Genomes and Genes
Summary: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
- Mlambo G, Vasquez Y, LeBlanc R, Sullivan D, Kumar N. A filter paper method for the detection of Plasmodium falciparum gametocytes by reverse transcription polymerase chain reaction. Am J Trop Med Hyg. 2008;78:114-6 pubmed..This assay will greatly facilitate bulk analysis of gametocyte RNA transcripts on filter paper, especially in areas where collection and preservation of liquid blood is not feasible. ..
- Dean S, Marchetti R, Kirk K, Matthews K. A surface transporter family conveys the trypanosome differentiation signal. Nature. 2009;459:213-7 pubmed publisher..As well as being molecular transducers of the differentiation signal in these parasites, PAD proteins provide the first example of a surface marker able to discriminate the transmission stage of trypanosomes in their mammalian host. ..
- Rochette A, Raymond F, Ubeda J, Smith M, Messier N, Boisvert S, et al. Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species. BMC Genomics. 2008;9:255 pubmed publisher..major and L. infantum. These important species-specific differences in stage-regulated gene expression may contribute to the disease tropism that distinguishes L. major from L. infantum. ..
- Le Roch K, Johnson J, Ahiboh H, Chung D, Prudhomme J, Plouffe D, et al. A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum. BMC Genomics. 2008;9:513 pubmed publisher..falciparum, and provide evidence for post-transcriptional regulations of parasite metabolism in response to external stimuli. ..
- Chen X, White W, Collins L, Penny D. Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis. PLoS ONE. 2008;3:e3106 pubmed publisher..Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes. ..
- Simoes Barbosa A, Meloni D, Wohlschlegel J, Konarska M, Johnson P. Spliceosomal snRNAs in the unicellular eukaryote Trichomonas vaginalis are structurally conserved but lack a 5'-cap structure. RNA. 2008;14:1617-31 pubmed publisher..Despite the lack of a cap structure, U1, U2, U4, and U5 genes are transcribed by RNA polymerase II, whereas the U6 gene is transcribed by RNA polymerase III. ..
- Deitsch K, Duraisingh M, Dzikowski R, Gunasekera A, Khan S, Le Roch K, et al. Mechanisms of gene regulation in Plasmodium. Am J Trop Med Hyg. 2007;77:201-8 pubmed
- Chen X, Rozhdestvensky T, Collins L, Schmitz J, Penny D. Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Res. 2007;35:4619-28 pubmed..Subsequent computational analysis has revealed additional putative C/D-box snoRNAs. Our results will lead towards a future understanding of RNA metabolism in the deep-branching eukaryote Giardia, as more ncRNAs are characterized. ..
- Gunasekera A, Myrick A, Le Roch K, Winzeler E, Wirth D. Plasmodium falciparum: genome wide perturbations in transcript profiles among mixed stage cultures after chloroquine treatment. Exp Parasitol. 2007;117:87-92 pubmed..Molecular Microbiology 50, 1229-1239]. These findings are important to report, given the striking contrast to similar studies in other model eukaryotic organisms. ..
- Jaillon O, Bouhouche K, Goût J, Aury J, Noel B, Saudemont B, et al. Translational control of intron splicing in eukaryotes. Nature. 2008;451:359-62 pubmed publisher..The results suggest that, independently of alternative splicing, species with large intron numbers universally rely on NMD to compensate for suboptimal splicing efficiency and accuracy. ..
- Clayton C, Shapira M. Post-transcriptional regulation of gene expression in trypanosomes and leishmanias. Mol Biochem Parasitol. 2007;156:93-101 pubmed..Thus the regulation of gene expression is post-transcriptional. We here discuss recent results concerning the enzymes required for mRNA degradation, and components of the translation initiation machinery, and how both are regulated. ..
- Mallick B, Ghosh Z, Chakrabarti J. MicroRNA switches in Trypanosoma brucei. Biochem Biophys Res Commun. 2008;372:459-63 pubmed publisher..2 corresponding to these clustered miRNAs play essential role in trypanosomiasis. These snippets can act as genetic switches modulating host-parasite interaction and provide useful clue toward treatment of trypanosomiasis. ..
- Chakrabarti K, Pearson M, Grate L, Sterne Weiler T, Deans J, Donohue J, et al. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA. 2007;13:1923-39 pubmed..These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts. ..
- Elemento O, Slonim N, Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell. 2007;28:337-50 pubmed
- Haile S, Papadopoulou B. Developmental regulation of gene expression in trypanosomatid parasitic protozoa. Curr Opin Microbiol. 2007;10:569-77 pubmed publisher..Several of these developments have greatly benefited from the recently completed genomic sequences and functional genomic studies...
- Kaestli M, Cockburn I, Cortes A, Baea K, Rowe J, Beck H. Virulence of malaria is associated with differential expression of Plasmodium falciparum var gene subgroups in a case-control study. J Infect Dis. 2006;193:1567-74 pubmed..Furthermore, parasites forming rosettes showed a significant up-regulation of var group A transcripts. ..
- Holzer T, McMaster W, Forney J. Expression profiling by whole-genome interspecies microarray hybridization reveals differential gene expression in procyclic promastigotes, lesion-derived amastigotes, and axenic amastigotes in Leishmania mexicana. Mol Biochem Parasitol. 2006;146:198-218 pubmed..Leishmania may represent an alternative paradigm for eukaryotic differentiation with minimal contributions from changes in mRNA abundance...
- Hinas A, Söderbom F. Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum. Curr Genet. 2007;51:141-59 pubmed..Old and recent findings are discussed and put in context of what we today know about ncRNAs in other organisms. ..
- De S, Pal D, Ghosh S. Entamoeba histolytica: computational identification of putative microRNA candidates. Exp Parasitol. 2006;113:239-43 pubmed..Putative microRNA identification in E. histolytica may act as a starting reference for cloning and characterization of miRNAs in Entamoeba genome. ..
- Leoni F, Amar C, Nichols G, Pedraza Diaz S, McLauchlin J. Genetic analysis of Cryptosporidium from 2414 humans with diarrhoea in England between 1985 and 2000. J Med Microbiol. 2006;55:703-7 pubmed..9 %), Cryptosporidium felis (0.2 %), Cryptosporidium andersoni (0.1 %), Cryptosporidium canis (0.04 %), Cryptosporidium suis (0.04 %) and the Cryptosporidium cervine type (0.04 %) were detected. ..
- Llinas M, Bozdech Z, Wong E, Adai A, Derisi J. Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res. 2006;34:1166-73 pubmed..The majority of these genes are uncharacterized and have no homology to other species. These tractable transcriptional differences provide important phenotypes for these otherwise highly related strains of Plasmodium. ..
- Hinas A, Larsson P, Avesson L, Kirsebom L, Virtanen A, Söderbom F. Identification of the major spliceosomal RNAs in Dictyostelium discoideum reveals developmentally regulated U2 variants and polyadenylated snRNAs. Eukaryot Cell. 2006;5:924-34 pubmed..Furthermore, all of the snRNAs could also be detected as polyadenylated species, and polyadenylated U1 RNA was demonstrated to be located in the cytoplasm. ..
- Cassago A, Rodrigues E, Prieto E, Gaston K, Alfonzo J, Iribar M, et al. Identification of Leishmania selenoproteins and SECIS element. Mol Biochem Parasitol. 2006;149:128-34 pubmed..To our knowledge this is the first report on the identification of selenocysteine insertion machinery in Kinetoplastida, more specifically in Leishmania, at the sequence level. ..
- Dobson D, Scholtes L, Myler P, Turco S, Beverley S. Genomic organization and expression of the expanded SCG/L/R gene family of Leishmania major: internal clusters and telomeric localization of SCGs mediating species-specific LPG modifications. Mol Biochem Parasitol. 2006;146:231-41 pubmed..Potentially, telomeric localization of SCG genes may function primarily to facilitate gene conversion and the elaboration of functional evolutionary diversity in the degree of PG sc-galactosylation observed in other strains of L. major. ..
- Mair G, Braks J, Garver L, Wiegant J, Hall N, Dirks R, et al. Regulation of sexual development of Plasmodium by translational repression. Science. 2006;313:667-9 pubmed..Genetic disruption of pbdozi inhibits the formation of the ribonucleoprotein complexes, and instead, at least 370 transcripts are diverted to a degradation pathway. ..
- Lobanov A, Gromer S, Salinas G, Gladyshev V. Selenium metabolism in Trypanosoma: characterization of selenoproteomes and identification of a Kinetoplastida-specific selenoprotein. Nucleic Acids Res. 2006;34:4012-24 pubmed..Overall, these data establish that Trypanosoma, Leishmania and likely other Kinetoplastida utilize and depend on the trace element selenium, and this dependence is due to occurrence of selenium in at least three selenoproteins. ..
- Rathjen T, Nicol C, McConkey G, Dalmay T. Analysis of short RNAs in the malaria parasite and its red blood cell host. FEBS Lett. 2006;580:5185-8 pubmed..Interestingly, mir-451 was not detectable in a series of immortalised cell lines representing progenitor stages of all major blood lineages, suggesting that mir-451 may play a role in the differentiation of erythroid cells. ..
- Nunes M, Goldring J, Doerig C, Scherf A. A novel protein kinase family in Plasmodium falciparum is differentially transcribed and secreted to various cellular compartments of the host cell. Mol Microbiol. 2007;63:391-403 pubmed..Our data suggest a role of FIKK proteins in the remodelling of the erythrocyte surface and reveal the existence of an adaptable parasite system able to sense intra- and possibly extracellular changes. ..
- Davids B, Reiner D, Birkeland S, Preheim S, Cipriano M, McArthur A, et al. A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein. PLoS ONE. 2006;1:e44 pubmed..HCNCp and the other HCMp provide a rich source for developing parasite-specific diagnostic reagents, vaccine candidates, and subjects for further research into Giardia biology. ..
- Colasante C, Robles A, Li C, Schwede A, Benz C, Voncken F, et al. Regulated expression of glycosomal phosphoglycerate kinase in Trypanosoma brucei. Mol Biochem Parasitol. 2007;151:193-204 pubmed..We also found that production of mRNAs using T7 polymerase can affect the apparent half-life, and that large amounts of CAT enzyme may be toxic in trypanosomes. ..
- Leifso K, Cohen Freue G, Dogra N, Murray A, McMaster W. Genomic and proteomic expression analysis of Leishmania promastigote and amastigote life stages: the Leishmania genome is constitutively expressed. Mol Biochem Parasitol. 2007;152:35-46 pubmed..The differential expression was validated by the identification of previously reported stage specific proteins and identified several amastigote and promastigote novel stage specific proteins. ..
- Saxena A, Lahav T, Holland N, Aggarwal G, Anupama A, Huang Y, et al. Analysis of the Leishmania donovani transcriptome reveals an ordered progression of transient and permanent changes in gene expression during differentiation. Mol Biochem Parasitol. 2007;152:53-65 pubmed..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. ..
- Oakley M, Kumar S, Anantharaman V, Zheng H, Mahajan B, Haynes J, et al. Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasites. Infect Immun. 2007;75:2012-25 pubmed..These studies enhance the possibility of designing vaccines and drugs on the basis of disruption in molecules and pathways of parasite survival and virulence activated in response to febrile temperatures. ..
- Macrae I, Zhou K, Li F, Repic A, Brooks A, Cande W, et al. Structural basis for double-stranded RNA processing by Dicer. Science. 2006;311:195-8 pubmed..The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end. ..
- Shen Z, Huang J, Lin X, Yi Z, Li J, Song W. Morphological and molecular characterization of Aspidisca hongkongensis spec. nov. (Ciliophora, Euplotida) from the South China Sea. Eur J Protistol. 2010;46:204-11 pubmed publisher..The SSU rRNA gene sequence similarity within the genus is about 75.3-92.1% which indicates that this is a distinct form. Phylogenetic trees based on SSU rRNA gene information show that A. hongkongensis groups with A. leptaspis. ..
- Li F, Ge P, Hui W, Atanasov I, Rogers K, Guo Q, et al. Structure of the core editing complex (L-complex) involved in uridine insertion/deletion RNA editing in trypanosomatid mitochondria. Proc Natl Acad Sci U S A. 2009;106:12306-10 pubmed publisher..The REL1 ligase was localized on the model to the base of the apex by decoration with REL1-specific IgG. This structure should prove useful for a detailed analysis of the editing reaction. ..
- Jerlström Hultqvist J, Franzén O, Ankarklev J, Xu F, Nohynkova E, Andersson J, et al. Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate. BMC Genomics. 2010;11:543 pubmed publisher..To further understand the genetic diversity between the Giardia intestinalis species, we have performed genome sequencing and analysis of a wild-type Giardia intestinalis sample from the assemblage E group, isolated from a pig...
- Simo G, Herder S, Cuny G, Hoheisel J. Identification of subspecies specific genes differentially expressed in procyclic forms of Trypanosoma brucei subspecies. Infect Genet Evol. 2010;10:229-37 pubmed publisher..These genes appear as potential targets for investigations on the development of vaccine blocking the transmission of trypanosomes in tsetse flies. ..
- Takishita K, Kakizoe N, Yoshida T, Maruyama T. Molecular evidence that phylogenetically diverged ciliates are active in microbial mats of deep-sea cold-seep sediment. J Eukaryot Microbiol. 2010;57:76-86 pubmed publisher..In addition, given that the environment studied is under highly reduced (anoxic) conditions, based on the prokaryotic community structure deduced from T-RFLP profiles, the ciliates detected may be obligatory or facultative anaerobes. ..
- Moreno A, Matz C, Kjelleberg S, Manefield M. Identification of ciliate grazers of autotrophic bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing. Appl Environ Microbiol. 2010;76:2203-11 pubmed publisher..We then demonstrated that (13)C-labeled protozoan RNA can be retrieved from activated sludge amended with (13)C-labeled protozoa or (13)C-labeled Escherichia coli ..
- Abe N, Makino I. Multilocus genotypic analysis of Cryptosporidium isolates from cockatiels, Japan. Parasitol Res. 2010;106:1491-7 pubmed publisher..Analyses identified three new genotypes in C. meleagridis, avian genotype III, and a new avian genotype V. ..
- Han J, Lee S, Jang H, Na K. Asymptomatic Babesia microti-like parasite infection in wild raccoon dogs (Nyctereutes procyonoides) in South Korea. J Wildl Dis. 2010;46:632-5 pubmed..This is the first description of natural B. microti-like parasite infection in raccoon dogs and suggests that the wild raccoon dog can be a source for B. microti-like parasite infection of domestic dogs and humans. ..
- Falk N, Kaestli M, Qi W, Ott M, Baea K, Cortes A, et al. Analysis of Plasmodium falciparum var genes expressed in children from Papua New Guinea. J Infect Dis. 2009;200:347-56 pubmed publisher..Despite this vast diversity, restricted disease-associated var genes were identified and might be used for innovative interventions based on PfEMP1. ..
- Lee S, Talsky K, Collins K. A single RNA-dependent RNA polymerase assembles with mutually exclusive nucleotidyl transferase subunits to direct different pathways of small RNA biogenesis. RNA. 2009;15:1363-74 pubmed publisher..The biochemical and biological phenotypes of RDRC subunit disruption reveal a previously unanticipated complexity of Rdr-dependent sRNA biogenesis in vivo. ..
- Jonikas M, Radmer R, Laederach A, Das R, Pearlman S, Herschlag D, et al. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA. 2009;15:189-99 pubmed publisher..thermophila group I intron, creating an integrated model of the entire molecule. Our software package is freely available at https://simtk.org/home/nast. ..
- Yi Z, Song W, Shao C, Warren A, Al Rasheid K, Roberts D, et al. Phylogeny of some systematically uncertain urostyloids--Apokeronopsis, Metaurostylopsis, Thigmokeronopsis (Ciliophora, Stichotrichia) estimated with small subunit rRNA gene sequence information: discrepancies and agreements with morphological data. Eur J Protistol. 2008;44:254-62 pubmed publisher
- Respuela P, Ferella M, Rada Iglesias A, Aslund L. Histone acetylation and methylation at sites initiating divergent polycistronic transcription in Trypanosoma cruzi. J Biol Chem. 2008;283:15884-92 pubmed publisher..cruzi with potential implications for transcriptional regulation; they indicate that both histone modifications and bidirectional transcription are evolutionarily conserved. ..
- Shaw P, Ponmee N, Karoonuthaisiri N, Kamchonwongpaisan S, Yuthavong Y. Characterization of human malaria parasite Plasmodium falciparum eIF4E homologue and mRNA 5' cap status. Mol Biochem Parasitol. 2007;155:146-55 pubmed..The putatively uncapped nuclear transcripts may represent a class of mRNAs targeted for storage and cap removal. ..
- Maciejewska A. Molecular phylogenetics of representative Paramecium species. Folia Biol (Krakow). 2007;55:1-8 pubmed..One of the directions of research in molecular phylogenetics include indirect methods that allow for an estimation of entire genomes, for example RAPD-PCR-fingerprinting. ..
- Lohan A, Gray M. Analysis of 5'- or 3'-terminal tRNA editing: mitochondrial 5' tRNA editing in Acanthamoeba castellanii as the exemplar. Methods Enzymol. 2007;424:223-42 pubmed
- Lagos M L, Moran O, Camacho M. Leishmania amazonensis: Anionic currents expressed in oocytes upon microinjection of mRNA from the parasite. Exp Parasitol. 2007;116:163-70 pubmed