thematic classes of repeats with different structures and genomic locations. We discuss how these repeat classes may interact with parasitic life-style and also how they can be used as experimental tools. The story which emerges is one of opportunism and upheaval which have been employed to add genetic diversity and genomic flexibility.
Collapse
Affiliation(s)
- Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | | | | |
Collapse
|
16
|
Worthey EA, Martinez-Calvillo S, Schnaufer A, Aggarwal G, Cawthra J, Fazelinia G, Fong C, Fu G, Hassebrock M, Hixson G, Ivens AC, Kiser P, Marsolini F, Rickel E, Rickell E, Salavati R, Sisk E, Sunkin SM, Stuart KD, Myler PJ. Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene. Nucleic Acids Res 2003; 31:4201-10. [PMID: 12853638 PMCID: PMC167632 DOI: 10.1093/nar/gkg469] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Leishmania parasites (order Kinetoplastida, family Trypanosomatidae) cause a spectrum of human diseases ranging from asymptomatic to lethal. The approximately 33.6 Mb genome is distributed among 36 chromosome pairs that range in size from approximately 0.3 to 2.8 Mb. The complete nucleotide sequence of Leishmania major Friedlin chromosome 1 revealed 79 protein-coding genes organized into two divergent polycistronic gene clusters with the mRNAs transcribed towards the telomeres. We report here the complete nucleotide sequence of chromosome 3 (384 518 bp) and an analysis revealing 95 putative protein-coding ORFs. The ORFs are primarily organized into two large convergent polycistronic gene clusters (i.e. transcribed from the telomeres). In addition, a single gene at the left end is transcribed divergently towards the telomere, and a tRNA gene separates the two convergent gene clusters. Numerous genes have been identified, including those for metabolic enzymes, kinases, transporters, ribosomal proteins, spliceosome components, helicases, an RNA-binding protein and a DNA primase subunit.
Collapse
Affiliation(s)
- E A Worthey
- Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109-1651, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Dubessay P, Ravel C, Bastien P, Crobu L, Dedet JP, Pagès M, Blaineau C. The switch region on Leishmania major chromosome 1 is not required for mitotic stability or gene expression, but appears to be essential. Nucleic Acids Res 2002; 30:3692-7. [PMID: 12202753 PMCID: PMC137432 DOI: 10.1093/nar/gkf510] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Leishmania genome project reference strain, Leishmania major Friedlin, is trisomic for chromosome 1. The complete sequence of this chromosome has revealed that the genes are grouped into two large clusters of the polycistronic type, each borne by one DNA strand and located on each side of a 1.6-kb sequence often termed the switch region. Several hypotheses concerning the role of this switch region have been put forward (region of initiation of transcription for both gene clusters, origin of replication or centromeric sequence). In the present study, we have deleted this region on the three copies of chromosome 1 by sequential targeted replacements. The absence of the switch region did not alter the mitotic stability of the three deleted chromosomes. This region therefore does not appear necessary for chromosomal replication or segregation. However, during the third targeting round, which aimed at knocking out the last switch region, a fourth copy of chromosome 1 that retained this region appeared in all clones analysed. This suggests that the persistence of this switch region is necessary for parasite survival. We then showed that the presence/absence of the switch region did not act upon the expression of a resistance marker gene inserted beforehand into the left gene cluster of the same chromosomal molecule. This result suggests that the presence of this 1.6-kb sequence is not necessary for the expression of all genes on chromosome 1.
Collapse
Affiliation(s)
- Pascal Dubessay
- CNRS UMR5093 'Génome et Biologie Moléculaire des Protozoaires Parasites', Laboratoire de Parasitologie-Mycologie, Faculté de Médecine, 163 Rue Auguste Broussonet, F-34090 Montpellier, France
| | | | | | | | | | | | | |
Collapse
|