An assembly of nuclear bodies associates with the active VSG expression site in African trypanosomes.
Cells, Cultured
Gene Expression Regulation
Membrane Glycoproteins
/ genetics
Nuclear Bodies
/ genetics
Organisms, Genetically Modified
Protozoan Proteins
/ genetics
RNA Polymerase I
/ genetics
RNA Splicing
RNA, Messenger
/ genetics
Transcription, Genetic
Trypanosoma brucei brucei
/ genetics
Variant Surface Glycoproteins, Trypanosoma
/ genetics
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
10 01 2022
10 01 2022
Historique:
received:
08
06
2021
accepted:
26
11
2021
entrez:
11
1
2022
pubmed:
12
1
2022
medline:
27
1
2022
Statut:
epublish
Résumé
A Variant Surface Glycoprotein (VSG) coat protects bloodstream form Trypanosoma brucei. Prodigious amounts of VSG mRNA (~7-10% total) are generated from a single RNA polymerase I (Pol I) transcribed VSG expression site (ES), necessitating extremely high levels of localised splicing. We show that splicing is required for processive ES transcription, and describe novel ES-associated T. brucei nuclear bodies. In bloodstream form trypanosomes, the expression site body (ESB), spliced leader array body (SLAB), NUFIP body and Cajal bodies all frequently associate with the active ES. This assembly of nuclear bodies appears to facilitate the extraordinarily high levels of transcription and splicing at the active ES. In procyclic form trypanosomes, the NUFIP body and SLAB do not appear to interact with the Pol I transcribed procyclin locus. The congregation of a restricted number of nuclear bodies at a single active ES, provides an attractive mechanism for how monoallelic ES transcription is mediated.
Identifiants
pubmed: 35013170
doi: 10.1038/s41467-021-27625-6
pii: 10.1038/s41467-021-27625-6
pmc: PMC8748868
doi:
Substances chimiques
Membrane Glycoproteins
0
Protozoan Proteins
0
RNA, Messenger
0
Variant Surface Glycoproteins, Trypanosoma
0
procyclic acidic repetitive protein, Trypanosoma
0
RNA Polymerase I
EC 2.7.7.6
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
101Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/L015129/1
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : R01 AI028798
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI110325
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : R01 AI165480
Pays : United States
Organisme : Wellcome Trust
ID : 108445/Z/15/Z
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 212211/Z/18/Z
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : R37 AI028798
Pays : United States
Organisme : Wellcome Trust
ID : 095161
Pays : United Kingdom
Informations de copyright
© 2022. The Author(s).
Références
Buscher, P., Cecchi, G., Jamonneau, V. & Priotto, G. Human African trypanosomiasis. Lancet 390, 2397–2409 (2017).
Schwede, A., Macleod, O. J., MacGregor, P. & Carrington, M. How does the VSG coat of bloodstream form African trypanosomes interact with external proteins? PLoS Pathog. 11, e1005259 (2015).
pubmed: 26719972
pmcid: 4697842
doi: 10.1371/journal.ppat.1005259
Cestari, I. & Stuart, K. Transcriptional regulation of telomeric expression sites and antigenic variation in trypanosomes. Curr. Genomics 19, 119–132 (2018).
pubmed: 29491740
pmcid: 5814960
doi: 10.2174/1389202918666170911161831
Horn, D. Antigenic variation in African trypanosomes. Mol. Biochem. Parasitol. 195, 123–129 (2014).
Clayton, C. E. Gene expression in Kinetoplastids. Curr. Opin. Microbiol 32, 46–51 (2016).
pubmed: 27177350
doi: 10.1016/j.mib.2016.04.018
Gunzl, A. et al. RNA polymerase I transcribes procyclin genes and variant surface glycoprotein gene expression sites in Trypanosoma brucei. Eukaryot. Cell 2, 542–551 (2003).
pubmed: 12796299
pmcid: 161450
doi: 10.1128/EC.2.3.542-551.2003
Navarro, M. & Gull, K. A pol I transcriptional body associated with VSG mono-allelic expression in Trypanosoma brucei. Nature 414, 759–763 (2001).
pubmed: 11742402
doi: 10.1038/414759a
Budzak, J. et al. Dynamic colocalization of 2 simultaneously active VSG expression sites within a single expression-site body in Trypanosoma brucei. Proc. Natl Acad. Sci. USA 116, 16561–16570 (2019).
pubmed: 31358644
pmcid: 6697882
doi: 10.1073/pnas.1905552116
Gunzl, A. The pre-mRNA splicing machinery of trypanosomes: complex or simplified? Eukaryot. Cell 9, 1159–1170 (2010).
pubmed: 20581293
pmcid: 2918933
doi: 10.1128/EC.00113-10
Machyna, M., Heyn, P. & Neugebauer, K. M. Cajal bodies: where form meets function. Wiley Interdiscip. Rev. RNA 4, 17–34 (2013).
pubmed: 23042601
doi: 10.1002/wrna.1139
Sawyer, I. A., Sturgill, D., Sung, M. H., Hager, G. L. & Dundr, M. Cajal body function in genome organization and transcriptome diversity. Bioessays 38, 1197–1208 (2016).
pubmed: 27767214
pmcid: 5225948
doi: 10.1002/bies.201600144
Wang, Q. et al. Cajal bodies are linked to genome conformation. Nat. Commun. 7, 10966 (2016).
pubmed: 26997247
pmcid: 4802181
doi: 10.1038/ncomms10966
Fadda, A. et al. Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Mol. Microbiol. 94, 307–326 (2014).
pubmed: 25145465
pmcid: 4285177
doi: 10.1111/mmi.12764
Ridewood S., et al. The role of genomic location and flanking 3’UTR in the generation of functional levels of variant surface glycoprotein in Trypanosoma brucei. Mol. Microbiol. 106, 614–634 (2017).
Kramer, S., Marnef, A., Standart, N. & Carrington, M. Inhibition of mRNA maturation in trypanosomes causes the formation of novel foci at the nuclear periphery containing cytoplasmic regulators of mRNA fate. J. Cell Sci. 125, 2896–2909 (2012).
pubmed: 22366449
pmcid: 3434824
Hertz-Fowler, C. et al. Telomeric expression sites are highly conserved in Trypanosoma brucei. PLoS ONE 3, e3527 (2008).
pubmed: 18953401
pmcid: 2567434
doi: 10.1371/journal.pone.0003527
Sheader, K. et al. Variant surface glycoprotein RNA interference triggers a precytokinesis cell cycle arrest in African trypanosomes. Proc. Natl Acad. Sci. USA 102, 8716–8721 (2005).
pubmed: 15937117
pmcid: 1150830
doi: 10.1073/pnas.0501886102
Dean, S., Sunter, J. D. & Wheeler, R. J. TrypTag.org: a trypanosome genome-wide protein localisation resource. Trends Parasitol. 33, 80–82 (2017).
pubmed: 27863903
pmcid: 5270239
doi: 10.1016/j.pt.2016.10.009
Glover, L., Hutchinson, S., Alsford, S. & Horn, D. VEX1 controls the allelic exclusion required for antigenic variation in trypanosomes. Proc. Natl Acad. Sci. USA 113, 7225–7230 (2016).
pubmed: 27226299
pmcid: 4932947
doi: 10.1073/pnas.1600344113
Faria, J. et al. Monoallelic expression and epigenetic inheritance sustained by a Trypanosoma brucei variant surface glycoprotein exclusion complex. Nat. Commun. 10, 3023 (2019).
pubmed: 31289266
pmcid: 6617441
doi: 10.1038/s41467-019-10823-8
Schimanski, B., Nguyen, T. N. & Gunzl, A. Characterization of a multisubunit transcription factor complex essential for spliced-leader RNA gene transcription in Trypanosoma brucei. Mol. Cell Biol. 25, 7303–7313 (2005).
pubmed: 16055738
pmcid: 1190248
doi: 10.1128/MCB.25.16.7303-7313.2005
Faria, J. et al. Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes. Nat. Microbiol 6, 289–300 (2021).
pubmed: 33432154
pmcid: 7610597
doi: 10.1038/s41564-020-00833-4
Kerry, L. E. et al. Selective inhibition of RNA polymerase I transcription as a potential approach to treat African trypanosomiasis. PLoS Negl. Trop. Dis. 11, e0005432 (2017).
pubmed: 28263991
pmcid: 5354456
doi: 10.1371/journal.pntd.0005432
Fare, C. M., Villani, A., Drake, L. E. & Shorter, J. Higher-order organization of biomolecular condensates. Open Biol. 11, 210137 (2021).
pubmed: 34129784
pmcid: 8205532
doi: 10.1098/rsob.210137
Bizarro, J. et al. Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control. J. Cell Biol. 207, 463–480 (2014).
pubmed: 25404746
pmcid: 4242836
doi: 10.1083/jcb.201404160
Bizarro, J. et al. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins. Nucleic Acids Res. 43, 8973–8989 (2015).
pubmed: 26275778
pmcid: 4605303
doi: 10.1093/nar/gkv809
Rothe, B. et al. Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly. Nucleic Acids Res. 42, 2015–2036 (2014).
pubmed: 24234454
doi: 10.1093/nar/gkt1091
Lopato, S., Gattoni, R., Fabini, G., Stevenin, J. & Barta, A. A novel family of plant splicing factors with a Zn knuckle motif: examination of RNA binding and splicing activities. Plant Mol. Biol. 39, 761–773 (1999).
pubmed: 10350090
doi: 10.1023/A:1006129615846
Vo, L. T., Minet, M., Schmitter, J. M., Lacroute, F. & Wyers, F. Mpe1, a zinc knuckle protein, is an essential component of yeast cleavage and polyadenylation factor required for the cleavage and polyadenylation of mRNA. Mol. Cell Biol. 21, 8346–8356 (2001).
pubmed: 11713271
pmcid: 99999
doi: 10.1128/MCB.21.24.8346-8356.2001
Brusini, L., D’Archivio, S., McDonald, J. & Wickstead, B. Trypanosome KKIP1 dynamically links the inner kinetochore to a kinetoplastid outer kinetochore complex. Front. Cell Infect. Microbiol. 11, 641174 (2021).
pubmed: 33834005
pmcid: 8023272
doi: 10.3389/fcimb.2021.641174
Nerusheva, O. O., Ludzia, P. & Akiyoshi, B. Identification of four unconventional kinetoplastid kinetochore proteins KKT22-25 in Trypanosoma brucei. Open Biol. 9, 190236 (2019).
pubmed: 31795916
pmcid: 6936259
doi: 10.1098/rsob.190236
Badjatia, N., Park, S. H., Ambrosio, D. L., Kirkham, J. K. & Gunzl, A. Cyclin-dependent kinase CRK9, required for spliced leader trans splicing of Pre-mRNA in trypanosomes, functions in a complex with a new L-type cyclin and a kinetoplastid-specific protein. PLoS Pathog. 12, e1005498 (2016).
pubmed: 26954683
pmcid: 4783070
doi: 10.1371/journal.ppat.1005498
Meier, U. T. RNA modification in Cajal bodies. RNA Biol. 14, 693–700 (2017).
pubmed: 27775477
doi: 10.1080/15476286.2016.1249091
Lopez-Farfan, D., Bart, J. M., Rojas-Barros, D. I. & Navarro, M. SUMOylation by the E3 ligase TbSIZ1/PIAS1 positively regulates VSG expression in Trypanosoma brucei. PLoS Pathog. 10, e1004545 (2014).
pubmed: 25474309
pmcid: 4256477
doi: 10.1371/journal.ppat.1004545
Saldi, T., Cortazar, M. A., Sheridan, R. M. & Bentley, D. L. Coupling of RNA polymerase II transcription elongation with Pre-mRNA splicing. J. Mol. Biol. 428, 2623–2635 (2016).
pubmed: 27107644
pmcid: 4893998
doi: 10.1016/j.jmb.2016.04.017
Scull, C. E. & Schneider, D. A. Coordinated control of rRNA processing by RNA polymerase I. Trends Genet 35, 724–733 (2019).
pubmed: 31358304
pmcid: 6744312
doi: 10.1016/j.tig.2019.07.002
Schneider, D. A. et al. Transcription elongation by RNA polymerase I is linked to efficient rRNA processing and ribosome assembly. Mol. Cell 26, 217–229 (2007).
pubmed: 17466624
pmcid: 1927085
doi: 10.1016/j.molcel.2007.04.007
Muller, L. S. M. et al. Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature 563, 121–125 (2018).
pubmed: 30333624
pmcid: 6784898
doi: 10.1038/s41586-018-0619-8
Vanhamme, L. et al. Differential RNA elongation controls the variant surface glycoprotein gene expression sites of Trypanosoma brucei. Mol. Microbiol 36, 328–340 (2000).
pubmed: 10792720
doi: 10.1046/j.1365-2958.2000.01844.x
Jae, N. et al. snRNA-specific role of SMN in trypanosome snRNP biogenesis in vivo. RNA Biol. 8, 90–100 (2011).
pubmed: 21282982
pmcid: 3127081
doi: 10.4161/rna.8.1.13985
Feric, M. et al. Coexisting liquid phases underlie nucleolar subcompartments. Cell 165, 1686–1697 (2016).
pubmed: 27212236
pmcid: 5127388
doi: 10.1016/j.cell.2016.04.047
Lafontaine, D. L. J., Riback, J. A., Bascetin, R. & Brangwynne, C. P. The nucleolus as a multiphase liquid condensate. Nat. Rev. Mol. Cell Biol. 22, 165–182 (2021).
pubmed: 32873929
doi: 10.1038/s41580-020-0272-6
Boulon, S. et al. The Hsp90 chaperone controls the biogenesis of L7Ae RNPs through conserved machinery. J. Cell Biol. 180, 579–595 (2008).
pubmed: 18268104
pmcid: 2234240
doi: 10.1083/jcb.200708110
Thul, P. J. et al. A subcellular map of the human proteome. Science 356, eaal3321 https://doi.org/10.1126/science.aal3321 (2017).
Rodor, J. et al. AtNUFIP, an essential protein for plant development, reveals the impact of snoRNA gene organisation on the assembly of snoRNPs and rRNA methylation in Arabidopsis thaliana. Plant J. 65, 807–819 (2011).
pubmed: 21261762
doi: 10.1111/j.1365-313X.2010.04468.x
Bardoni, B., Schenck, A. & Mandel, J. L. A novel RNA-binding nuclear protein that interacts with the fragile X mental retardation (FMR1) protein. Hum. Mol. Genet. 8, 2557–2566 (1999).
pubmed: 10556305
doi: 10.1093/hmg/8.13.2557
Poon, S. K., Peacock, L., Gibson, W., Gull, K. & Kelly, S. A modular and optimized single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor. Open Biol. 2, 110037 (2012).
pubmed: 22645659
pmcid: 3352093
doi: 10.1098/rsob.110037
Schumann Burkard, G., Jutzi, P. & Roditi, I. Genome-wide RNAi screens in bloodstream form trypanosomes identify drug transporters. Mol. Biochem Parasitol. 175, 91–94 (2011).
pubmed: 20851719
doi: 10.1016/j.molbiopara.2010.09.002
Kelly, S. et al. Functional genomics in Trypanosoma brucei: a collection of vectors for the expression of tagged proteins from endogenous and ectopic gene loci. Mol. Biochem. Parasitol. 154, 103–109 (2007).
pubmed: 17512617
pmcid: 2705915
doi: 10.1016/j.molbiopara.2007.03.012
Waldner, C., Roose, M. & Ryffel, G. U. Red fluorescent Xenopus laevis: a new tool for grafting analysis. BMC Dev. Biol. 9, 37 (2009).
pubmed: 19549299
pmcid: 2706234
doi: 10.1186/1471-213X-9-37
Dean, S. et al. A toolkit enabling efficient, scalable and reproducible gene tagging in trypanosomatids. Open Biol. 5, 140197 (2015).
pubmed: 25567099
pmcid: 4313374
doi: 10.1098/rsob.140197
Davies, C. et al. TbSAP is a novel chromatin protein repressing metacyclic variant surface glycoprotein expression sites in bloodstream form Trypanosoma brucei. Nucleic Acids Res. 49, 3242–3262 (2021).
pubmed: 33660774
pmcid: 8034637
doi: 10.1093/nar/gkab109
Wickstead, B., Ersfeld, K. & Gull, K. Targeting of a tetracycline-inducible expression system to the transcriptionally silent minichromosomes of Trypanosoma brucei. Mol. Biochem Parasitol. 125, 211–216 (2002).
pubmed: 12467990
doi: 10.1016/S0166-6851(02)00238-4
Redmond, S., Vadivelu, J. & Field, M. C. RNAit: an automated web-based tool for the selection of RNAi targets in Trypanosoma brucei. Mol. Biochem Parasitol. 128, 115–118 (2003).
pubmed: 12706807
doi: 10.1016/S0166-6851(03)00045-8
Bertrand, E. et al. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 2, 437–445 (1998).
pubmed: 9809065
doi: 10.1016/S1097-2765(00)80143-4
Devaux, S. et al. Diversification of function by different isoforms of conventionally shared RNA polymerase subunits. Mol. Biol. Cell 18, 1293–1301 (2007).
pubmed: 17267688
pmcid: 1838988
doi: 10.1091/mbc.e06-09-0841
Ball, G. et al. SIMcheck: a toolbox for successful super-resolution structured illumination microscopy. Sci. Rep. 5, 15915 (2015).
pubmed: 26525406
pmcid: 4648340
doi: 10.1038/srep15915
Hutchinson, S., Glover, L. & Horn, D. High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes. BMC Genomics 17, 806 (2016).
pubmed: 27756224
pmcid: 5070307
doi: 10.1186/s12864-016-3154-8
Hoek, M., Zanders, T. & Cross, G. A. Trypanosoma brucei expression-site-associated-gene-8 protein interacts with a Pumilio family protein. Mol. Biochem Parasitol. 120, 269–283 (2002).
pubmed: 11897132
doi: 10.1016/S0166-6851(02)00009-9
Haanstra, J. R. et al. Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei. J. Biol. Chem. 283, 2495–2507 (2008).
pubmed: 17991737
doi: 10.1074/jbc.M705782200
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
pubmed: 29722887
pmcid: 5967553
doi: 10.1093/molbev/msy096
Clamp, M., Cuff, J., Searle, S. M. & Barton, G. J. The Jalview Java alignment editor. Bioinformatics 20, 426–427 (2004).
pubmed: 14960472
doi: 10.1093/bioinformatics/btg430
Bailey, T. L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).
pubmed: 19458158
pmcid: 2703892
doi: 10.1093/nar/gkp335