Genomes and Genes
Summary: The functional hereditary units of protozoa.
- A Elbasit I, Alifrangis M, Khalil I, Bygbjerg I, Masuadi E, Elbashir M, et al. The implication of dihydrofolate reductase and dihydropteroate synthetase gene mutations in modification of Plasmodium falciparum characteristics. Malar J. 2007;6:108 pubmed..However, these mutations have a survival advantage as they were associated with increased gametocytogenesis. The above implications of dhfr/dhps mutations were associated with MOM 2 to 5, regardless of the gene/codon locus. ..
- Imwong M, Pukrittayakamee S, Pongtavornpinyo W, Nakeesathit S, Nair S, Newton P, et al. Gene amplification of the multidrug resistance 1 gene of Plasmodium vivax isolates from Thailand, Laos, and Myanmar. Antimicrob Agents Chemother. 2008;52:2657-9 pubmed publisher..02). Five coding mutations in pvmdr1, independent of gene amplification, were also found. ..
- Weedall G, Polley S, Conway D. Gene-specific signatures of elevated non-synonymous substitution rates correlate poorly across the Plasmodium genus. PLoS ONE. 2008;3:e2281 pubmed publisher..Thus it is essential to complete the genome sequences of particular species of phylogenetic importance, such as P. reichenowi. ..
- Linford A, Moreno H, Good K, Zhang H, Singh U, Petri W. Short hairpin RNA-mediated knockdown of protein expression in Entamoeba histolytica. BMC Microbiol. 2009;9:38 pubmed publisher..Use of the U6 promoter to drive expression of 29-basepair short hairpin RNAs is effective at knocking down protein expression for unrelated genes in Entamoeba histolytica, providing a useful tool for the study of this parasite. ..
- Singh N, Almeida R, Kothari H, Kumar P, Mandal G, Chatterjee M, et al. Differential gene expression analysis in antimony-unresponsive Indian kala azar (visceral leishmaniasis) clinical isolates by DNA microarray. Parasitology. 2007;134:777-87 pubmed..This study provides preliminary clues to the role of a thiol-dependent efflux system in antimonial resistant clinical isolates of Leishmania donovani...
- Picot S, Olliaro P, de Monbrison F, Bienvenu A, Price R, Ringwald P. A systematic review and meta-analysis of evidence for correlation between molecular markers of parasite resistance and treatment outcome in falciparum malaria. Malar J. 2009;8:89 pubmed publisher..Genetic molecular markers were related to an increased risk of therapeutic failure. Guidelines are discussed and a checklist for further studies is proposed. ..
- Dahlbäck M, Lavstsen T, Salanti A, Hviid L, Arnot D, Theander T, et al. Changes in var gene mRNA levels during erythrocytic development in two phenotypically distinct Plasmodium falciparum parasites. Malar J. 2007;6:78 pubmed
- Mirelman D, Anbar M, Bracha R. Epigenetic transcriptional gene silencing in Entamoeba histolytica. IUBMB Life. 2008;60:598-604 pubmed publisher..The nonvirulent phenotype of the gene-silenced amoeba was demonstrated in various assays and the results suggest that they may have a potential use for vaccination. ..
- Wang C, Magistrado P, Nielsen M, Theander T, Lavstsen T. Preferential transcription of conserved rif genes in two phenotypically distinct Plasmodium falciparum parasite lines. Int J Parasitol. 2009;39:655-64 pubmed publisher..This conclusion is experimentally supported by group-specific rif transcription in parasites with different VSA and PfEMP1 expression phenotypes. ..
- Sanderson S, Xia D, Prieto H, Yates J, Heiges M, Kissinger J, et al. Determining the protein repertoire of Cryptosporidium parvum sporozoites. Proteomics. 2008;8:1398-414 pubmed publisher..For approximately half the proteome there was limited functional and structural information, highlighting the limitations in the current understanding of Cryptosporidium biology. ..
- Glockner G, Golderer G, Werner Felmayer G, Meyer S, Marwan W. A first glimpse at the transcriptome of Physarum polycephalum. BMC Genomics. 2008;9:6 pubmed publisher..It now can be genetically manipulated, opening up the possibility of targeted functional analysis in this organism...
- Clark C, Alsmark U, Tazreiter M, Saito Nakano Y, Ali V, Marion S, et al. Structure and content of the Entamoeba histolytica genome. Adv Parasitol. 2007;65:51-190 pubmed..In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes. ..
- Nair S, Miller B, Barends M, Jaidee A, Patel J, Mayxay M, et al. Adaptive copy number evolution in malaria parasites. PLoS Genet. 2008;4:e1000243 pubmed publisher..More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation. ..
- Tsao C, Gorovsky M. Different effects of Tetrahymena IFT172 domains on anterograde and retrograde intraflagellar transport. Mol Biol Cell. 2008;19:1450-61 pubmed publisher..These results implicate different regions of Ift172p in different steps of the IFT process...
- Santorelli L, Thompson C, Villegas E, Svetz J, Dinh C, Parikh A, et al. Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae. Nature. 2008;451:1107-10 pubmed publisher..The opportunities for evolutionary moves and countermoves in such conflicts may select for the involvement of multiple pathways and numerous genes...
- Haanstra J, Stewart M, Luu V, van Tuijl A, Westerhoff H, Clayton C, et al. Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei. J Biol Chem. 2008;283:2495-507 pubmed..Yet regulation of mRNA levels does not occur by transcription, but by adjusting mRNA degradation. The contribution of splicing to regulation is negligible, as for all cases where splicing is faster than RNA precursor degradation. ..
- Shock J, Fischer K, Derisi J. Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biol. 2007;8:R134 pubmed..This type of genome-wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum. ..
- Gunasekera A, Myrick A, Militello K, Sims J, Dong C, Gierahn T, et al. Regulatory motifs uncovered among gene expression clusters in Plasmodium falciparum. Mol Biochem Parasitol. 2007;153:19-30 pubmed..Together, both the bioinformatic and functional data reported here imply that multiple forms of gene regulation, including post-transcriptional control, may be important in the malarial system. ..
- Alsmark U, Sicheritz Ponten T, Foster P, Hirt R, Embley T. Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis. Methods Mol Biol. 2009;532:489-500 pubmed publisher..We found a broad range of prokaryotic lineages represented among the donors, but organisms that share similar environmental niches with E. histolytica and T. vaginalis, such as the gut and the vaginal mucosa, dominate...
- Sanchez C, Rotmann A, Stein W, Lanzer M. Polymorphisms within PfMDR1 alter the substrate specificity for anti-malarial drugs in Plasmodium falciparum. Mol Microbiol. 2008;70:786-98 pubmed publisher..falciparum digestive vacuole, and that this contributes to accumulation of, and susceptibility to, the drug in question...
- Frankel M, Mordue D, Knoll L. Discovery of parasite virulence genes reveals a unique regulator of chromosome condensation 1 ortholog critical for efficient nuclear trafficking. Proc Natl Acad Sci U S A. 2007;104:10181-6 pubmed..This protein divergence may represent a unique mechanism of nucleocytoplasmic transport. This study illustrates the power of this forward genetics approach to identify atypical virulence mechanisms. ..
- De Silva E, Gehrke A, Olszewski K, León I, Chahal J, Bulyk M, et al. Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A. 2008;105:8393-8 pubmed publisher..Because of their origin in the plant lineage, ApiAP2 proteins have no homologues in the human host and may prove to be ideal antimalarial targets. ..
- Cooper M, Adam R, Worobey M, Sterling C. Population genetics provides evidence for recombination in Giardia. Curr Biol. 2007;17:1984-8 pubmed..These observations provide genetic data supportive of sexual reproduction in Giardia. ..
- Fernandez Becerra C, Yamamoto M, Vencio R, Lacerda M, Rosanas Urgell A, del Portillo H. Plasmodium vivax and the importance of the subtelomeric multigene vir superfamily. Trends Parasitol. 2009;25:44-51 pubmed publisher..vivax and from data gathered from experimental infections in reticulocyte-prone non-lethal malaria parasites and natural P. vivax infections. ..
- Epp C, Li F, Howitt C, Chookajorn T, Deitsch K. Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum. RNA. 2009;15:116-27 pubmed publisher..These sterile transcripts therefore might act in a manner analogous to noncoding RNAs associated with silent, condensed chromatin found in other eukaryotic systems. ..
- Scholz S, Simon N, Lavazec C, Dude M, Templeton T, Pradel G. PfCCp proteins of Plasmodium falciparum: gametocyte-specific expression and role in complement-mediated inhibition of exflagellation. Int J Parasitol. 2008;38:327-40 pubmed..We conclude that the six PfCCp proteins are specifically expressed during gametocytogenesis and gamete formation, and that select members may represent prospective candidates for transmission blocking vaccines. ..
- Carlton J, Hirt R, Silva J, Delcher A, Schatz M, Zhao Q, et al. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science. 2007;315:207-12 pubmed..The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria...
- 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. ..
- Brayton K, Lau A, Herndon D, Hannick L, Kappmeyer L, Berens S, et al. Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa. PLoS Pathog. 2007;3:1401-13 pubmed..The genome sequence provides a greater understanding of B. bovis metabolism and potential avenues for drug therapies and vaccine development. ..
- Horrocks P, Wong E, Russell K, Emes R. Control of gene expression in Plasmodium falciparum - ten years on. Mol Biochem Parasitol. 2009;164:9-25 pubmed publisher..and apicomplexan parasites. Specifically, however, we will address the current polarised debate regarding the level at which control is mediated, and attempt to identify some of the challenges this field faces in the next 10 years. ..
- Ehrenkaufer G, Haque R, Hackney J, Eichinger D, Singh U. Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite. Cell Microbiol. 2007;9:1426-44 pubmed..These advances lay the groundwork for dissection of the molecular signals that initiate stage conversion and development of novel diagnostic and therapeutic measures targeting E. histolytica cysts. ..
- MARTINEZ CALVILLO S, Saxena A, Green A, Leland A, Myler P. Characterization of the RNA polymerase II and III complexes in Leishmania major. Int J Parasitol. 2007;37:491-502 pubmed
- Baudry C, Malinsky S, Restituito M, Kapusta A, Rosa S, Meyer E, et al. PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia. Genes Dev. 2009;23:2478-83 pubmed publisher..This is the first in vivo evidence suggesting an essential endonucleolytic function of a domesticated piggyBac transposase...
- Pain A, Böhme U, Berry A, Mungall K, Finn R, Jackson A, et al. The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature. 2008;455:799-803 pubmed publisher..One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry...
- Natalang O, Bischoff E, Deplaine G, Proux C, Dillies M, Sismeiro O, et al. Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate. BMC Genomics. 2008;9:388 pubmed publisher..Further work is needed to clarify which transcriptome alterations observed reflect a specific response to overcome artesunate toxicity or more general perturbations on the path to cellular death. ..
- Su X, Hayton K, Wellems T. Genetic linkage and association analyses for trait mapping in Plasmodium falciparum. Nat Rev Genet. 2007;8:497-506 pubmed..Rapidly increasing genetic and genomic information on Plasmodium parasites, mosquitoes and humans will combine as a rich resource for new advances in our understanding of malaria, its transmission and its manifestations of disease. ..
- Cong P, Luo Y, Bao W, Hu S. Genomic organization and promoter analysis of the Trichomonas vaginalis core histone gene families. Parasitol Int. 2010;59:29-34 pubmed publisher..vaginalis genome. Those findings reveal that both genomic organization and cis-acting transcription elements facilitate these large number of T. vaginalis core histone genes under the control of the same transcription machine. ..
- Gubbels M, Lehmann M, Muthalagi M, Jerome M, Brooks C, Szatanek T, et al. Forward genetic analysis of the apicomplexan cell division cycle in Toxoplasma gondii. PLoS Pathog. 2008;4:e36 pubmed publisher..The genes identified include regulators of spindle formation, nuclear trafficking, and protein degradation. The genetic approach described here should be widely applicable to numerous essential aspects of parasite biology. ..
- Carter R, Hunt P, Cheesman S. Linkage Group Selection--a fast approach to the genetic analysis of malaria parasites. Int J Parasitol. 2007;37:285-93 pubmed..We have called the method Linkage Group Selection. ..
- Mita T, Tanabe K, Takahashi N, Tsukahara T, Eto H, Dysoley L, et al. Independent evolution of pyrimethamine resistance in Plasmodium falciparum isolates in Melanesia. Antimicrob Agents Chemother. 2007;51:1071-7 pubmed..The other lineage had a unique, previously undescribed microsatellite haplotype, indicative of the de novo emergence of pyrimethamine resistance in Melanesia. ..
- Mok B, Ribacke U, Winter G, Yip B, Tan C, Fernandez V, et al. Comparative transcriptomal analysis of isogenic Plasmodium falciparum clones of distinct antigenic and adhesive phenotypes. Mol Biochem Parasitol. 2007;151:184-92 pubmed..The present data provides evidence for complex transcriptional differences between closely related isogenic P. falciparum of distinct adhesive and antigenic characteristics. ..
- Petter M, Bonow I, Klinkert M. Diverse expression patterns of subgroups of the rif multigene family during Plasmodium falciparum gametocytogenesis. PLoS ONE. 2008;3:e3779 pubmed publisher..Therefore, our data provide a first foundation and point to new directions for future investigations of the potential role of RIFINs in gametocyte immune evasion. ..
- Scherf A, Lopez Rubio J, Rivière L. Antigenic variation in Plasmodium falciparum. Annu Rev Microbiol. 2008;62:445-70 pubmed publisher..In addition, controversies surrounding var genetic elements in antigenic variation are discussed. ..
- Cui J, Smith T, Samuelson J. Gene expansion in Trichomonas vaginalis: a case study on transmembrane cyclases. Genome Inform. 2007;18:35-43 pubmed..We gave three possible hypotheses for that observation: a) Sequencing error or stop-codon read-through; b) Recency of duplication and mutation; c) The likelihood of functional pseudogene. ..
- Hunt P, Afonso A, Creasey A, Culleton R, Sidhu A, Logan J, et al. Gene encoding a deubiquitinating enzyme is mutated in artesunate- and chloroquine-resistant rodent malaria parasites. Mol Microbiol. 2007;65:27-40 pubmed..No mutations in the UBP-1 gene encoding the P. falciparum orthologue of the deubiquitinating enzyme were observed. The possible significance of these mutations in parasite responses to chloroquine or artemisinin is discussed...
- Hackney J, Ehrenkaufer G, Singh U. Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference. Nucleic Acids Res. 2007;35:2141-52 pubmed..Our analysis suggests that transcriptional regulatory networks can be identified using limited expression data. Thus, this approach is applicable to the multitude of systems for which microarray and genome sequence data are emerging. ..
- Ferreira I, Lopes D, Martinelli A, Ferreira C, Do Rosario V, Cravo P. In vitro assessment of artesunate, artemether and amodiaquine susceptibility and molecular analysis of putative resistance-associated mutations of Plasmodium falciparum from São Tomé and Príncipe. Trop Med Int Health. 2007;12:353-62 pubmed..Mutations in the pfcrt and pfmdr1 genes are near fixation, most likely because of high levels of chloroquine resistance, whereas only one protein type of the artemisinin resistance candidate, PfATPase6, was identified. ..
- 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. ..