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Lajevardi MS, Taheri T, Gholami E, Seyed N, Rafati S. Structural analysis of PpSP15 and PsSP9 sand fly salivary proteins designed with a self-cleavable linker as a live vaccine candidate against cutaneous leishmaniasis. Parasit Vectors 2022; 15:377. [PMID: 36261836 PMCID: PMC9580450 DOI: 10.1186/s13071-022-05437-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background Leishmania parasites are deposited in the host through sand fly bites along with sand fly saliva. Therefore, salivary proteins are promising vaccine candidates for controlling leishmaniasis. Herein, two immunogenic salivary proteins, PpSP15 from Phlebotomus papatasi and PsSP9 from Phlebotomus sergenti, were selected as vaccine candidates to be delivered by live Leishmania tarentolae as vector. The stepwise in silico protocol advantaged in this study for multi-protein design in L. tarentolae is then described in detail. Methods All possible combinations of two salivary proteins, PpSP15 and PsSP9, with or without T2A peptide were designed at the mRNA and protein levels. Then, the best combination for the vaccine candidate was selected based on mRNA and protein stability along with peptide analysis. Results At the mRNA level, the most favored secondary structure was PpSP15-T2A-PsSP9. At the protein level, the refined three-dimensional models of all combinations were structurally valid; however, local quality estimation showed that the PpSp15-T2A-PsSP9 fusion had higher stability for each amino acid position, with low root-mean-square deviation (RMSD), compared with the original proteins. In silico evaluation confirmed the PpSP15-T2A-PsSP9 combination as a good Th1-polarizing candidate in terms of high IFN-γ production and low IL-10/TGF-β ratio in response to three consecutive immunizations. Potential protein expression was then confirmed by Western blotting. Conclusions The approach presented herein is among the first studies to have privileged protein homology modeling along with mRNA analysis for logical live vaccine design-coding multi-proteins. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05437-x.
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Affiliation(s)
- Mahya Sadat Lajevardi
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran.,Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Tahereh Taheri
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Gholami
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran
| | - Negar Seyed
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran.
| | - Sima Rafati
- Department of Immunotherapy and Leishmania Vaccine Research, Pasteur Institute of Iran, Tehran, Iran.
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Calvelo J, Juan H, Musto H, Koziol U, Iriarte A. SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem. BMC Bioinformatics 2020; 21:293. [PMID: 32640978 PMCID: PMC7346339 DOI: 10.1186/s12859-020-03610-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced. RESULTS In this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing. CONCLUSIONS SLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation.
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Affiliation(s)
- Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Hernán Juan
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Héctor Musto
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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Ling Z, Brockmöller T, Baldwin IT, Xu S. Evolution of Alternative Splicing in Eudicots. FRONTIERS IN PLANT SCIENCE 2019; 10:707. [PMID: 31244865 PMCID: PMC6581728 DOI: 10.3389/fpls.2019.00707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/13/2019] [Indexed: 05/30/2023]
Abstract
Alternative pre-mRNA splicing (AS) is prevalent in plants and is involved in many interactions between plants and environmental stresses. However, the patterns and underlying mechanisms of AS evolution in plants remain unclear. By analyzing the transcriptomes of four eudicot species, we revealed that the divergence of AS is largely due to the gains and losses of AS events among orthologous genes. Furthermore, based on a subset of AS, in which AS can be directly associated with specific transcripts, we found that AS that generates transcripts containing premature termination codons (PTC), are likely more conserved than those that generate non-PTC containing transcripts. This suggests that AS coupled with nonsense-mediated decay (NMD) might play an important role in affecting mRNA levels post-transcriptionally. To understand the mechanisms underlying the divergence of AS, we analyzed the key determinants of AS using a machine learning approach. We found that the presence/absence of alternative splice site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5' donor site and 3' acceptor site among the studied species, suggesting a relatively conserved AS mechanism. The comparative analysis further demonstrated that variations of the identified AS determinants significantly contributed to the AS divergence among closely related species in both Solanaceae and Brassicaceae taxa. Together, these results provide detailed insights into the evolution of AS in plants.
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Affiliation(s)
- Zhihao Ling
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Ian T. Baldwin
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Shuqing Xu
- Plant Adaptation-in-action Group, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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Radío S, Fort RS, Garat B, Sotelo-Silveira J, Smircich P. UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes. Front Genet 2018; 9:671. [PMID: 30619487 PMCID: PMC6305552 DOI: 10.3389/fgene.2018.00671] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/04/2018] [Indexed: 11/23/2022] Open
Abstract
Most signals involved in post-transcriptional regulatory networks are located in the untranslated regions (UTRs) of the mRNAs. Therefore, to deepen our understanding of gene expression regulation, delimitation of these regions with high accuracy is needed. The trypanosomatid lineage includes a variety of parasitic protozoans causing a significant worldwide burden on human health. Given their peculiar mechanisms of gene expression, these organisms depend on post-transcriptional regulation as the main level of gene expression control. In this context, the definition of the UTR regions becomes of key importance. We have developed UTR-mini-exon (UTRme), a graphical user interface (GUI) stand-alone application to identify and annotate 5′ and 3′ UTR regions in a highly accurate way. UTRme implements a multiple scoring system tailored to address the issue of false positive UTR assignment that frequently arise because of the characteristics of the intergenic regions. Even though it was developed for trypanosomatids, the tool can be used to predict 3′ sites in any eukaryote and 5′ UTRs in any organism where trans-splicing occurs (such as the model organism C. elegans). UTRme offers a way for non-bioinformaticians to precisely determine UTRs from transcriptomic data. The tool is freely available via the conda and github repositories.
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Affiliation(s)
- Santiago Radío
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, Uruguay.,Laboratory of Molecular Interactions, Facultad de Ciencias. Universidad de la República, Montevideo, Uruguay
| | - Rafael Sebastián Fort
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, Uruguay.,Laboratory of Molecular Interactions, Facultad de Ciencias. Universidad de la República, Montevideo, Uruguay
| | - Beatriz Garat
- Laboratory of Molecular Interactions, Facultad de Ciencias. Universidad de la República, Montevideo, Uruguay
| | - José Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, Uruguay.,Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Pablo Smircich
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, Uruguay.,Laboratory of Molecular Interactions, Facultad de Ciencias. Universidad de la República, Montevideo, Uruguay
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Abstract
The ciliate Oxytricha is a microbial eukaryote with two genomes, one of which experiences extensive genome remodeling during development. Each round of conjugation initiates a cascade of events that construct a transcriptionally active somatic genome from a scrambled germline genome, with considerable help from both long and small noncoding RNAs. This process of genome remodeling entails massive DNA deletion and reshuffling of remaining DNA segments to form functional genes from their interrupted and scrambled germline precursors. The use of Oxytricha as a model system provides an opportunity to study an exaggerated form of programmed genome rearrangement. Furthermore, studying the mechanisms that maintain nuclear dimorphism and mediate genome rearrangement has demonstrated a surprising plasticity and diversity of noncoding RNA pathways, with new roles that go beyond conventional gene silencing. Another aspect of ciliate genetics is their unorthodox patterns of RNA-mediated, epigenetic inheritance that rival Mendelian inheritance. This review takes the reader through the key experiments in a model eukaryote that led to fundamental discoveries in RNA biology and pushes the biological limits of DNA processing.
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SLaP mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes. Mol Biochem Parasitol 2014; 196:71-4. [PMID: 25111964 PMCID: PMC4222701 DOI: 10.1016/j.molbiopara.2014.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 11/24/2022]
Abstract
A web-server for identification of spliced-leader and polyadenylation addition sites. Fully automated site quantification and gene assignment. Multiple species within the Kinetoplastida.
The Kinetoplastida are a diverse and globally distributed class of free-living and parasitic single-celled eukaryotes that collectively cause a significant burden on human health and welfare. In kinetoplastids individual genes do not have promoters, but rather all genes are arranged downstream of a small number of RNA polymerase II transcription initiation sites and are thus transcribed in polycistronic gene clusters. Production of individual mRNAs from this continuous transcript occurs co-transcriptionally by trans-splicing of a ∼39 nucleotide capped RNA and subsequent polyadenylation of the upstream mRNA. SLaP mapper (Spliced-Leader and Polyadenylation mapper) is a fully automated web-service for identification, quantitation and gene-assignment of both spliced-leader and polyadenylation addition sites in Kinetoplastid genomes. SLaP mapper only requires raw read data from paired-end Illumina RNAseq and performs all read processing, mapping, quality control, quantification, and analysis in a fully automated pipeline. To provide usage examples and estimates of the quantity of sequence data required we use RNAseq obtained from two different library preparations from both Trypanosoma brucei and Leishmania mexicana to show the number of expected reads that are obtained from each preparation type. SLaP mapper is an easy to use, platform independent webserver that is freely available for use at http://www.stevekellylab.com/software/slap. Example files are provided on the website.
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Miranda A, Samudio F, Saldaña A, Castillo J, Brandão A, Calzada JE. The calmodulin intergenic spacer as molecular target for characterization of Leishmania species. Parasit Vectors 2014; 7:35. [PMID: 24438764 PMCID: PMC4021611 DOI: 10.1186/1756-3305-7-35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/14/2014] [Indexed: 11/18/2022] Open
Abstract
Background Human leishmaniasis is a neglected disease caused by parasites of the genus Leishmania. Clinical aspects of this disease can vary significantly, reflecting the wide range of parasites in the genus Leishmania. Knowing accurately the Leishmania species infecting humans is important for clinical case management and evaluation of epidemiological risk. Calmodulin is an essential gene in trypanosomatids that modulates the calcium metabolism in various cellular activities. Despite its strong conservation in trypanosomatids, it has been recently observed that its untranslated regions (UTR) diverge among species. Methods In this study we analyzed the sequences and the absolute dinucleotide frequency of the intergenic spacer of the calmodulin gene (containing both, 3′ and 5′UTR) in nine reference Leishmania species and ten clinical isolates obtained from patients with cutaneous leishmaniasis. Results We show that the short calmodulin intergenic spacers exhibit features that make them interesting for applications in molecular characterization and phylogenetic studies of Leishmania. Dendrograms based on sequence alignments and on the dinucleotide frequency indicate that this particular region of calmodulin gene might be useful for species typing between the Leishmania and Viannia subgenera. Conclusions Mutations and composition of the calmodulin intergenic spacer from Leishmania species might have taxonomic value as parameters to define if an isolate is identical to a certain species or belongs to one of the two current subgenera.
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Affiliation(s)
| | | | | | | | | | - Jose E Calzada
- Instituto Conmemorativo Gorgas de Estudios de Salud, Ciudad de Panamá, Panamá.
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8
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McLean TI. "Eco-omics": a review of the application of genomics, transcriptomics, and proteomics for the study of the ecology of harmful algae. MICROBIAL ECOLOGY 2013; 65:901-915. [PMID: 23553002 DOI: 10.1007/s00248-013-0220-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/14/2013] [Indexed: 06/02/2023]
Abstract
The implementation of molecular techniques has been widely adopted throughout the life sciences except in the marine sciences. The latter trend is quickly being reversed as even more cutting-edge molecular platforms, referred to collectively as 'omics-related technologies, are being used in a number of laboratories that study various aspects of life in the marine environment. This review provides a brief overview of just a few representative studies that have used genomics, transcriptomics, or proteomics approaches to deepen our understanding, specifically, about the underlying molecular biology of harmful algae. The examples of the studies described here are particularly relevant in showing how the information gleaned from these technologies can uncover the genetic capacity of harmful algal bloom-forming species, can generate new hypotheses about mechanistic relationships that bridge gene-environment interactions, and can impinge on our understanding surrounding the ecology of these organisms.
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Affiliation(s)
- T I McLean
- The Department of Biological Sciences, The University of Southern Mississippi, 118 College Drive #5018, Hattiesburg, MS 39406-0001, USA.
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9
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SL RNA Biogenesis in Kinetoplastids: A Long and Winding Road. RNA METABOLISM IN TRYPANOSOMES 2012. [DOI: 10.1007/978-3-642-28687-2_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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10
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Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation. PLoS One 2011; 6:e25666. [PMID: 21991330 PMCID: PMC3185004 DOI: 10.1371/journal.pone.0025666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 09/08/2011] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The rapid increase in the availability of genome information has created considerable demand for both comparative and ab initio predictive bioinformatic analyses. The biology laid bare in the genomes of many organisms is often novel, presenting new challenges for bioinformatic interrogation. A paradigm for this is the collected genomes of the kinetoplastid parasites, a group which includes Trypanosoma brucei the causative agent of human African trypanosomiasis. These genomes, though outwardly simple in organisation and gene content, have historically challenged many theories for gene expression regulation in eukaryotes. METHODOLOGY/PRINCIPLE FINDINGS Here we utilise a Bayesian approach to identify local changes in nucleotide composition in the genome of T. brucei. We show that there are several elements which are found at the starts and ends of multicopy gene arrays and that there are compositional elements that are common to all intergenic regions. We also show that there is a composition-inversion element that occurs at the position of the trans-splice site. CONCLUSIONS/SIGNIFICANCE The nature of the elements discovered reinforces the hypothesis that context dependant RNA secondary structure has an important influence on gene expression regulation in Trypanosoma brucei.
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Genomic organization of leishmania species. IRANIAN JOURNAL OF PARASITOLOGY 2011; 6:1-18. [PMID: 22347292 PMCID: PMC3279888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 07/18/2011] [Indexed: 10/31/2022]
Abstract
Leishmania is a protozoan parasite belonging to the family Trypanosomatidae, which is found among 88 different countries. The parasite lives as an amastigote in vertebrate macrophages and as a promastigote in the digestive tract of sand fly. It can be cultured in the laboratory using appropriate culture media. Although the sexual cycle of Leishmania has not been observed during the promastigote and amastigote stages, it has been reported by some researchers. Leishmania has eukaryotic cell organization. Cell culture is convenient and cost effective, and because posttranslational modifications are common processes in the cultured cells, the cells are used as hosts for preparing eukaryotic recombinant proteins for research. Several transcripts of rDNA in the Leishmania genome are suitable regions for conducting gene transfer. Old World Leishmania spp. has 36 chromosomes, while New World Leishmania spp. has 34 or 35 chromosomes. The genomic organization and parasitic characteristics have been investigated. Leishmania spp. has a unique genomic organization among eukaryotes; the genes do not have introns, and the chromosomes are smaller with larger numbers of genes confined to a smaller space within the nucleus. Leishmania spp. genes are organized on one or both DNA strands and are transcribed as polycistronic (prokaryotic-like) transcripts from undefined promoters. Regulation of gene expression in the members of Trypanosomatidae differs from that in other eukaryotes. The trans-splicing phenomenon is a necessary step for mRNA processing in lower eukaryotes and is observed in Leishmania spp. Another particular feature of RNA editing in Leishmania spp. is that mitochondrial genes encoding respiratory enzymes are edited and transcribed. This review will discuss the chromosomal and mitochondrial (kinetoplast) genomes of Leishmania spp. as well as the phenomenon of RNA editing in the kinetoplast genome.
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The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog 2010; 6:e1001090. [PMID: 20838601 PMCID: PMC2936537 DOI: 10.1371/journal.ppat.1001090] [Citation(s) in RCA: 225] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 08/06/2010] [Indexed: 12/30/2022] Open
Abstract
The genome of Trypanosoma brucei, the causative agent of African trypanosomiasis, was published five years ago, yet identification of all genes and their transcripts remains to be accomplished. Annotation is challenged by the organization of genes transcribed by RNA polymerase II (Pol II) into long unidirectional gene clusters with no knowledge of how transcription is initiated. Here we report a single-nucleotide resolution genomic map of the T. brucei transcriptome, adding 1,114 new transcripts, including 103 non-coding RNAs, confirming and correcting many of the annotated features and revealing an extensive heterogeneity of 5′ and 3′ ends. Some of the new transcripts encode polypeptides that are either conserved in T. cruzi and Leishmania major or were previously detected in mass spectrometry analyses. High-throughput RNA sequencing (RNA-Seq) was sensitive enough to detect transcripts at putative Pol II transcription initiation sites. Our results, as well as recent data from the literature, indicate that transcription initiation is not solely restricted to regions at the beginning of gene clusters, but may occur at internal sites. We also provide evidence that transcription at all putative initiation sites in T. brucei is bidirectional, a recently recognized fundamental property of eukaryotic promoters. Our results have implications for gene expression patterns in other important human pathogens with similar genome organization (Trypanosoma cruzi, Leishmania sp.) and revealed heterogeneity in pre-mRNA processing that could potentially contribute to the survival and success of the parasite population in the insect vector and the mammalian host. Identifying genes essential for survival in the host is fundamental to unraveling the biology of human pathogens and understanding mechanisms of pathogenesis. The protozoan parasite Trypanosoma brucei causes devastating diseases in humans and animals in sub-Saharan Africa, and the publication in 2005 of the genome sequence provided the first glance at the coding potential of this organism. Although at present there is a catalogue of predicted protein coding genes, the challenge remains to identify all authentic genes, including their boundaries. We used next generation RNA sequencing (RNA-Seq) to map transcribed regions and RNA polymerase II transcription initiation sites on a genome-wide scale. This approach allowed us to improve and correct the current annotation, to reveal a widespread heterogeneity of RNA processing sites (trans-splicing and polyadenylation) and to estimate that most genes are expressed at levels corresponding to 1 to 10 mRNAs per cell. Our data indicate that different transcript forms representing the same gene are present stochastically within the mRNA population. This unanticipated scenario may contribute to determining gene expression landscapes to adapt to different environments in the parasite life cycle.
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Paape D, Lippuner C, Schmid M, Ackermann R, Barrios-Llerena ME, Zimny-Arndt U, Brinkmann V, Arndt B, Pleissner KP, Jungblut PR, Aebischer T. Transgenic, fluorescent Leishmania mexicana allow direct analysis of the proteome of intracellular amastigotes. Mol Cell Proteomics 2008; 7:1688-701. [PMID: 18474515 DOI: 10.1074/mcp.m700343-mcp200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Investigating the proteome of intracellular pathogens is often hampered by inadequate methodologies to purify the pathogen free of host cell material. This has also precluded direct proteome analysis of the intracellular, amastigote form of Leishmania spp., protozoan parasites that cause a spectrum of diseases that affect some 12 million patients worldwide. Here a method is presented that combines classic, isopycnic density centrifugation with fluorescent particle sorting for purification by exploiting transgenic, fluorescent parasites to allow direct proteome analysis of the purified organisms. By this approach the proteome of intracellular Leishmania mexicana amastigotes was compared with that of extracellular promastigotes that are transmitted by insect vectors. In total, 509 different proteins were identified by mass spectrometry and database search. This number corresponds to approximately 6% of gene products predicted from the reference genome of Leishmania major. Intracellular amastigotes synthesized significantly more proteins with basic pI and showed a greater abundance of enzymes of fatty acid catabolism, which may reflect their living in acidic habitats and metabolic adaptation to nutrient availability, respectively. Bioinformatics analyses of the genes corresponding to the protein data sets produced clear evidence for skewed codon usage and translational bias in these organisms. Moreover analysis of the subset of genes whose products were more abundant in amastigotes revealed characteristic sequence motifs in 3'-untranslated regions that have been linked to translational control elements. This suggests that proteome data sets may be used to identify regulatory elements in mRNAs. Last but not least, at 6% coverage the proteome identified all vaccine antigens tested to date. Thus, the present data set provides a valuable resource for selection of candidate vaccine antigens.
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Affiliation(s)
- Daniel Paape
- Institute of Immunology and Infection Research, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom
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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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Developmental regulation of gene expression in trypanosomatid parasitic protozoa. Curr Opin Microbiol 2008; 10:569-77. [PMID: 18177626 DOI: 10.1016/j.mib.2007.10.001] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 10/02/2007] [Accepted: 10/03/2007] [Indexed: 12/21/2022]
Abstract
Kinetoplastids branched early from the eukaryotic lineage and include several parasitic protozoan species. Up to several hundred kinetoplastid genes are co-transcribed into polycistronic RNAs and individual mRNAs are resolved by coupled co-transcriptional trans-splicing of a universal splice-leader RNA (SL-RNA) and 3'-end maturation processes. Protein-coding genes lack RNA polymerase II promoters. Consequently, most of gene regulation in these organisms occurs post-transcriptionally. Over the last few years, many more genes that are regulated at the mRNA stability level and a few at the translation level have been reported. Almost all major trypanosome homologues of yeast/mammalian mRNA degradation enzymes have been functionally characterized and major pathways identified. Novel paradigms have also recently emerged: regulated post-transcriptional processing of cytoplasmic RNAs, SL-RNA transcriptional silencing-mediated global stress response, and Leishmania-specific large-scale modulation of post-transcriptional gene expression via inactive degenerated retroelements. Several of these developments have greatly benefited from the recently completed genomic sequences and functional genomic studies.
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Horn D. Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids. BMC Genomics 2008; 9:2. [PMID: 18173843 PMCID: PMC2217535 DOI: 10.1186/1471-2164-9-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 01/03/2008] [Indexed: 11/16/2022] Open
Abstract
Background Different proteins are required in widely different quantities to build a living cell. In most organisms, transcription control makes a major contribution to differential expression. This is not the case in trypanosomatids where most genes are transcribed at an equivalent rate within large polycistronic clusters. Thus, trypanosomatids must use post-transcriptional control mechanisms to balance gene expression requirements. Results Here, the evidence for translational selection, the enrichment of 'favoured' codons in more highly expressed genes, is explored. A set of highly expressed, tandem-repeated genes display codon bias in Trypanosoma cruzi, Trypanosoma brucei and Leishmania major. The tRNA complement reveals forty-five of the sixty-one possible anticodons indicating widespread use of 'wobble' tRNAs. Consistent with translational selection, cognate tRNA genes for favoured codons are over-represented. Importantly, codon usage (Codon Adaptation Index) correlates with predicted and observed expression level. In addition, relative codon bias is broadly conserved among syntenic genes from different trypanosomatids. Conclusion Synonymous codon bias is correlated with tRNA gene copy number and with protein expression level in trypanosomatids. Taken together, the results suggest that translational selection is the dominant mechanism underlying the control of differential protein expression in these organisms. The findings reveal how trypanosomatids may compensate for a paucity of canonical Pol II promoters and subsequent widespread constitutive RNA polymerase II transcription.
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Affiliation(s)
- David Horn
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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17
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Robertson HM, Navik JA, Walden KKO, Honegger HW. The bursicon gene in mosquitoes: an unusual example of mRNA trans-splicing. Genetics 2007; 176:1351-3. [PMID: 17435221 PMCID: PMC1894596 DOI: 10.1534/genetics.107.070938] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2007] [Accepted: 04/02/2007] [Indexed: 11/18/2022] Open
Abstract
The bursicon gene in Anopheles gambiae is encoded by two loci. Burs124 on chromosome arm 2L contains exons 1, 2, and 4, while burs3 on arm 2R contains exon 3. Exon 3 is efficiently spliced into position in the mature transcript. This unusual gene arrangement is ancient within mosquitoes, being shared by Aedes aegypti and Culex pipiens.
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Affiliation(s)
- Hugh M Robertson
- Department of Entomology, University of Illinois, 505 S. Goodwin Ave., Urbana, IL 61801, USA.
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18
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Brandão A. The untranslated regions of genes from Trypanosoma cruzi: perspectives for functional characterization of strains and isolates. Mem Inst Oswaldo Cruz 2007; 101:775-7. [PMID: 17160286 DOI: 10.1590/s0074-02762006000700011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 08/15/2006] [Indexed: 11/21/2022] Open
Abstract
The sequencing of Trypanosoma cruzi genome has been completed and a great deal of information is now available. However, the organization of protozoa genomes is somewhat elusive and much effort must be applied to reveal all the information coded in the nucleotide sequences. Among the DNA segments that needs further investigation are the untranslated regions of genes. Many of the T. cruzi genes that were revealed by the genome sequencing lack information about the untranslated regions. In this paper, some features of these untranslated segments as well as their applications in T. cruzi populations are discussed.
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Affiliation(s)
- Adeilton Brandão
- Departamento de Medicina Tropical, Instituto Oswaldo Cruz-Fiocruz, 21045-900 Rio de Janeiro, RJ, Brazil.
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19
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Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S. Spliced leader RNA trans-splicing in dinoflagellates. Proc Natl Acad Sci U S A 2007; 104:4618-23. [PMID: 17360573 PMCID: PMC1838650 DOI: 10.1073/pnas.0700258104] [Citation(s) in RCA: 290] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Indexed: 12/31/2022] Open
Abstract
Through the analysis of hundreds of full-length cDNAs from fifteen species representing all major orders of dinoflagellates, we demonstrate that nuclear-encoded mRNAs in all species, from ancestral to derived lineages, are trans-spliced with the addition of the 22-nt conserved spliced leader (SL), DCCGUAGCCAUUUUGGCUCAAG (D = U, A, or G), to the 5' end. SL trans-splicing has been documented in a limited but diverse number of eukaryotes, in which this process makes it possible to translate polycistronically transcribed nuclear genes. In SL trans-splicing, SL-donor transcripts (SL RNAs) contain two functional domains: an exon that provides the SL for mRNA and an intron that contains a spliceosomal (Sm) binding site. In dinoflagellates, SL RNAs are unusually short at 50-60 nt, with a conserved Sm binding motif (AUUUUGG) located in the SL (exon) rather than the intron. The initiation nucleotide is predominantly U or A, an unusual feature that may affect capping, and hence the translation and stability of the recipient mRNA. The core SL element was found in mRNAs coding for a diverse array of proteins. Among the transcripts characterized were three homologs of Sm-complex subunits, indicating that the role of the Sm binding site is conserved, even if the location on the SL is not. Because association with an Sm-complex often signals nuclear import for U-rich small nuclear RNAs, it is unclear how this Sm binding site remains on mature mRNAs without impeding cytosolic localization or translation of the latter. The sequences reported in this paper have been deposited in the GenBank database (accession nos. AF 512889, DQ 864761-DQ 864971, DQ 867053-DQ 867070, DQ 884413-DQ 884451, EF 133854-EF 133905, EF 133961-EF 134003, EF 134083-EF 134402, EF 141835, and EF 143070-EF 143105).
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Affiliation(s)
- Huan Zhang
- *Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340
| | - Yubo Hou
- *Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340
| | - Lilibeth Miranda
- *Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340
| | - David A. Campbell
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, 609 Charles Young Drive, Los Angeles, CA 90095; and
| | - Nancy R. Sturm
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, 609 Charles Young Drive, Los Angeles, CA 90095; and
| | - Terry Gaasterland
- Scripps Institution of Oceanography, University of California at San Diego, 8602 La Jolla Shores Drive, La Jolla, CA 92037
| | - Senjie Lin
- *Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Road, Groton, CT 06340
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20
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Forgber M, Basu R, Roychoudhury K, Theinert S, Roy S, Sundar S, Walden P. Mapping the antigenicity of the parasites in Leishmania donovani infection by proteome serology. PLoS One 2006; 1:e40. [PMID: 17183669 PMCID: PMC1762392 DOI: 10.1371/journal.pone.0000040] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 10/12/2006] [Indexed: 11/21/2022] Open
Abstract
Background Leishmaniasis defines a cluster of protozoal diseases with diverse clinical manifestations. The visceral form caused by Leishmania donovani is the most severe. So far, no vaccines exist for visceral leishmaniasis despite indications of naturally developing immunity, and sensitive immunodiagnostics are still at early stages of development. Methodology/Principle Findings Establishing a proteome-serological methodology, we mapped the antigenicity of the parasites and the specificities of the immune responses in human leishmaniasis. Using 2-dimensional Western blot analyses with sera and parasites isolated from patients in India, we detected immune responses with widely divergent specificities for up to 330 different leishmanial antigens. 68 antigens were assigned to proteins in silver- and fluorochrome-stained gels. The antigenicity of these proteins did not correlate with the expression levels of the proteins. Although some antigens are shared among different parasite isolates, there are extensive differences and no immunodominant antigens, but indications of antigenic drift in the parasites. Six antigens were identified by mass spectrometry. Conclusions/Significance Proteomics-based dissection of the serospecificities of leishmaniasis patients provides a comprehensive inventory of the complexity and interindividual heterogeneity of the host-responses to and variations in the antigenicity of the Leishmania parasites. This information can be instrumental in the development of vaccines and new immune monitoring and diagnostic devices.
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MESH Headings
- Adolescent
- Adult
- Amino Acid Sequence
- Animals
- Antibodies, Protozoan/blood
- Antibody Specificity
- Antigens, Protozoan/genetics
- Antigens, Protozoan/isolation & purification
- Blotting, Western
- Child
- Electrophoresis, Gel, Two-Dimensional
- Epitope Mapping
- Female
- Humans
- India
- Leishmania donovani/genetics
- Leishmania donovani/immunology
- Leishmaniasis, Visceral/immunology
- Leishmaniasis, Visceral/parasitology
- Male
- Middle Aged
- Molecular Sequence Data
- Proteome
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Young Adult
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Affiliation(s)
- Michael Forgber
- Department of Dermatology, Venerology and Allergy, Charité - Universitätsmedizin Berlin, Humboldt UniversityBerlin, Germany
| | - Rajatava Basu
- Department of Immunology, Indian Institute of Chemical BiologyCalcutta, West Bengal, India
| | - Kaushik Roychoudhury
- Department of Immunology, Indian Institute of Chemical BiologyCalcutta, West Bengal, India
| | - Stephan Theinert
- Department of Dermatology, Venerology and Allergy, Charité - Universitätsmedizin Berlin, Humboldt UniversityBerlin, Germany
| | - Syamal Roy
- Department of Immunology, Indian Institute of Chemical BiologyCalcutta, West Bengal, India
| | - Shyam Sundar
- Kala-Azar Medical Research Center, Banaras Hindu UniversityVaranasi, Uttar Pradesh, India
| | - Peter Walden
- Department of Dermatology, Venerology and Allergy, Charité - Universitätsmedizin Berlin, Humboldt UniversityBerlin, Germany
- * To whom correspondence should be addressed. E-mail:
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Thompson J, Gopal S. Correction: genetic algorithm learning as a robust approach to RNA editing site site prediction. BMC Bioinformatics 2006; 7:406. [PMID: 16956416 PMCID: PMC1569880 DOI: 10.1186/1471-2105-7-406] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 09/06/2006] [Indexed: 11/10/2022] Open
Abstract
After the publication of [1], we were alerted to an error in our data. The error was an one-off miscalculation in the extraction of position information for our set of true negatives. Our data set should have used randomly selected non-edited cytosines (C) as true negatives, but the data generation phase resulted in a set of nucleotides that were each one nucleotide downstream of known, unedited cytosines. The consequences of this error are reflected in changes to our results, although the general conclusions presented in our original publication remain largely unchanged.
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Affiliation(s)
- James Thompson
- Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Shuba Gopal
- Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
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