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Galat A, Bua J. Molecular aspects of cyclophilins mediating therapeutic actions of their ligands. Cell Mol Life Sci 2010; 67:3467-88. [PMID: 20602248 PMCID: PMC11115621 DOI: 10.1007/s00018-010-0437-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/04/2010] [Accepted: 06/10/2010] [Indexed: 12/14/2022]
Abstract
Cyclosporine A (CsA) is an immunosuppressive cyclic peptide that binds with a high affinity to 18 kDa human cyclophilin-A (hCyPA). CsA and its several natural derivatives have some pharmacological potential in treatment of diverse immune disorders. More than 20 paralogues of CyPA are expressed in the human body while expression levels and functions of numerous ORFs encoding cyclophilin-like sequences remain unknown. Certain derivatives of CsA devoid of immunosuppressive activity may have some potential in treatments of Alzheimer diseases, Hepatitis C and HIV infections, amyotrophic lateral sclerosis, congenital muscular dystrophy, asthma and various parasitic infections. Here, we discuss structural and functional aspects of the human cyclophilins and their interaction with various intra-cellular targets that can be under the control of CsA or its complexes with diverse cyclophilins that are selectively expressed in different cellular compartments. Some molecular aspects of the cyclophilins expressed in parasites invading humans and causing diseases were also analyzed.
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Affiliation(s)
- Andrzej Galat
- SIMOPRO, Institute de Biologie et de Technologies de Saclay, DSV/CEA, Bat. 152, CE-Saclay, Gif-sur-Yvette Cedex, France.
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2
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Cribb P, Serra E. One- and two-hybrid analysis of the interactions between components of the Trypanosoma cruzi spliced leader RNA gene promoter binding complex. Int J Parasitol 2009; 39:525-32. [DOI: 10.1016/j.ijpara.2008.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 09/10/2008] [Accepted: 09/14/2008] [Indexed: 01/06/2023]
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3
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Majumder HK. Searching the Tritryp genomes for drug targets. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 625:133-40. [PMID: 18365664 PMCID: PMC7123030 DOI: 10.1007/978-0-387-77570-8_11] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent publication of the complete genome sequences of Leishmania major, Trypanosoma brucei and Trypanosoma cruzi revealed that each genome contains 8300-12,000 protein-coding genes, of which approximately 6500 are common to all three genomes, and ushers in a new, post-genomic, era for trypanosomatid drug discovery. This vast amount of new information makes possible more comprehensive and accurate target identification using several new computational approaches, including identification of metabolic "choke-points", searching the parasite proteomes for orthologues of known drug targets, and identification of parasite proteins likely to interact with known drugs and drug-like small molecules. In this chapter, we describe several databases (such as GENEDB, BRENDA, KEGG, METACYC, the THERAPEUTIC TARGET DATABASE, and CHEMBANK) and algorithms (including PATHOLOGIC, PATHWAY HUNTER TOOL, AND AUToDOCK) which have been developed to facilitate the bioinformatic analyses underlying these approaches. While target identification is only the first step in the drug development pipeline, these new approaches give rise to renewed optimism for the discovery of new drugs to combat the devastating diseases caused by these parasites. Traditionally, drug discovery in the trypanosomatids (and other organisms) has proceeded from two different starting points: screening large numbers of existing compounds for activity against whole parasites or more focused screening of compounds for activity against defined molecular targets. Most existing anti-trypanosomatids drugs were developed using the former approach, although the latter has gained much attention in the last twenty years under the rubric of "rational drug design". Until recently, one of the major bottlenecks in anti-trypanosomatid drug development has been our ability to identify good targets, since only a very small percentage of the total number of trypanosomatid genes were known. That has now changed forever, with the recent (July, 2005) publication of the "Tritryp" (Trypanosoma brucei, Trypanosoma cruzi and Leishmania major) genome sequences. This vast amount of information now makes possible several new approaches for target identification and ushers in a post-genomic era for trypanosomatid drug discovery.
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Affiliation(s)
- Hemanta K. Majumder
- Molecular Parasitology Laboratory, Indian Institute of Chemical Biology, Kolkata, India
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4
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Saxena A, Lahav T, Holland N, Aggarwal G, Anupama A, Huang Y, Volpin H, Myler PJ, Zilberstein D. Analysis of the Leishmania donovani transcriptome reveals an ordered progression of transient and permanent changes in gene expression during differentiation. Mol Biochem Parasitol 2006; 152:53-65. [PMID: 17204342 PMCID: PMC1904838 DOI: 10.1016/j.molbiopara.2006.11.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 11/18/2006] [Accepted: 11/22/2006] [Indexed: 01/22/2023]
Abstract
Leishmania donovani is an intracellular protozoan parasite that causes kala-azar in humans. During infection the extracellular insect forms (promastigotes) undergo rapid differentiation to intracellular amastigotes that proliferates in phagolysosomes of mammalian macrophages. We used microarray-based expression profiling to investigate the time-course of changes in RNA abundance during promastigote-to-amastigote differentiation in a host-free system that mimics this process. These studies revealed that several hundred genes underwent an ordered progression of transient or permanent up- and down-regulation during differentiation. Genes that were permanently up-regulated in amastigotes were enriched for transporters and surface proteins, but under-represented in genes involved in protein and other metabolism. Most of these changes occurred late in the differentiation process, when morphological differentiation was essentially complete. Down-regulated genes were over-represented in those involved in cell motility, growth and/or maintenance, and these changes generally occurred earlier in the process. Genes that were transiently up- or down-regulated during differentiation included those encoding heat shock proteins, ubiquitin hydrolases, RNA binding proteins, protein kinases, a protein phosphatase, and a histone deacetylase. These results suggest that changes in mRNA abundance may be important in signal transduction, as well as protein and mRNA turnover, during differentiation. In addition to these mRNA changes, other transcripts including one or more rRNAs and snoRNAs, and non-coding RNAs from several telomeres, also showed substantial changes in abundance during the differentiation process. This paper provides the first genome-scale quantitative analysis of gene expression during the transition from promastigotes to amastigotes and demonstrates the utility of the host-free differentiation system.
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Affiliation(s)
- A Saxena
- Seattle Biomedical Research Institute, 307 Westlake Avenue N, Seattle, WA 98109-5219, USA
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5
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Worthey EA, Myler PJ. Protozoan genomes: gene identification and annotation. Int J Parasitol 2005; 35:495-512. [PMID: 15826642 DOI: 10.1016/j.ijpara.2005.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Revised: 01/25/2005] [Accepted: 02/06/2005] [Indexed: 12/01/2022]
Abstract
The draft sequence of several complete protozoan genomes is now available and genome projects are ongoing for a number of other species. Different strategies are being implemented to identify and annotate protein coding and RNA genes in these genomes, as well as study their genomic architecture. Since the genomes vary greatly in size, GC-content, nucleotide composition, and degree of repetitiveness, genome structure is often a factor in choosing the methodology utilised for annotation. In addition, the approach taken is dictated, to a greater or lesser extent, by the particular reasons for carrying out genome-wide analyses and the level of funding available for projects. Nevertheless, these projects have provided a plethora of material that will aid in understanding the biology and evolution of these parasites, as well as identifying new targets that can be used to design urgently required drug treatments for the diseases they cause.
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Affiliation(s)
- E A Worthey
- Seattle Biomedical Research Institute, 307 Westlake Ave N., Seattle, WA 98109-2591, USA
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6
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Worthey EA, Martinez-Calvillo S, Schnaufer A, Aggarwal G, Cawthra J, Fazelinia G, Fong C, Fu G, Hassebrock M, Hixson G, Ivens AC, Kiser P, Marsolini F, Rickel E, Rickell E, Salavati R, Sisk E, Sunkin SM, Stuart KD, Myler PJ. Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene. Nucleic Acids Res 2003; 31:4201-10. [PMID: 12853638 PMCID: PMC167632 DOI: 10.1093/nar/gkg469] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Leishmania parasites (order Kinetoplastida, family Trypanosomatidae) cause a spectrum of human diseases ranging from asymptomatic to lethal. The approximately 33.6 Mb genome is distributed among 36 chromosome pairs that range in size from approximately 0.3 to 2.8 Mb. The complete nucleotide sequence of Leishmania major Friedlin chromosome 1 revealed 79 protein-coding genes organized into two divergent polycistronic gene clusters with the mRNAs transcribed towards the telomeres. We report here the complete nucleotide sequence of chromosome 3 (384 518 bp) and an analysis revealing 95 putative protein-coding ORFs. The ORFs are primarily organized into two large convergent polycistronic gene clusters (i.e. transcribed from the telomeres). In addition, a single gene at the left end is transcribed divergently towards the telomere, and a tRNA gene separates the two convergent gene clusters. Numerous genes have been identified, including those for metabolic enzymes, kinases, transporters, ribosomal proteins, spliceosome components, helicases, an RNA-binding protein and a DNA primase subunit.
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Affiliation(s)
- E A Worthey
- Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109-1651, USA
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7
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Sunkin SM, McDonagh P, Cunningham ML, Beverley SM, Stuart K, Myler PJ. Conservation of the LD1 region in Leishmania includes DNA implicated in LD1 amplification. Mol Biochem Parasitol 2001; 113:315-21. [PMID: 11295186 DOI: 10.1016/s0166-6851(01)00215-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- S M Sunkin
- Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle 98109-1651, USA
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8
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Hummel HS, Gillespie RD, Swindle J. Mutational analysis of 3' splice site selection during trans-splicing. J Biol Chem 2000; 275:35522-31. [PMID: 10938269 DOI: 10.1074/jbc.m002424200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
trans-Splicing is essential for mRNA maturation in trypanosomatids. A conserved AG dinucleotide serves as the 3' splice acceptor site, and analysis of native processing sites suggests that selection of this site is determined according to a 5'-3' scanning model. A series of stable gene replacement lines were generated that carried point mutations at or near the 3' splice site within the intergenic region separating CUB2.65, the calmodulin-ubiquitin associated gene, and FUS1, the ubiquitin fusion gene of Trypanosoma cruzi. In one stable line, the elimination of the native 3' splice acceptor site led to the accumulation of Y-branched splicing intermediates, which served as templates for mapping the first trans-splicing branch points in T. cruzi. In other lines, point mutations shifted the position of the first consensus AG dinucleotide either upstream or downstream of the wild-type 3' splice acceptor site in this intergenic region. Consistent with the scanning model, the first AG dinucleotide downstream of the branch points was used as the predominant 3' splice acceptor site. In all of the stable lines, the point mutations affected splicing efficiency in this region.
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Affiliation(s)
- H S Hummel
- Department of Microbiology and Immunology, University of Tennessee, Memphis, Tennessee 38163, USA
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9
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Abstract
A first generation cosmid contig map of the Leishmania major Friedlin genome has been constructed, and genomic sequencing is well underway. Chromosome 1 (Chr1) and Chr3 have been completely sequenced, and Chr4 is virtually complete. Sequencing of several other chromosomes is in progress and the complete genome sequence may be available as soon as 2003. More than 600 completely sequenced new genes have been identified, representing approximately 8% of the total gene complement (approximately 8,600 genes) of Leishmania. Notably, a large proportion (approximately 69%) of the genes remain unclassified, with 40% of these being potentially Leishmania- (or kinetoplastid-) specific. Most interestingly, the genes are organized into large (>100-300 kb) polycistronic clusters of adjacent genes on the same DNA strand. Chr1 contains two such clusters organized in a 'divergent' manner, whereas Chr3 contains two 'convergent' clusters, with a single 'divergent' gene at one telomere, with the two large clusters separated by a tRNA gene. Statistical analyses of Chr1 show that the 'divergent junction' region between the two polycistronic gene clusters may be a candidate for an origin of DNA replication.
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Affiliation(s)
- P J Myler
- Seattle Biomedical Research Institute, WA 98109-1651, USA.
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10
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Wilson JE, Powell MJ, Hoover SE, Sarnow P. Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 2000; 20:4990-9. [PMID: 10866656 PMCID: PMC85949 DOI: 10.1128/mcb.20.14.4990-4999.2000] [Citation(s) in RCA: 259] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cricket paralysis virus is a member of a group of insect picorna-like viruses. Cloning and sequencing of the single plus-strand RNA genome revealed the presence of two nonoverlapping open reading frames, ORF1 and ORF2, that encode the nonstructural and structural proteins, respectively. We show that each ORF is preceded by one internal ribosome entry site (IRES). The intergenic IRES is located 6,024 nucleotides from the 5' end of the viral RNA and is more active than the IRES located at the 5' end of the RNA, providing a mechanistic explanation for the increased abundance of structural proteins relative to nonstructural proteins in infected cells. Mutational analysis of this intergenic-region IRES revealed that ORF2 begins with a noncognate CCU triplet. Complementarity of this CCU triplet with sequences in the IRES is important for IRES function, pointing to an involvement of RNA-RNA interactions in translation initiation. Thus, the cricket paralysis virus genome is an example of a naturally occurring, functionally dicistronic eukaryotic mRNA whose translation is controlled by two IRES elements located at the 5' end and in the middle of the mRNA. This finding argues that eukaryotic mRNAs can express multiple proteins not only by polyprotein processing, reinitiation and frameshifting but also by using multiple IRES elements.
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Affiliation(s)
- J E Wilson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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11
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Teixeira MM, Serrano MG, Camargo EP. New data from old Trypanosomatid preparations. PARASITOLOGY TODAY (PERSONAL ED.) 2000; 16:261-3. [PMID: 10827436 DOI: 10.1016/s0169-4758(00)01653-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Assessing the diversity of the Trypanosomatidae is difficult because of the relatively small number of species that can be cultured. This same problem thwarts efforts to identify the hosts and insect vectors of Phytomonas, a genus of parasites of plants that includes species responsible for devastating epiphytotics of economically important plantations. Here, Myrna Serrano, Marta Teixeira and Erney Camargo review the studies that have led to the development of a PCR-based technique for processing insect and plant juices fixed on glass slides. The method overcomes the need for cultivation, facilitates field collections and also permits the molecular examination of archival smears of Phytomonas. In principle, the method can be adapted to any trypanosomatid as well as to any fastidious parasitic or free-living organism.
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Affiliation(s)
- M M Teixeira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo. Av. Lineu Prestes 1374, São Paulo 05508-900, SP, Brazil
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12
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Myler PJ, Audleman L, deVos T, Hixson G, Kiser P, Lemley C, Magness C, Rickel E, Sisk E, Sunkin S, Swartzell S, Westlake T, Bastien P, Fu G, Ivens A, Stuart K. Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes. Proc Natl Acad Sci U S A 1999; 96:2902-6. [PMID: 10077609 PMCID: PMC15867 DOI: 10.1073/pnas.96.6.2902] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Leishmania are evolutionarily ancient protozoans (Kinetoplastidae) and important human pathogens that cause a spectrum of diseases ranging from the asymptomatic to the lethal. The Leishmania genome is relatively small [ approximately 34 megabases (Mb)], lacks substantial repetitive DNA, and is distributed among 36 chromosomes pairs ranging in size from 0.3 Mb to 2.5 Mb, making it a useful candidate for complete genome sequence determination. We report here the nucleotide sequence of the smallest chromosome, chr1. The sequence of chr1 has a 257-kilobase region that is densely packed with 79 protein-coding genes. This region is flanked by telomeric and subtelomeric repetitive elements that vary in number and content among the chr1 homologs, resulting in an approximately 27.5-kilobase size difference. Strikingly, the first 29 genes are all encoded on one DNA strand, whereas the remaining 50 genes are encoded on the opposite strand. Based on the gene density of chr1, we predict a total of approximately 9,800 genes in Leishmania, of which 40% may encode unknown proteins.
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Affiliation(s)
- P J Myler
- Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109-1651, USA
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13
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Bringaud F, Vedrenne C, Cuvillier A, Parzy D, Baltz D, Tetaud E, Pays E, Venegas J, Merlin G, Baltz T. Conserved organization of genes in trypanosomatids. Mol Biochem Parasitol 1998; 94:249-64. [PMID: 9747975 DOI: 10.1016/s0166-6851(98)00080-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Trypanosomatids are unicellular protozoan parasites which constitute some of the most primitive eukaryotes. Leishmania spp, Trypanosoma cruzi and members of the Trypanosoma brucei group, which cause human diseases, are the most studied representatives of this large family. Here we report a comparative analysis of a large genomic region containing glucose transporter genes in three Salivarian trypanosomes (T. brucei, T. congolense and T. vivax), T. cruzi and Leishmania donovani. In T. brucei, the 8 kb (upstream) and 14 kb (downstream) regions flanking the glucose transporter genes cluster contain two and six new genes, respectively, six of them encoding proteins homologous to known eukaryotic proteins (phosphatidylinositol 3 kinase, ribosomal protein S12, DNAJ and three small G-proteins--Rab1, YPT6 and ARL3). This gene organization is identical in T. brucei, T. congolense and T. vivax suggesting that Salivarian trypanosomes have a high level of conservation in gene organization. In T. cruzi and Leishmania, the overall organization of this cluster is conserved, with insertion of additional genes when compared with T. brucei. Phylogenetic reconstitution based on glucose transporters is in accord with the monophyly of the genus Trypanosoma and the early separation of T. vivax within Salivarian trypanosomes. On the basis of gene organization, biochemical characteristics of isoforms and phylogeny, we discuss the genesis of the glucose transporter multigene family in Salivarian trypanosomes.
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Affiliation(s)
- F Bringaud
- Laboratoire de Parasitologie Moléculaire, Université Victor Ségolène de Bordeaux II, France.
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14
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Nunes LR, Carvalho MR, Shakarian AM, Buck GA. The transcription promoter of the spliced leader gene from Trypanosoma cruzi. Gene 1997; 188:157-68. [PMID: 9133587 DOI: 10.1016/s0378-1119(96)00726-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A putative promoter element responsible for transcription of the spliced leader (SL) gene of Trypanosoma cruzi was identified by overlapping deletion and linker scanning analyses of the upstream flanking sequences using the bacterial chloramphenicol acetyltransferase (CAT) gene as a reporter in transient transfections of cultured epimastigotes. Deletion or substitution of a proximal sequence element (PSE) between positions -53 and -40 relative to the transcription start point eliminated CAT gene expression. Comparison of SL genes from several strains of T. cruzi revealed two alternative sequence patterns for the putative SL PSE, both composed of a short run of purines followed by a run of pyrimidines. Moreover, an examination of these sequences supports the subdivision of T. cruzi isolates into two divergent groups. Double-stranded oligonucleotides containing the sequence of the PSE exhibited specific gel mobility shifts after incubation with T. cruzi nuclear extracts, suggesting that a transcription factor binds this site. Finally, experiments designed to increase the level of CAT expression from the SL promoter suggest that it is not a strong promoter in cultured T. cruzi epimastigotes.
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Affiliation(s)
- L R Nunes
- Department of Microbiology and Immunology, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond 23298-0678, USA
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15
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Affiliation(s)
- A K Cruz
- Departamento de Bioquímica, Faculdade de Medicina de Ribeirao Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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16
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Wong AK, Curotto de Lafaille MA, Wirth DF. Identification of a cis-acting gene regulatory element from the lemdr1 locus of Leishmania enriettii. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)47222-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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17
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Abstract
U3 nucleolar small RNA (snRNA) is involved in early processing of the primary rRNA transcript. A secondary structure model for the unusually small Trypanosoma brucei U3 snRNA was deduced by chemical modification and enzymatic cleavage of U3 snRNA in deproteinized and ribonucleoprotein (RNP) forms. Comprehensive alignment of U3 snRNAs from vertebrate, plant, fungal and protozoan species clearly delineated conserved and divergent features. The 5' domain of the T. brucei U3 snRNA appears to form one small, flexible 5' stem loop structure followed by a long single-stranded region; this model is a variation on 5' domain structures proposed for other U3 snRNAs which do not conform to a single model. The 3' domain of T. brucei U3 snRNA contains four single-stranded sequences conserved between U3 snRNAs. Of these, structural probing determined that the configurations of GAU region and box B and C sequences are altered by protein interactions in U3 snRNP. Conspicuously, the 3' domains of trypanosomal U3 snRNAs lack stem loops II and III, indicating that these structures are not required for conserved U3 snRNA functions.
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Affiliation(s)
- T Hartshorne
- Intercampus Program in Molecular Parasitology, School of Pharmacy, University of California, San Francisco 94143-1204
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18
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Merello S, Xavier M, Parodi A. Novel (rhamnosyl and ribosyl) and uncommon (xylosyl) monosaccharide residues are present in asparagine-linked oligosaccharides of the trypanosomatid Blastocrithidia culicis. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31990-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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19
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Abstract
The spliced leader RNA from Leptomonas collosoma has two competing secondary structures of nearly equal free energy. Short, complementary oligonucleotides can drive the structure from one form of the other. We report stopped-flow rapid-mixing and temperature-jump measurements of the kinetics of the structural switch. At high concentrations of oligonucleotide, the rate of binding becomes limited by the rate of the structural switch, which occurs on a time scale of a fraction of a second. The low activation energy observed for the process implies a branch migration type of mechanism in which portions of the two competing helices transiently coexist.
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Affiliation(s)
- K A LeCuyer
- Department of Chemistry, Yale University, New Haven, CT 06511
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20
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Carruthers VB, Cross GA. High-efficiency clonal growth of bloodstream- and insect-form Trypanosoma brucei on agarose plates. Proc Natl Acad Sci U S A 1992; 89:8818-21. [PMID: 1528898 PMCID: PMC50012 DOI: 10.1073/pnas.89.18.8818] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
This report describes a method for growing both bloodstream- and procyclic-form Trypanosoma brucei as colonies on agarose plates. Procyclic colonies, which took 2 weeks to develop, grew with approximately 17% plating efficiency on SDM-79/0.65% agarose supplemented with 20% (vol/vol) conditioned medium. Bloodstream forms were adapted to in vitro growth in liquid HMI-9 medium and then spread on HMI-9/0.65% agarose plates, where they grew to visible colonies in 3-5 days. Plating efficiencies were from 3 to 80%, depending upon the trypanosome variant and experiment. Colonies were proven to be the result of growth from a single cell and contained approximately 10(6) cells at maturity. Colonies were transferred to filters and probed for multicopy and single-copy genes. Potential uses of this method in conjunction with classical and reverse genetic approaches to studying trypanosomes are discussed.
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Affiliation(s)
- V B Carruthers
- Laboratory of Molecular Parasitology, Rockefeller University, New York, NY 10021
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21
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Stuart KD, Weeks R, Guilbride L, Myler PJ. Molecular organization of Leishmania RNA virus 1. Proc Natl Acad Sci U S A 1992; 89:8596-600. [PMID: 1382295 PMCID: PMC49967 DOI: 10.1073/pnas.89.18.8596] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The complete 5284-nucleotide sequence of the double-stranded RNA genome of Leishmania RNA virus 1 (LRV1) was determined and contains three open reading frames (ORFs) on the plus (+) (mRNA) strand. The predicted amino acid sequence of ORF3 has motifs characteristic of viral RNA-dependent RNA polymerases. ORF2, which may encode the major viral coat protein, overlaps ORF3 by 71 nucleotides, suggesting a +1 translational frameshift to produce a gag-pol type of fusion protein. Two alternative models for the frameshift are presented. The 5' splice leader sequence of kinetoplastid mRNAs is not in LRV1 RNA. This suggests that the 450-base region at the 5' end of the LRV1 (+)-strand, which contains ORF1 and is highly conserved among viral strains, does not encode protein but has a role in initiation of translation and/or RNA stability. The similarity of LRV1 genomic organization, replication cycle, and RNA-dependent RNA polymerase sequence to those of the yeast virus ScV L-A suggests a common ancestral origin. The possibility that LRV1 affects pathogenesis in leishmaniasis is intriguing.
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Affiliation(s)
- K D Stuart
- Seattle Biomedical Research Institute, WA 98109-1651
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