#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Organising the cell cycle in the absence of transcriptional control: Dynamic phosphorylation co-ordinates the Trypanosoma brucei cell cycle post-transcriptionally


Autoři: Corinna Benz aff001;  Michael D. Urbaniak aff001
Působiště autorů: Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom aff001
Vyšlo v časopise: Organising the cell cycle in the absence of transcriptional control: Dynamic phosphorylation co-ordinates the Trypanosoma brucei cell cycle post-transcriptionally. PLoS Pathog 15(12): e32767. doi:10.1371/journal.ppat.1008129
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.ppat.1008129

Souhrn

The cell division cycle of the unicellular eukaryote Trypanosome brucei is tightly regulated despite the paucity of transcriptional control that results from the arrangement of genes in polycistronic units and lack of dynamically regulated transcription factors. To identify the contribution of dynamic phosphorylation to T. brucei cell cycle control we have combined cell cycle synchronisation by centrifugal elutriation with quantitative phosphoproteomic analysis. Cell cycle regulated changes in phosphorylation site abundance (917 sites, average 5-fold change) were more widespread and of a larger magnitude than changes in protein abundance (443 proteins, average 2-fold change) and were mostly independent of each other. Hierarchical clustering of co-regulated phosphorylation sites according to their cell cycle profile revealed that a bulk increase in phosphorylation occurs across the cell cycle, with a significant enrichment of known cell cycle regulators and RNA binding proteins (RBPs) within the largest clusters. Cell cycle regulated changes in essential cell cycle kinases are temporally co-ordinated with differential phosphorylation of components of the kinetochore and eukaryotic initiation factors, along with many RBPs not previously linked to the cell cycle such as eight PSP1-C terminal domain containing proteins. The temporal profiles demonstrate the importance of dynamic phosphorylation in co-ordinating progression through the cell cycle, and provide evidence that RBPs play a central role in post-transcriptional regulation of the T. brucei cell cycle.

Data are available via ProteomeXchange with identifier PXD013488.

Klíčová slova:

Cell cycle and cell division – Parasitic cell cycles – Phosphorylation – Protein domains – RNA interference – RNA-binding proteins – Trypanosoma brucei gambiense – Stable isotope labeling by amino acids in cell culture


Zdroje

1. Simon Itamar, Barnett John, Hannett Nancy, Harbison Christopher T., Rinaldi Nicola J., Volkert Thomas L., et al. Serial Regulation of Transcriptional Regulators in the Yeast Cell cycle. Cell. 2001;106:697–708. doi: 10.1016/s0092-8674(01)00494-9 11572776

2. Morgan DO. Principles of CDK regulation. Nature. 1995;374:131–4. doi: 10.1038/374131a0 7877684

3. Pagliuca FW, Collins MO, Lichawska A, Zegerman P, Choudhary JS, Pines J. Quantitative proteomics reveals the basis for the biochemical specificity of the cell-cycle machinery. Mol Cell. 2011;43(3):406–17. doi: 10.1016/j.molcel.2011.05.031 21816347

4. Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, et al. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal. 2010;3(104):ra3. doi: 10.1126/scisignal.2000475 20068231

5. Clayton C. The regulation of trypanosome gene expression by RNA-binding proteins. PLoS Pathog. 2013;9(11):e1003680. doi: 10.1371/journal.ppat.1003680 24244152

6. Clayton CE. Life without transcritpional control? From fly to man and back again. EMBO J. 2002;21(8):881–1888.

7. Vasquez JJ, Hon CC, Vanselow JT, Schlosser A, Siegel TN. Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages. Nucleic Acids Res. 2014.

8. Manful T, Fadda A, Clayton C. The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA degradation. RNA. 2011;17(11):2039–47. doi: 10.1261/rna.2837311 21947264

9. McKean PG. Coordination of cell cycle and cytokinesis in Trypanosoma brucei. Curr Opin Microbiol. 2003;6(6):600–7. doi: 10.1016/j.mib.2003.10.010 14662356

10. Li Z. Regulation of the cell division cycle in Trypanosoma brucei. Eukaryot Cell. 2012;11(10):1180–90. doi: 10.1128/EC.00145-12 22865501

11. Li Z, Wang CC. A PHO80-like cyclin and a B-type cyclin control the cell cycle of the procyclic form of Trypanosoma brucei. J Biol Chem. 2003;278(23):20652–8. doi: 10.1074/jbc.M301635200 12665514

12. Tu X, Wang CC. The involvement of two cdc2-related kinases (CRKs) in Trypanosoma brucei cell cycle regulation and the distinctive stage-specific phenotypes caused by CRK3 depletion. J Biol Chem. 2004;279(19):20519–28. doi: 10.1074/jbc.M312862200 15010459

13. Archer SK, Inchaustegui D, Queiroz R, Clayton C. The cell cycle regulated transcriptome of Trypanosoma brucei. PloS one. 2011;6(3):e18425. doi: 10.1371/journal.pone.0018425 21483801

14. Crozier TWM, Tinti M, Wheeler RJ, Ly T, Ferguson MAJ, Lamond AI. Proteomic Analysis of the Cell Cycle of Procylic Form Trypanosoma brucei. Mol Cell Proteomics. 2018;17(6):1184–95. doi: 10.1074/mcp.RA118.000650 29555687

15. Archer SK, Luu VD, de Queiroz RA, Brems S, Clayton C. Trypanosoma brucei PUF9 regulates mRNAs for proteins involved in replicative processes over the cell cycle. PLoS Pathog. 2009;5(8):e1000565. doi: 10.1371/journal.ppat.1000565 19714224

16. Pasion SG, Brown GW, Brown LM, Ray DS. Periodic expression of nuclear and mitochondrial DNA replication genes during the trypanosomatid cell cycle. J Cell Sci. 1994;107:3515–20. 7706402

17. Mittra B, Ray DS. Presence of a poly(A) binding protein and two proteins with cell cycle-dependent phosphorylation in Crithidia fasciculata mRNA cycling sequence binding protein II. Eukaryot Cell. 2004;3(5):1185–97. doi: 10.1128/EC.3.5.1185-1197.2004 15470247

18. Urbaniak MD, Martin DM, Ferguson MA. Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei. Journal of proteome research. 2013;12(5):2233–44. doi: 10.1021/pr400086y 23485197

19. Benz C, Dondelinger F, McKean PG, Urbaniak MD. Cell cycle synchronisation of Trypanosoma brucei by centrifugal counter-flow elutriation reveals the timing of nuclear and kinetoplast DNA replication. Sci Rep. 2017;7(1):17599. doi: 10.1038/s41598-017-17779-z 29242601

20. Urbaniak MD, Guther MLS, Ferguson MAJ. Comparative SILAC Proteomic Analysis of Trypanosoma brucei Bloodstream and Procyclic Lifecycle Stages. PloS one. 2012;7(5):e36619. doi: 10.1371/journal.pone.0036619 22574199

21. Ishihama Y, Sato T, Tabata T, Miyamoto N, Sagane K, Nagasu T, et al. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat Biotechnol. 2005;23(5):617–21. doi: 10.1038/nbt1086 15834404

22. Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods. 2009;6(5):359–62. doi: 10.1038/nmeth.1322 19377485

23. Ruprecht B, Koch H, Medard G, Mundt M, Kuster B, Lemeer S. Comprehensive and reproducible phosphopeptide enrichment using iron immobilized metal ion affinity chromatography (Fe-IMAC) columns. Mol Cell Proteomics. 2015;14(1):205–15. doi: 10.1074/mcp.M114.043109 25394399

24. Yang F, Shen Y, Camp DG, 2nd, Smith RD. High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Rev Proteomics. 2012;9(2):129–34. doi: 10.1586/epr.12.15 22462785

25. Parsons M, Worthey EA, Ward PN, Mottram JC. Comparative analysis of the kinomes of three pathogenic trypanosomatids: Leishmania major, Trypanosoma brucei and Trypanosoma cruzi. BMC Genomics. 2005;6:127. doi: 10.1186/1471-2164-6-127 16164760

26. Urbaniak MD, Mathieson T, Bantscheff M, Eberhard D, Grimaldi R, Miranda-Saavedra D, et al. Chemical proteomic analysis reveals the drugability of the kinome of Trypanosoma brucei. ACS chemical biology. 2012;7(11):1858–65. doi: 10.1021/cb300326z 22908928

27. Jones NG, Thomas EB, Brown E, Dickens NJ, Hammarton TC, Mottram JC. Regulators of Trypanosoma brucei cell cycle progression and differentiation identified using a kinome-wide RNAi screen. PLoS Pathog. 2014;10(1):e1003886. doi: 10.1371/journal.ppat.1003886 24453978

28. Hammarton TC, Kramer S, Tetley L, Boshart M, Mottram JC. Trypanosoma brucei Polo-like kinase is essential for basal body duplication, kDNA segregation and cytokinesis. Mol Microbiol. 2007;65(5):1229–48. doi: 10.1111/j.1365-2958.2007.05866.x 17662039

29. Wei Y, Li Z. Distinct roles of a mitogen-activated protein kinase in cytokinesis between different life cycle forms of Trypanosoma brucei. Eukaryot Cell. 2014;13(1):110–8. doi: 10.1128/EC.00258-13 24213350

30. Gomes FC, Ali NO, Brown E, Walker RG, Grant KM, Mottram JC. Recombinant Leishmania mexicana CRK3:CYCA has protein kinase activity in the absence of phosphorylation on the T-loop residue Thr178. Mol Biochem Parasitol. 2010;171(2):89–96. doi: 10.1016/j.molbiopara.2010.03.002 20338198

31. Hayashi H, Akiyoshi B. Degradation of cyclin B is critical for nuclear division in Trypanosoma brucei. Biol Open. 2018;7(3).

32. Umeyama T, Wang CC. Polo-like kinase is expressed in S/G2/M phase and associated with the flagellum attachment zone in both procyclic and bloodstream forms of Trypanosoma brucei. Eukaryot Cell. 2008;7(9):1582–90. doi: 10.1128/EC.00150-08 18621923

33. de Graffenried CL, Ho HH, Warren G. Polo-like kinase is required for Golgi and bilobe biogenesis in Trypanosoma brucei. J Cell Biol. 2008;181(3):431–8. doi: 10.1083/jcb.200708082 18443217

34. McAllaster MR, Ikeda KN, Lozano-Nunez A, Anrather D, Unterwurzacher V, Gossenreiter T, et al. Proteomic identification of novel cytoskeletal proteins associated with TbPLK, an essential regulator of cell morphogenesis in Trypanosoma brucei. Mol Biol Cell. 2015;26(17):3013–29. doi: 10.1091/mbc.E15-04-0219 26133384

35. Hu H, Zhou Q, Li Z. A Novel Basal Body Protein That Is a Polo-like Kinase Substrate Is Required for Basal Body Segregation and Flagellum Adhesion in Trypanosoma brucei. J Biol Chem. 2015;290(41):25012–22. doi: 10.1074/jbc.M115.674796 26272611

36. Hu H, Zhou Q, Li Z. SAS-4 Protein in Trypanosoma brucei Controls Life Cycle Transitions by Modulating the Length of the Flagellum Attachment Zone Filament. J Biol Chem. 2015;290(51):30453–63. doi: 10.1074/jbc.M115.694109 26504079

37. Hilton NA, Sladewski TE, Perry JA, Pataki Z, Sinclair-Davis AN, Muniz RS, et al. Identification of TOEFAZ1-interacting proteins reveals key regulators of Trypanosoma brucei cytokinesis. Mol Microbiol. 2018;109(3):306–26. doi: 10.1111/mmi.13986 29781112

38. Akiyoshi B, Gull K. Discovery of unconventional kinetochores in kinetoplastids. Cell. 2014;156(6):1247–58. doi: 10.1016/j.cell.2014.01.049 24582333

39. D'Archivio S, Wickstead B. Trypanosome outer kinetochore proteins suggest conservation of chromosome segregation machinery across eukaryotes. J Cell Biol. 2017;216(2):379–91. 28034897

40. Saldivia M, Rao SPS, Fang E, Myburgh E, Brown E, Wollman AJM, et al. Targeting the trypanosome kinetochore with CLK1 protein kinase inhibitors. BioRxiv. 2019.

41. Lueong S, Merce C, Fischer B, Hoheisel JD, Erben ED. Gene expression regulatory networks in Trypanosoma brucei: insights into the role of the mRNA-binding proteome. Mol Microbiol. 2016;100(3):457–71. doi: 10.1111/mmi.13328 26784394

42. Erben ED, Fadda A, Lueong S, Hoheisel JD, Clayton C. A genome-wide tethering screen reveals novel potential post-transcriptional regulators in Trypanosoma brucei. PLoS Pathog. 2014;10(6):e1004178. doi: 10.1371/journal.ppat.1004178 24945722

43. Naguleswaran A, Gunasekera K, Schimanski B, Heller M, Hemphill A, Ochsenreiter T, et al. Trypanosoma brucei RRM1 is a nuclear RNA-binding protein and modulator of chromatin structure. MBio. 2015;6(2):e00114. doi: 10.1128/mBio.00114-15 25784696

44. Levy GV, Banuelos CP, Nittolo AG, Ortiz GE, Mendiondo N, Moretti G, et al. Depletion of the SR-Related Protein TbRRM1 Leads to Cell Cycle Arrest and Apoptosis-Like Death in Trypanosoma brucei. PloS one. 2015;10(8):e0136070. doi: 10.1371/journal.pone.0136070 26284933

45. Freire ER, Moura DMN, Bezerra MJR, Xavier CC, Morais-Sobral MC, Vashisht AA, et al. Trypanosoma brucei EIF4E2 cap-binding protein binds a homolog of the histone-mRNA stem-loop-binding protein. Curr Genet. 2018;64(4):821–39. doi: 10.1007/s00294-017-0795-3 29288414

46. Koseoglu MM, Graves LM, Marzluff WF. Phosphorylation of threonine 61 by cyclin a/Cdk1 triggers degradation of stem-loop binding protein at the end of S phase. Mol Cell Biol. 2008;28(14):4469–79. doi: 10.1128/MCB.01416-07 18490441

47. An T, Liu Y, Gourguechon S, Wang CC, Li Z. CDK Phosphorylation of Translation Initiation Factors Couples Protein Translation with Cell-Cycle Transition. Cell Rep. 2018;25(11):3204–14 e5. doi: 10.1016/j.celrep.2018.11.063 30540951

48. Freire ER, Dhalia R, Moura DM, da Costa Lima TD, Lima RP, Reis CR, et al. The four trypanosomatid eIF4E homologues fall into two separate groups, with distinct features in primary sequence and biological properties. Mol Biochem Parasitol. 2011;176(1):25–36. doi: 10.1016/j.molbiopara.2010.11.011 21111007

49. Zinoviev A, Akum Y, Yahav T, Shapira M. Gene duplication in trypanosomatids—two DED1 paralogs are functionally redundant and differentially expressed during the life cycle. Mol Biochem Parasitol. 2012;185(2):127–36. doi: 10.1016/j.molbiopara.2012.08.001 22910033

50. Formosa T, Nittis T. Suppressors of the temperature sensitivity of DNA polymerase alpha mutations in Saccharomyces cerevisiae. Mol Gen Genet. 1998;257(4):461–8. doi: 10.1007/s004380050670 9529527

51. Benz C, Lo W, Fathallah N, Connor-Guscott A, Benns HJ, Urbaniak MD. Dynamic regulation of the Trypanosoma brucei transferrin receptor in response to iron starvation is mediated via the 3'UTR. PloS one. 2018;13(12):e0206332. doi: 10.1371/journal.pone.0206332 30596656

52. Domingo-Sananes MR, Szoor B, Ferguson MA, Urbaniak MD, Matthews KR. Molecular control of irreversible bistability during trypanosome developmental commitment. J Cell Biol. 2015;211(2):455–68. doi: 10.1083/jcb.201506114 26483558

53. Nett IRE, Martin DMA, Miranda-Saavedra D, Lamont D, Barber JD, Mehlert A, et al. The phopshoproteome of bloodstream form Trypanosoma brucei, causative agent of African sleeping sickness. Mol Cell Proteomics. 2009;8.7:1527–38. doi: 10.1074/mcp.M800556-MCP200 19346560

54. Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, et al. TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res. 2010;38(Database issue):D457–62. doi: 10.1093/nar/gkp851 19843604

55. Mitchell Alex L, Attwood Teresa K, Babbitt Patricia C, Blum Matthias, Bork Peer, Bridge Alan, et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acid Res. 2019;47:D351–D60. doi: 10.1093/nar/gky1100 30398656

56. Schroeder MJ, Shabanowitz J, Schwartz JC, Hunt DF, Coon JJ. A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Analytical chemistry. 2004;76(13):3590–8. doi: 10.1021/ac0497104 15228329

57. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26(12):1367–72. doi: 10.1038/nbt.1511 19029910

58. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. Journal of proteome research. 2011;10(4):1794–805. doi: 10.1021/pr101065j 21254760

59. Vizcaino JA, Cote RG, Csordas A, Dianes JA, Fabregat A, Foster JM, et al. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013;41(Database issue):D1063–9. doi: 10.1093/nar/gks1262 23203882

60. Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat Methods. 2016;13(9):731–40. doi: 10.1038/nmeth.3901 27348712

61. Poon SK, 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. 2012;2(2):110037. doi: 10.1098/rsob.110037 22645659

62. Benz C, Clucas C, Mottram JC, Hammarton TC. Cytokinesis in bloodstream stage Trypanosoma brucei requires a family of katanins and spastin. PloS one. 2012;7(1):e30367. doi: 10.1371/journal.pone.0030367 22279588

63. Wickstead B, Ersfeld K, Gull K. Targeting of a tetracycline-inducible expression system to the transcriptionally silent minichromosomes of Trypanosoma brucei. Mol Biochem Parasitol. 2002;125:211–6. doi: 10.1016/s0166-6851(02)00238-4 12467990

64. Dean S, Sunter J, Wheeler RJ, Hodkinson I, Gluenz E, Gull K. A toolkit enabling efficient, scalable and reproducible gene tagging in trypanosomatids. Open Biol. 2015;5(1):140197. doi: 10.1098/rsob.140197 25567099

Štítky
Hygiena a epidemiologie Infekční lékařství Laboratoř

Článek vyšel v časopise

PLOS Pathogens


2019 Číslo 12
Nejčtenější tento týden
Nejčtenější v tomto čísle
Kurzy Podcasty Doporučená témata Časopisy
Přihlášení
Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se

#ADS_BOTTOM_SCRIPTS#