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Gao P, Zhao Y, Xu G, Zhong Y, Sun C. Unique features of conventional and nonconventional introns in Euglena gracilis. BMC Genomics 2024; 25:595. [PMID: 38872102 PMCID: PMC11170887 DOI: 10.1186/s12864-024-10495-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Nuclear introns in Euglenida have been understudied. This study aimed to investigate nuclear introns in Euglenida by identifying a large number of introns in Euglena gracilis (E. gracilis), including cis-spliced conventional and nonconventional introns, as well as trans-spliced outrons. We also examined the sequence characteristics of these introns. RESULTS A total of 28,337 introns and 11,921 outrons were identified. Conventional and nonconventional introns have distinct splice site features; the former harbour canonical GT/C-AG splice sites, whereas the latter are capable of forming structured motifs with their terminal sequences. We observed that short introns had a preference for canonical GT-AG introns. Notably, conventional introns and outrons in E. gracilis exhibited a distinct cytidine-rich polypyrimidine tract, in contrast to the thymidine-rich tracts observed in other organisms. Furthermore, the SL-RNAs in E. gracilis, as well as in other trans-splicing species, can form a recently discovered motif called the extended U6/5' ss duplex with the respective U6s. We also describe a novel type of alternative splicing pattern in E. gracilis. The tandem repeat sequences of introns in this protist were determined, and their contents were comparable to those in humans. CONCLUSIONS Our findings highlight the unique features of E. gracilis introns and provide insights into the splicing mechanism of these introns, as well as the genomics and evolution of Euglenida.
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Affiliation(s)
- Pingwei Gao
- Scientific Research Center, Chengdu Medical College, Chengdu, 610500, China
| | - Yali Zhao
- Scientific Research Center, Chengdu Medical College, Chengdu, 610500, China
| | - Guangjie Xu
- Scientific Research Center, Chengdu Medical College, Chengdu, 610500, China
| | - Yujie Zhong
- Clinical Laboratory Department, Zigong Hospital of Women's and Children's Healthcare, Zigong, 643002, China.
| | - Chengfu Sun
- Scientific Research Center, Chengdu Medical College, Chengdu, 610500, China.
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2
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Soysa R, Tran KD, Ullman B, Yates PA. Integrating ribosomal promoter vectors that offer a choice of constitutive expression profiles in Leishmania donovani. Mol Biochem Parasitol 2016; 204:89-92. [PMID: 26844641 DOI: 10.1016/j.molbiopara.2016.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 01/05/2016] [Accepted: 01/28/2016] [Indexed: 12/17/2022]
Abstract
We have designed a novel series of integrating ribosomal RNA promoter vectors with five incrementally different constitutive expression profiles, covering a 250-fold range. Differential expression was achieved by placing different combinations of synthetic or leishmanial DNA sequences upstream and downstream of the transgene coding sequence in order to modulate pre-mRNA processing efficiency and mRNA stability, respectively. All of the vectors have extensive multiple cloning sites, and versions are available for producing N- or C- terminal GFP fusions at each of the possible relative expression levels. In addition, the modular configuration of the vectors allows drug resistance cassettes and other components to be readily exchanged. In toto, these vectors should be useful additions to the toolkit available for molecular and genetic studies of Leishmania donovani.
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Affiliation(s)
- Radika Soysa
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Khoa D Tran
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Buddy Ullman
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A Yates
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA.
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Dillon LAL, Okrah K, Hughitt VK, Suresh R, Li Y, Fernandes MC, Belew AT, Corrada Bravo H, Mosser DM, El-Sayed NM. Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation. Nucleic Acids Res 2015; 43:6799-813. [PMID: 26150419 PMCID: PMC4538839 DOI: 10.1093/nar/gkv656] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Protozoan parasites of the genus Leishmania are the etiological agents of leishmaniasis, a group of diseases with a worldwide incidence of 0.9–1.6 million cases per year. We used RNA-seq to conduct a high-resolution transcriptomic analysis of the global changes in gene expression and RNA processing events that occur as L. major transforms from non-infective procyclic promastigotes to infective metacyclic promastigotes. Careful statistical analysis across multiple biological replicates and the removal of batch effects provided a high quality framework for comprehensively analyzing differential gene expression and transcriptome remodeling in this pathogen as it acquires its infectivity. We also identified precise 5′ and 3′ UTR boundaries for a majority of Leishmania genes and detected widespread alternative trans-splicing and polyadenylation. An investigation of possible correlations between stage-specific preferential trans-splicing or polyadenylation sites and differentially expressed genes revealed a lack of systematic association, establishing that differences in expression levels cannot be attributed to stage-regulated alternative RNA processing. Our findings build on and improve existing expression datasets and provide a substantially more detailed view of L. major biology that will inform the field and potentially provide a stronger basis for drug discovery and vaccine development efforts.
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Affiliation(s)
- Laura A L Dillon
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Kwame Okrah
- Department of Mathematics, University of Maryland, College Park, MD 20742, USA
| | - V Keith Hughitt
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Rahul Suresh
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA
| | - Yuan Li
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Maria Cecilia Fernandes
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - A Trey Belew
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
| | - Hector Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - David M Mosser
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA
| | - Najib M El-Sayed
- Department of Cell Biology and Molecular Genetics, 3128 Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
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Rastrojo A, Carrasco-Ramiro F, Martín D, Crespillo A, Reguera RM, Aguado B, Requena JM. The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq. BMC Genomics 2013; 14:223. [PMID: 23557257 PMCID: PMC3637525 DOI: 10.1186/1471-2164-14-223] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 02/25/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the genome sequence of the protozoan parasite Leishmania major was determined several years ago, the knowledge of its transcriptome was incomplete, both regarding the real number of genes and their primary structure. RESULTS Here, we describe the first comprehensive transcriptome analysis of a parasite from the genus Leishmania. Using high-throughput RNA sequencing (RNA-seq), a total of 10285 transcripts were identified, of which 1884 were considered novel, as they did not match previously annotated genes. In addition, our data indicate that current annotations should be modified for many of the genes. The detailed analysis of the transcript processing sites revealed extensive heterogeneity in the spliced leader (SL) and polyadenylation addition sites. As a result, around 50% of the genes presented multiple transcripts differing in the length of the UTRs, sometimes in the order of hundreds of nucleotides. This transcript heterogeneity could provide an additional source for regulation as the different sizes of UTRs could modify RNA stability and/or influence the efficiency of RNA translation. In addition, for the first time for the Leishmania major promastigote stage, we are providing relative expression transcript levels. CONCLUSIONS This study provides a concise view of the global transcriptome of the L. major promastigote stage, providing the basis for future comparative analysis with other development stages or other Leishmania species.
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Affiliation(s)
- Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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Gerald NJ, Coppens I, Dwyer DM. Molecular characterization and expression of a novel kinesin which localizes with the kinetoplast in the human pathogen,Leishmania donovani. ACTA ACUST UNITED AC 2008; 65:269-80. [DOI: 10.1002/cm.20259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Smith M, Blanchette M, Papadopoulou B. Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania. BMC Bioinformatics 2008; 9:158. [PMID: 18366710 PMCID: PMC2335281 DOI: 10.1186/1471-2105-9-158] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 03/20/2008] [Indexed: 11/23/2022] Open
Abstract
Background Leishmania and other members of the Trypanosomatidae family diverged early on in eukaryotic evolution and consequently display unique cellular properties. Their apparent lack of transcriptional regulation is compensated by complex post-transcriptional control mechanisms, including the processing of polycistronic transcripts by means of coupled trans-splicing and polyadenylation. Trans-splicing signals are often U-rich polypyrimidine (poly(Y)) tracts, which precede AG splice acceptor sites. However, as opposed to higher eukaryotes there is no consensus polyadenylation signal in trypanosomatid mRNAs. Results We refined a previously reported method to target 5' splice junctions by incorporating the pyrimidine content of query sequences into a scoring function. We also investigated a novel approach for predicting polyadenylation (poly(A)) sites in-silico, by comparing query sequences to polyadenylated expressed sequence tags (ESTs) using position-specific scanning matrices (PSSMs). An additional analysis of the distribution of putative splice junction to poly(A) distances helped to increase prediction rates by limiting the scanning range. These methods were able to simplify splice junction prediction without loss of precision and to increase polyadenylation site prediction from 22% to 47% within 100 nucleotides. Conclusion We propose a simplified trans-splicing prediction tool and a novel poly(A) prediction tool based on comparative sequence analysis. We discuss the impact of certain regions surrounding the poly(A) sites on prediction rates and contemplate correlating biological mechanisms. This work aims to sharpen the identification of potentially functional untranslated regions (UTRs) in a large-scale, comparative genomics framework.
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Affiliation(s)
- Martin Smith
- Research Centre in Infectious Diseases, CHUL Research Centre, 2705 Laurier Blvd,, Quebec, QC G1V 4G2, Canada.
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Lukes J, Paris Z, Regmi S, Breitling R, Mureev S, Kushnir S, Pyatkov K, Jirků M, Alexandrov KA. Translational initiation in Leishmania tarentolae and Phytomonas serpens (Kinetoplastida) is strongly influenced by pre-ATG triplet and its 5' sequence context. Mol Biochem Parasitol 2006; 148:125-32. [PMID: 16644031 DOI: 10.1016/j.molbiopara.2006.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 03/13/2006] [Accepted: 03/17/2006] [Indexed: 10/24/2022]
Abstract
To investigate the influence of sequence context of translation initiation codon on translation efficiency in Kinetoplastida, we constructed a library of expression plasmids randomized in the three nucleotides prefacing ATG of a reporter gene encoding enhanced green fluorescent protein (EGFP). All 64 possible combinations of pre-ATG triplets were individually stably integrated into the rDNA locus of Leishmania tarentolae and the resulting cell lines were assessed for EGFP expression. The expression levels were quantified directly by measuring the fluorescence of EGFP protein in living cells and confirmed by Western blotting. We observed a strong influence of the pre-ATG triplet on the level of protein expression over a 20-fold range. To understand the degree of evolutionary conservation of the observed effect, we transformed Phytomonas serpens, a trypanosomatid parasite of plants, with a subset of the constructs. The pattern of translational efficiency mediated by individual pre-ATG triplets in this species was similar to that observed in L. tarentolae. However, the pattern of translational efficiency of two other proteins (red fluorescent protein and tetracycline repressor) containing selected pre-ATG triplets did not correlate with either EGFP or each other. Thus, we conclude that a conserved mechanism of translation initiation site selection exists in kinetoplastids that is strongly influenced not only by the pre-ATG sequences but also by the coding region of the gene.
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Affiliation(s)
- Julius Lukes
- Institute of Parasitology, Czech Academy of Sciences and Faculty of Biology, University of South Bohemia, Ceské Budejovice, Czech Republic.
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Martínez-Calvillo S, Stuart K, Myler PJ. Ploidy changes associated with disruption of two adjacent genes on Leishmania major chromosome 1. Int J Parasitol 2005; 35:419-29. [PMID: 15777918 DOI: 10.1016/j.ijpara.2004.12.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 12/24/2004] [Accepted: 12/24/2004] [Indexed: 11/29/2022]
Abstract
Leishmania major Friedlin (LmjF) is a kinetoplastid protozoan whose genomic sequence has been recently elucidated. About 60% of the identified genes do not have a known function, and many are trypanosomatid-specific. Here we characterise two adjacent genes from LmjF chromosome 1 (chr1): LmjF01.0750, which encodes a predicted protein with a serine/threonine protein kinase motif and LmjF01.0760, which encodes a product with no similarity to other known proteins. Orthologues of both genes are present in Trypanosoma cruzi, but neither occur in Trypanosoma brucei. We have mapped polyadenylation and spliced-leader acceptor sites for both genes, and show that they differ between Leishmania species. Attempts to generate null mutants of LmjF01.0750 by homologous recombination were unsuccessful and led to the apparent triploidy of the entire genome, suggesting that it is an essential gene. Interestingly, at least two copies of LmjF01.0750 are required for cell survival. Further evidence of genome plasticity in Leishmania was provided by changes in chr1 copy number that occurred during in vitro growth of wild-type LmjF promastigotes and following replacement of a single copy of LmjF01.0760.
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Campbell K, Popov V, Soong L. Identification and molecular characterization of a gene encoding a protective Leishmania amazonensis Trp-Asp (WD) protein. Infect Immun 2004; 72:2194-202. [PMID: 15039343 PMCID: PMC375213 DOI: 10.1128/iai.72.4.2194-2202.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2003] [Revised: 12/01/2003] [Accepted: 12/31/2003] [Indexed: 11/20/2022] Open
Abstract
Several Leishmania proteins have been identified and characterized in pursuit of understanding pathogenesis and protection in cutaneous leishmaniasis. In the present study, we utilized sera from infected BALB/c mice to screen a Leishmania amazonensis amastigote cDNA expression library and obtained the full-length gene that encodes a novel Trp-Asp (WD) protein designated LAWD (for Leishmania antigenic WD protein). The WD family of proteins mediates protein-protein interactions and coordinates the formation of protein complexes. The single-copy LAWD gene is transcribed as a approximately 3.1-kb mRNA in both promastigotes and amastigotes, with homologues being detected in several other Leishmania species. Immunoelectron microscopy revealed a predominant localization of the LAWD protein in the flagellar pocket. Analyses of sera from human patients with cutaneous and mucocutaneous leishmaniasis indicated that these individuals mounted significant humoral responses against LAWD. Given that recombinant LAWD protein elicited the production of high levels of gamma interferon, but no detectable levels of interleukin-10 (IL-10), in CD4(+) cells of L. amazonensis-infected mice, we further examined whether LAWD could elicit protective immunity. DNA vaccination with the LAWD and IL-12 genes significantly delayed lesion development, which correlated with a dramatic reduction in parasite burdens. Thus, we have successfully identified a promising vaccine candidate and antigenic vehicle to aid in the dissection of the complicated pathogenic immune response of L. amazonensis.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Protozoan/blood
- Antibodies, Protozoan/immunology
- Antigens, Protozoan/administration & dosage
- Antigens, Protozoan/chemistry
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- Aspartic Acid
- CD4-Positive T-Lymphocytes/immunology
- Cricetinae
- Female
- Humans
- Immunization
- Leishmania/genetics
- Leishmania/immunology
- Leishmania/metabolism
- Leishmaniasis, Cutaneous/immunology
- Leishmaniasis, Cutaneous/parasitology
- Mesocricetus
- Mice
- Mice, Inbred BALB C
- Molecular Sequence Data
- Protozoan Proteins/administration & dosage
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/immunology
- Protozoan Vaccines/administration & dosage
- Protozoan Vaccines/immunology
- Recombinant Proteins/administration & dosage
- Recombinant Proteins/immunology
- Sequence Analysis, DNA
- Tryptophan
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Affiliation(s)
- Kimberly Campbell
- Department of Microbiology and Immunology, Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas 77555-1070, USA
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