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Camacho E, González-de la Fuente S, Solana JC, Rastrojo A, Carrasco-Ramiro F, Requena JM, Aguado B. Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain. Genes (Basel) 2021; 12:genes12091359. [PMID: 34573340 PMCID: PMC8468144 DOI: 10.3390/genes12091359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.
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Bel Hadj Ali I, Chouaieb H, Saadi Ben Aoun Y, Harigua-Souiai E, Souguir H, Yaacoub A, El Dbouni O, Harrat Z, Mukhtar MM, Ben Said M, Haddad N, Fathallah-Mili A, Guizani I. Dipeptidyl peptidase III as a DNA marker to investigate epidemiology and taxonomy of Old World Leishmania species. PLoS Negl Trop Dis 2021; 15:e0009530. [PMID: 34310607 PMCID: PMC8341715 DOI: 10.1371/journal.pntd.0009530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 08/05/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Dipeptidyl peptidase III (DPPIII) member of M49 peptidase family is a zinc-dependent metallopeptidase that cleaves dipeptides sequentially from the N-terminus of its substrates. In Leishmania, DPPIII, was reported with other peptidases to play a significant role in parasites' growth and survival. In a previous study, we used a coding sequence annotated as DPPIII to develop and evaluate a PCR assay that is specific to dermotropic Old World (OW) Leishmania species. Thus, our objective was to further assess use of this gene for Leishmania species identification and for phylogeny, and thus for diagnostic and molecular epidemiology studies of Old World Leishmania species. METHODOLOGY Orthologous DDPIII genes were searched in all Leishmania genomes and aligned to design PCR primers and identify relevant restriction enzymes. A PCR assays was developed and seventy-two Leishmania fragment sequences were analyzed using MEGA X genetics software to infer evolution and phylogenetic relationships of studied species and strains. A PCR-RFLP scheme was also designed and tested on 58 OW Leishmania strains belonging to 8 Leishmania species and evaluated on 75 human clinical skin samples. FINDINGS Sequence analysis showed 478 variable sites (302 being parsimony informative). Test of natural selection (dN-dS) (-0.164, SE = 0.013) inferred a negative selection, characteristic of essential genes, corroborating the DPPIII importance for parasite survival. Inter- and intra-specific genetic diversity was used to develop universal amplification of a 662bp fragment. Sequence analyses and phylogenies confirmed occurrence of 6 clusters congruent to L. major, L. tropica, L. aethiopica, L. arabica, L. turanica, L. tarentolae species, and one to the L. infantum and L. donovani species complex. A PCR-RFLP algorithm for Leishmania species identification was designed using double digestions with HaeIII and KpnI and with SacI and PvuII endonucleases. Overall, this PCR-RFLP yielded distinct profiles for each of the species L. major, L. tropica, L. aethiopica, L. arabica and L. turanica and the L. (Sauroleishmania) L. tarentolae. The species L. donovani, and L. infantum shared the same profile except for strains of Indian origin. When tested on clinical samples, the DPPIII PCR showed sensitivities of 82.22% when compared to direct examination and was able to identify 84.78% of the positive samples. CONCLUSION The study demonstrates that DPPIII gene is suitable to detect and identify Leishmania species and to complement other molecular methods for leishmaniases diagnosis and epidemiology. Thus, it can contribute to evidence-based disease control and surveillance.
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Affiliation(s)
- Insaf Bel Hadj Ali
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
| | - Hamed Chouaieb
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
- Service de parasitologie, EPS Farhat Hached, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Yusr Saadi Ben Aoun
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
| | - Emna Harigua-Souiai
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
| | - Hejer Souguir
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
| | - Alia Yaacoub
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
- Service de parasitologie, EPS Farhat Hached, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Oussaïma El Dbouni
- Department of Infectious Diseases, Rafik Hariri Hospital, Beirut, Lebanon
| | - Zoubir Harrat
- Laboratoire d’Eco-épidémiologie Parasitaire et Génétique des Populations, Institut Pasteur d’Algérie, Algiers, Algeria
| | | | - Moncef Ben Said
- Service de parasitologie, EPS Farhat Hached, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Nabil Haddad
- Laboratory of Immunology and Vector-Borne Diseases, Faculty of Public Health Lebanese University, Hadath, Lebanon
| | - Akila Fathallah-Mili
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
- Service de parasitologie, EPS Farhat Hached, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunisia
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Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation. Sci Rep 2019; 9:6127. [PMID: 30992521 PMCID: PMC6467909 DOI: 10.1038/s41598-019-42511-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/02/2019] [Indexed: 01/05/2023] Open
Abstract
Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L. donovani is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an L. donovani genome attained to date. The use of a combination of sequencing platforms enabled to assemble, without any sequence gap, the 36 chromosomes for this species. Additionally, based on this assembly and using RNA-seq reads derived from poly-A + RNA, the transcriptome for this species, not yet available, was delineated. Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes. After a complete annotation of the transcriptome, 2,410 novel transcripts were defined. Additionally, the relative expression for all transcripts present in the promastigote stage was determined. Events of cis-splicing have been documented to occur during the maturation of the transcripts derived from genes LDHU3_07.0430 and LDHU3_29.3990. The complete genome assembly and the availability of the gene models (including annotation of untranslated regions) are important pieces to understand how differential gene expression occurs in this pathogen, and to decipher phenotypic peculiarities like tissue tropism, clinical disease, and drug susceptibility.
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Akhoundi M, Downing T, Votýpka J, Kuhls K, Lukeš J, Cannet A, Ravel C, Marty P, Delaunay P, Kasbari M, Granouillac B, Gradoni L, Sereno D. Leishmania infections: Molecular targets and diagnosis. Mol Aspects Med 2017; 57:1-29. [PMID: 28159546 DOI: 10.1016/j.mam.2016.11.012] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/08/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022]
Abstract
Progress in the diagnosis of leishmaniases depends on the development of effective methods and the discovery of suitable biomarkers. We propose firstly an update classification of Leishmania species and their synonymies. We demonstrate a global map highlighting the geography of known endemic Leishmania species pathogenic to humans. We summarize a complete list of techniques currently in use and discuss their advantages and limitations. The available data highlights the benefits of molecular markers in terms of their sensitivity and specificity to quantify variation from the subgeneric level to species complexes, (sub) species within complexes, and individual populations and infection foci. Each DNA-based detection method is supplied with a comprehensive description of markers and primers and proposal for a classification based on the role of each target and primer in the detection, identification and quantification of leishmaniasis infection. We outline a genome-wide map of genes informative for diagnosis that have been used for Leishmania genotyping. Furthermore, we propose a classification method based on the suitability of well-studied molecular markers for typing the 21 known Leishmania species pathogenic to humans. This can be applied to newly discovered species and to hybrid strains originating from inter-species crosses. Developing more effective and sensitive diagnostic methods and biomarkers is vital for enhancing Leishmania infection control programs.
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Affiliation(s)
- Mohammad Akhoundi
- Service de Parasitologie-Mycologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France; MIVEGEC, UMR CNRS5290-IRD224-Université de Montpellier Centre IRD, Montpellier, France.
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Jan Votýpka
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Katrin Kuhls
- Division of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic; Canadian Institute for Advanced Research, Toronto, Canada
| | - Arnaud Cannet
- Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Université de Nice-Sophia Antipolis, Nice, France
| | - Christophe Ravel
- French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France
| | - Pierre Marty
- Service de Parasitologie-Mycologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France; Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Université de Nice-Sophia Antipolis, Nice, France
| | - Pascal Delaunay
- Service de Parasitologie-Mycologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France; Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Université de Nice-Sophia Antipolis, Nice, France; MIVEGEC, UMR CNRS5290-IRD224-Université de Montpellier Centre IRD, Montpellier, France
| | - Mohamed Kasbari
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, ANSES, Laboratoire de Santé Animale, Maisons-Alfort, Cedex, France
| | - Bruno Granouillac
- IRD/UMI 233, INSERM U1175, Montpellier University, Montpellier, France; MIVEGEC, UMR CNRS5290-IRD224-Université de Montpellier Centre IRD, Montpellier, France
| | - Luigi Gradoni
- Unit of Vector-borne Diseases and International Health, Istituto Superiore di Sanità, Rome, Italy
| | - Denis Sereno
- MIVEGEC, UMR CNRS5290-IRD224-Université de Montpellier Centre IRD, Montpellier, France; Intertryp UMR IRD177, Centre IRD de Montpellier, Montpellier, France
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Depledge DP, MacLean LM, Hodgkinson MR, Smith BA, Jackson AP, Ma S, Uliana SRB, Smith DF. Leishmania-specific surface antigens show sub-genus sequence variation and immune recognition. PLoS Negl Trop Dis 2010; 4:e829. [PMID: 20927190 PMCID: PMC2946902 DOI: 10.1371/journal.pntd.0000829] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 08/31/2010] [Indexed: 11/25/2022] Open
Abstract
Background A family of hydrophilic acylated surface (HASP) proteins, containing extensive and variant amino acid repeats, is expressed at the plasma membrane in infective extracellular (metacyclic) and intracellular (amastigote) stages of Old World Leishmania species. While HASPs are antigenic in the host and can induce protective immune responses, the biological functions of these Leishmania-specific proteins remain unresolved. Previous genome analysis has suggested that parasites of the sub-genus Leishmania (Viannia) have lost HASP genes from their genomes. Methods/Principal Findings We have used molecular and cellular methods to analyse HASP expression in New World Leishmania mexicana complex species and show that, unlike in L. major, these proteins are expressed predominantly following differentiation into amastigotes within macrophages. Further genome analysis has revealed that the L. (Viannia) species, L. (V.) braziliensis, does express HASP-like proteins of low amino acid similarity but with similar biochemical characteristics, from genes present on a region of chromosome 23 that is syntenic with the HASP/SHERP locus in Old World Leishmania species and the L. (L.) mexicana complex. A related gene is also present in Leptomonas seymouri and this may represent the ancestral copy of these Leishmania-genus specific sequences. The L. braziliensis HASP-like proteins (named the orthologous (o) HASPs) are predominantly expressed on the plasma membrane in amastigotes and are recognised by immune sera taken from 4 out of 6 leishmaniasis patients tested in an endemic region of Brazil. Analysis of the repetitive domains of the oHASPs has shown considerable genetic variation in parasite isolates taken from the same patients, suggesting that antigenic change may play a role in immune recognition of this protein family. Conclusions/Significance These findings confirm that antigenic hydrophilic acylated proteins are expressed from genes in the same chromosomal region in species across the genus Leishmania. These proteins are surface-exposed on amastigotes (although L. (L.) major parasites also express HASPB on the metacyclic plasma membrane). The central repetitive domains of the HASPs are highly variant in their amino acid sequences, both within and between species, consistent with a role in immune recognition in the host. Single-celled Leishmania parasites, transmitted by sand flies, infect humans and other mammals in many tropical and sub-tropical regions, giving rise to a spectrum of diseases called the leishmaniases. Species of parasite within the Leishmania genus can be divided into two groups (referred to as sub-genera) that are separated by up to 100 million years of evolution yet are highly related at the genome level. Our research is focused on identifying gene differences between these sub-genera that may identify proteins that impact on the transmission and pathogenicity of different Leishmania species. Here we report the presence of a highly-variant genomic locus (OHL) that was previously described as absent in parasites of the L. (Viannia) subgenus (on the basis of lack of key genes) but is present and well-characterised (as the LmcDNA16 locus) in all members of the alternative subgenus, L. (Leishmania). We demonstrate that the proteins encoded within the LmcDNA16 and OHL loci are similar in their structure and surface localisation in mammalian-infective amastigotes, despite significant differences in their DNA sequences. Most importantly, we demonstrate that the OHL locus proteins, like the HASP proteins from the LmcDNA16 locus, contain highly variable amino acid repeats that are antigenic in man and may therefore contribute to future vaccine development.
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Affiliation(s)
- Daniel P Depledge
- Centre for Immunology and Infection, Department of Biology, Hull York Medical School, University of York, York, United Kingdom
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Dávila López M, Martínez Guerra JJ, Samuelsson T. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. PLoS One 2010; 5:e10654. [PMID: 20498846 PMCID: PMC2871058 DOI: 10.1371/journal.pone.0010654] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 04/26/2010] [Indexed: 01/03/2023] Open
Abstract
The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.
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Affiliation(s)
- Marcela Dávila López
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
| | - Juan José Martínez Guerra
- Departmento de Química, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Aguascalientes, Mexico
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Göteborg, Sweden
- * E-mail:
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Folgueira C, Quijada L, Soto M, Abanades DR, Alonso C, Requena JM. The translational efficiencies of the two Leishmania infantum HSP70 mRNAs, differing in their 3'-untranslated regions, are affected by shifts in the temperature of growth through different mechanisms. J Biol Chem 2005; 280:35172-83. [PMID: 16105831 DOI: 10.1074/jbc.m505559200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Exposure of Leishmania promastigotes to the temperature of their mammalian hosts induces a typical heat-shock response. In Leishmania infantum, HSP70 is encoded by two types of genes that differ in their 3'-untranslated regions (3'-UTRs). Previously, we have shown that specific transcripts for each gene are present in promastigotes growing at normal temperature (26 degrees C), but only transcripts with 3'-UTR-type I (3'-UTRI) accumulate in a temperature-dependent manner. Here, we have investigated the translational efficiencies of both types of HSP70 transcripts at the different temperatures that the parasite encounters in the insect (26 degrees C, normal temperature) or in the mammalian host (heat-shock temperatures). Interestingly, 3'-UTRI-bearing transcripts (HSP70-I) were found associated with ribosomes in promastigotes at normal and heat-shock temperatures, whereas the HSP70-II transcripts appear to be preferentially translated at heat-shock temperatures but not at 26 degrees C. We have analyzed the function of these UTRs in the translational control by use of plasmid constructs in which the CAT reporter gene was flanked by UTRs of the HSP70 genes. Unexpectedly, it was found that CAT transcripts with 3'-UTRII bind to ribosomes at 26 degrees C, and, indeed, the CAT protein is synthesized. A valid conclusion of these experiments was that both types of 3'-UTRs are essential for translation of HSP70 mRNAs at heat shock temperatures, although the 3'-UTRII is more efficient during severe heat shock (39 degrees C). In addition, these results suggest that sequence region other than the 3'-UTR of HSP70-II gene is involved in the translational silent state of HSP70-II transcripts at 26 degrees C. Finally, a null mutant has been created by targeted disruption of both HSP70-II alleles. Remarkably, the deltaHSP70 mutant synthesizes HSP70 at a lower rate than the wild-type parasites. Overall, our data suggest that the biological function of the HSP70-II gene is to top up HSP70 levels under conditions of stress.
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Affiliation(s)
- Cristina Folgueira
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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