2019
The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA
Kolev NG, Rajan KS, Tycowski KT, Toh JY, Shi H, Lei Y, Michaeli S, Tschudi C. The vault RNA of Trypanosoma brucei plays a role in the production of trans-spliced mRNA. Journal Of Biological Chemistry 2019, 294: 15559-15574. PMID: 31439669, PMCID: PMC6816085, DOI: 10.1074/jbc.ra119.008580.Peer-Reviewed Original ResearchConceptsTelomerase-associated protein 1Vault RNAY RNAsRNA quality controlRNA polymerase IIISmall nuclear RNATrans-spliced mRNAPermeabilized cell systemNcRNA repertoireRNP biogenesisMRNA metabolismRNA speciesSequence similarityRNA classesMammalian cellsNuclear RNAPolymerase IIIRo functionTrypanosoma bruceiVtRNAsGene expressionRo proteinBloodstream formsRNACell nuclei
2018
Temperature shift activates bloodstream VSG expression site promoters in Trypanosoma brucei
Kolev NG, Ramsdell TK, Tschudi C. Temperature shift activates bloodstream VSG expression site promoters in Trypanosoma brucei. Molecular And Biochemical Parasitology 2018, 226: 20-23. PMID: 30399391, PMCID: PMC6258174, DOI: 10.1016/j.molbiopara.2018.10.003.Peer-Reviewed Original Research
2017
The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion
Christiano R, Kolev NG, Shi H, Ullu E, Walther TC, Tschudi C. The proteome and transcriptome of the infectious metacyclic form of Trypanosoma brucei define quiescent cells primed for mammalian invasion. Molecular Microbiology 2017, 106: 74-92. PMID: 28742275, PMCID: PMC5607103, DOI: 10.1111/mmi.13754.Peer-Reviewed Original ResearchConceptsInfectious metacyclic formsTsetse fly vectorMetacyclic formsVariant surface glycoprotein expression sitesQuiescent cellsGene expression profilesFly vectorsAvailability of nutrientsMammalian invasionsCell surface componentsCell divisionProcyclic trypanosomesMammalian hostsTrypanosoma bruceiMRNA sequencingExpression profilesExpression sitesMetabolic enzymesBloodstream formsInfectious metacyclicsProtein 6TranscriptomeTsetse fliesProteomeProtein levelsMetacyclic VSG expression site promoters are recognized by the same general transcription factor that is required for RNA polymerase I transcription of bloodstream expression sites
Kolev NG, Günzl A, Tschudi C. Metacyclic VSG expression site promoters are recognized by the same general transcription factor that is required for RNA polymerase I transcription of bloodstream expression sites. Molecular And Biochemical Parasitology 2017, 216: 52-55. PMID: 28716719, PMCID: PMC5582990, DOI: 10.1016/j.molbiopara.2017.07.002.Peer-Reviewed Original ResearchConceptsBloodstream VSG expression sitesVSG expression sitesVSG ES promoterExpression sitesPol IVSG genesES promoterRNA polymerase I transcriptionGeneral transcription factorsBloodstream expression sitesVariant surface glycoprotein (VSG) coatPolymerase I transcriptionRNA polymerase IDistinct promoter sequencesMetacyclic VSG geneTrypanosoma brucei cellsProcyclin genesTypes of promotersBrucei cellsDevelopmental programDistinct binding affinitiesTranscription factorsI transcriptionInitiation factorsPromoter sequencesThe Canonical Poly (A) Polymerase PAP1 Polyadenylates Non-Coding RNAs and Is Essential for snoRNA Biogenesis in Trypanosoma brucei
Chikne V, Gupta SK, Doniger T, K. SR, Cohen-Chalamish S, Ben-Asher HW, Kolet L, Yahia NH, Unger R, Ullu E, Kolev NG, Tschudi C, Michaeli S. The Canonical Poly (A) Polymerase PAP1 Polyadenylates Non-Coding RNAs and Is Essential for snoRNA Biogenesis in Trypanosoma brucei. Journal Of Molecular Biology 2017, 429: 3301-3318. PMID: 28456523, DOI: 10.1016/j.jmb.2017.04.015.Peer-Reviewed Original ResearchConceptsNon-coding RNAsPoly (ADP-ribose) polymeraseUnique RNA processing mechanismsCis-spliced intronsRNA processing mechanismsSmall nucleolar RNAsLong non-coding RNAsPolyadenylation of mRNAParasite Trypanosoma bruceiSnoRNA biogenesisTrans splicingPrecursor snoRNASnoRNA processingNucleolar RNAsPAP1Trypanosoma bruceiPolyadenylationMajor substrateSnoRNAsTrypanosoma cruziPAP2RNAPolymerase Pap1TrypanosomesCausative agent
2016
Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans
Savage AF, Kolev NG, Franklin JB, Vigneron A, Aksoy S, Tschudi C. Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans. PLOS ONE 2016, 11: e0168877. PMID: 28002435, PMCID: PMC5176191, DOI: 10.1371/journal.pone.0168877.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsElectron Transport Complex IVGene Expression ProfilingGene LibraryHigh-Throughput Nucleotide SequencingInsect VectorsIntestinal MucosaLife Cycle StagesMembrane GlycoproteinsProtozoan ProteinsProventriculusSalivary GlandsSequence Analysis, RNATranscriptomeTrypanosoma brucei bruceiTsetse FliesUp-RegulationConceptsSalivary gland transcriptomeMetacyclic VSGsInsect vectorsHigh-throughput RNA sequencingBlood-feeding tsetse fliesDigenetic life cycleRNA-binding proteinGene ontology analysisAlanine-rich proteinCytochrome oxidase complexTsetse fliesMidgut transcriptomeGlobal regulatorDNA metabolismTrypanosome developmentOntology analysisDNA replicationSignal transductionTransporter familyMammalian hostsRNA sequencingDistinct tissuesTranscript levelsTranscriptomeRich protein
2015
Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA
Eliaz D, Doniger T, Tkacz ID, Biswas VK, Gupta SK, Kolev NG, Unger R, Ullu E, Tschudi C, Michaeli S. Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA. RNA Biology 2015, 12: 1222-1255. PMID: 25970223, PMCID: PMC4829279, DOI: 10.1080/15476286.2015.1038019.Peer-Reviewed Original ResearchConceptsSmall nucleolar RNAsNucleolar RNAsGenome-wide analysisRNA processing mechanismsRRNA secondary structurePost-transcriptional levelCore proteinProcessing of rRNARNA-seq analysisFunctional homologueGene clusterRNA speciesTrypanosoma bruceiSnoRNAsComplete repertoireGene expressionRRNA cleavageAnalogous functionsSecondary structureRNAProtozoan parasiteRich repertoireOrganismsSpeciesProteinSynchronous expression of individual metacyclic variant surface glycoprotein genes in Trypanosoma brucei
Ramey-Butler K, Ullu E, Kolev NG, Tschudi C. Synchronous expression of individual metacyclic variant surface glycoprotein genes in Trypanosoma brucei. Molecular And Biochemical Parasitology 2015, 200: 1-4. PMID: 25896436, PMCID: PMC4470760, DOI: 10.1016/j.molbiopara.2015.04.001.Peer-Reviewed Original ResearchConceptsVariant surface glycoproteinMetacyclic variant surface glycoproteinInfectious metacyclic formsVariant surface glycoprotein genesVSG gene expressionSurface glycoprotein genesNew mammalian hostInsect vectorsParasite biologyMammalian hostsDifferentiation systemGene expressionTsetse vectorBloodstream trypanosomesDifferential expressionGlycoprotein geneProtein 6Molecular aspectsIndividual cellsMetacyclic formsBlood mealProtein levelsDiscrete populationsSurface glycoproteinLife cycle
2014
Construction of Trypanosoma brucei Illumina RNA-Seq Libraries Enriched for Transcript Ends
Kolev NG, Ullu E, Tschudi C. Construction of Trypanosoma brucei Illumina RNA-Seq Libraries Enriched for Transcript Ends. Methods In Molecular Biology 2014, 1201: 165-175. PMID: 25388113, DOI: 10.1007/978-1-4939-1438-8_9.Peer-Reviewed Original ResearchConceptsHuman pathogen Trypanosoma bruceiHigh-throughput RNA sequencingLong polycistronic precursorsGenome-wide scaleIllumina RNA-seqPathogen Trypanosoma bruceiRNA polymerase IIRNA-seq librariesSingle-nucleotide resolutionTranscript endsTranscript boundariesTranscriptome annotationUnannotated genesPolymerase IICellular abundancePolycistronic precursorsTranscription initiationGene clusterRNA-seqPolyadenylation sitesRNA sequencingMRNA precursorsTrypanosoma bruceiRNA moleculesMRNA moleculesThe emerging role of RNA‐binding proteins in the life cycle of Trypanosoma brucei
Kolev NG, Ullu E, Tschudi C. The emerging role of RNA‐binding proteins in the life cycle of Trypanosoma brucei. Cellular Microbiology 2014, 16: 482-489. PMID: 24438230, PMCID: PMC3974610, DOI: 10.1111/cmi.12268.Peer-Reviewed Original ResearchConceptsParasitic protozoan Trypanosoma bruceiIdentification of RBPsTargets of RBPsSpecific gene networksProtozoan Trypanosoma bruceiPost-transcriptional mechanismsGene regulatory networksGene expression patternsRelated trypanosomatidsTranscriptional machineryCellular fateGene networksRegulatory networksTrypanosoma bruceiExpression patternsRegulatory mechanismsDifferent hostsRBPsLife cyclePathogenic organismsRNAOrganismsProteinDifferent environmentsCrucial role
2012
Developmental Progression to Infectivity in Trypanosoma brucei Triggered by an RNA-Binding Protein
Kolev NG, Ramey-Butler K, Cross GA, Ullu E, Tschudi C. Developmental Progression to Infectivity in Trypanosoma brucei Triggered by an RNA-Binding Protein. Science 2012, 338: 1352-1353. PMID: 23224556, PMCID: PMC3664091, DOI: 10.1126/science.1229641.Peer-Reviewed Original ResearchComparative Genomics Reveals Two Novel RNAi Factors in Trypanosoma brucei and Provides Insight into the Core Machinery
Barnes RL, Shi H, Kolev NG, Tschudi C, Ullu E. Comparative Genomics Reveals Two Novel RNAi Factors in Trypanosoma brucei and Provides Insight into the Core Machinery. PLOS Pathogens 2012, 8: e1002678. PMID: 22654659, PMCID: PMC3359990, DOI: 10.1371/journal.ppat.1002678.Peer-Reviewed Original ResearchConceptsRNA interferenceT. bruceiComparative genomicsTrypanosoma bruceiMechanism of RNAiCatalog of genesCore RNAi machineryWide RNAi screenArgonaute 1 proteinNext-generation IlluminaRepertoire of factorsLoss of fitnessDistinct developmental stagesAncient eukaryotesRNAi factorsCore machineryRNAi machineryRNAi screenRNAi toolTrypanosomatid protozoaDuplex siRNAsRNAi efficiencyHuman parasitesMolecular explorationBruceiA single-cloning-step procedure for the generation of RNAi plasmids producing long stem–loop RNA
Atayde VD, Ullu E, Kolev NG. A single-cloning-step procedure for the generation of RNAi plasmids producing long stem–loop RNA. Molecular And Biochemical Parasitology 2012, 184: 55-58. PMID: 22542486, PMCID: PMC3358476, DOI: 10.1016/j.molbiopara.2012.04.003.Peer-Reviewed Original Research
2011
RNA Interference in Protozoan Parasites: Achievements and Challenges
Kolev NG, Tschudi C, Ullu E. RNA Interference in Protozoan Parasites: Achievements and Challenges. MSphere 2011, 10: 1156-1163. PMID: 21764910, PMCID: PMC3187059, DOI: 10.1128/ec.05114-11.Peer-Reviewed Original Research
2010
The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution
Kolev NG, Franklin JB, Carmi S, Shi H, Michaeli S, Tschudi C. The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution. PLOS Pathogens 2010, 6: e1001090. PMID: 20838601, PMCID: PMC2936537, DOI: 10.1371/journal.ppat.1001090.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceGene Expression ProfilingGenome, BacterialHigh-Throughput Nucleotide SequencingHumansMolecular Sequence DataRNA Polymerase IIRNA PrecursorsRNA, BacterialSequence Homology, Nucleic AcidTranscription Initiation SiteTranscription, GeneticTrypanosoma brucei bruceiTrypanosomiasis, AfricanConceptsGene clusterNew transcriptsHigh-throughput RNA sequencingInitiation siteOrganization of genesRNA polymerase IISimilar genome organizationPutative initiation siteSingle-nucleotide resolutionTranscription initiation siteGene expression patternsPre-mRNA processingNon-coding RNAsGenome organizationPolymerase IIGenomic mapTranscription initiationInsect vectorsEukaryotic promotersMass spectrometry analysisImportant human pathogenMammalian hostsRNA sequencingTrypanosoma bruceiT. brucei
2009
Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei
Patrick KL, Shi H, Kolev NG, Ersfeld K, Tschudi C, Ullu E. Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 17933-17938. PMID: 19815526, PMCID: PMC2764927, DOI: 10.1073/pnas.0907766106.Peer-Reviewed Original ResearchConceptsDicer-like enzymesRNA interferenceRNAi pathwayBiogenesis of siRNAsDicer-like proteinsNuclear RNAi pathwaySingle Argonaute proteinEnd modificationReverse genetic analysisRNAi-deficient cellsRNA interference (RNAi) pathwayWild-type cellsAncient eukaryotesArgonaute proteinsRNAi responseAncient traitRepeat transcriptsInterference pathwayCytoplasmic proteinsImportant human pathogenTrypanosoma bruceiGenetic analysisRNAi triggersFunctional analysisIntermediate transcriptssnoRNAs in Giardia lamblia: a novel role in RNA silencing?
Kolev NG, Ullu E. snoRNAs in Giardia lamblia: a novel role in RNA silencing? Trends In Parasitology 2009, 25: 348-350. PMID: 19616476, DOI: 10.1016/j.pt.2009.05.001.Peer-Reviewed Original Research
2008
A manganese-dependent ribozyme in the 3′-untranslated region of Xenopus Vg1 mRNA
Kolev NG, Hartland EI, Huber PW. A manganese-dependent ribozyme in the 3′-untranslated region of Xenopus Vg1 mRNA. Nucleic Acids Research 2008, 36: 5530-5539. PMID: 18753150, PMCID: PMC2553595, DOI: 10.1093/nar/gkn530.Peer-Reviewed Original ResearchConserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3′‐end maturation
Kolev NG, Yario TA, Benson E, Steitz JA. Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3′‐end maturation. EMBO Reports 2008, 9: 1013-1018. PMID: 18688255, PMCID: PMC2572124, DOI: 10.1038/embor.2008.146.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceBase SequenceCell LineCleavage And Polyadenylation Specificity FactorConserved SequenceEndonucleasesEnzyme ActivationHeLa CellsHistonesHumansMolecular Sequence DataProtein Structure, TertiaryProtein SubunitsRNA 3' End ProcessingRNA PrecursorsRNA, MessengerConceptsPre-messenger RNAPolyadenylation specificity factorMammalian proteinsRNase ZConserved motifsHistone mRNASpecificity factorEndonucleolytic cleavageActive endonucleaseEndonuclease activityMBL familyComplex machineryMessenger RNAPoint mutationsCPSF73CPSF100Process of maturationMaturation processRNAProteinMotifMRNAMaturationEukaryotesCleavageMinor-class splicing occurs in the nucleus of the Xenopus oocyte
Friend K, Kolev NG, Shu MD, Steitz JA. Minor-class splicing occurs in the nucleus of the Xenopus oocyte. RNA 2008, 14: 1459-1462. PMID: 18567814, PMCID: PMC2491479, DOI: 10.1261/rna.1119708.Peer-Reviewed Original ResearchConceptsSmall nuclear ribonucleoproteinMinor class intronsU12-type splicingXenopus oocytesU12-dependent intronsNuclear envelope breakdownCertain eukaryotesMinor spliceosomeVertebrate cellsSplicing substrateNuclear compartmentNuclear ribonucleoproteinRNA intronsAccurate splicingEnvelope breakdownSplicingIntronsCytoplasmOocytesEukaryotesSpliceosomeMeiosisRibonucleoproteinNucleusSmall fraction