Systematic functional analysis of Leishmania protein kinases identifies regulators of differentiation or survival
Jazyk angličtina Země Anglie, Velká Británie Médium electronic
Typ dokumentu časopisecké články, práce podpořená grantem
Grantová podpora
MR/L00092X/1
Medical Research Council - United Kingdom
MR/P027989/1
Medical Research Council - United Kingdom
200807/Z/16/Z
Wellcome Trust - United Kingdom
Wellcome Trust - United Kingdom
200807
Wellcome Trust - United Kingdom
PubMed
33623024
PubMed Central
PMC7902614
DOI
10.1038/s41467-021-21360-8
PII: 10.1038/s41467-021-21360-8
Knihovny.cz E-zdroje
- MeSH
- biologické modely MeSH
- buněčná diferenciace * MeSH
- CRISPR-Cas systémy genetika MeSH
- delece genu MeSH
- flagella enzymologie MeSH
- Leishmania mexicana cytologie enzymologie MeSH
- leishmanióza parazitologie patologie MeSH
- mutace genetika MeSH
- myši inbrední BALB C MeSH
- myši MeSH
- protein Cas9 metabolismus MeSH
- proteinkinasy genetika metabolismus MeSH
- proteom metabolismus MeSH
- Psychodidae parazitologie MeSH
- viabilita buněk MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- protein Cas9 MeSH
- proteinkinasy MeSH
- proteom MeSH
Differentiation between distinct stages is fundamental for the life cycle of intracellular protozoan parasites and for transmission between hosts, requiring stringent spatial and temporal regulation. Here, we apply kinome-wide gene deletion and gene tagging in Leishmania mexicana promastigotes to define protein kinases with life cycle transition roles. Whilst 162 are dispensable, 44 protein kinase genes are refractory to deletion in promastigotes and are likely core genes required for parasite replication. Phenotyping of pooled gene deletion mutants using bar-seq and projection pursuit clustering reveal functional phenotypic groups of protein kinases involved in differentiation from metacyclic promastigote to amastigote, growth and survival in macrophages and mice, colonisation of the sand fly and motility. This unbiased interrogation of protein kinase function in Leishmania allows targeted investigation of organelle-associated signalling pathways required for successful intracellular parasitism.
Department of Biology University of York York UK
Department of Mathematics University of York York UK
Department of Parasitology Faculty of Science Charles University Prague Czech Republic
Department of Physics University of York York UK
York Biomedical Research Institute University of York York UK
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Matthews KR. Controlling and coordinating development in vector-transmitted parasites. Science. 2011;331:1149–1153. doi: 10.1126/science.1198077. PubMed DOI PMC
Solyakov L, et al. Global kinomic and phospho-proteomic analyses of the human malaria parasite Plasmodium falciparum. Nat. Commun. 2011;2:565. doi: 10.1038/ncomms1558. PubMed DOI
Stanway RR, et al. Genome-scale identification of essential metabolic processes for targeting the Plasmodium liver stage. Cell. 2019;179:1112–1128.e26. doi: 10.1016/j.cell.2019.10.030. PubMed DOI PMC
Mony BM, et al. Genome-wide dissection of the quorum sensing signalling pathway in Trypanosoma brucei. Nature. 2014;505:681–685. doi: 10.1038/nature12864. PubMed DOI PMC
Cayla M, McDonald L, MacGregor P, Matthews K. An atypical DYRK kinase connects quorum-sensing with posttranscriptional gene regulation in Trypanosoma brucei. Elife. 2020;9:e51620. doi: 10.7554/eLife.51620. PubMed DOI PMC
Volf P, Hajmova M, Sadlova J, Votypka J. Blocked stomodeal valve of the insect vector: similar mechanism of transmission in two trypanosomatid models. Int. J. Parasitol. 2004;34:1221–1227. doi: 10.1016/j.ijpara.2004.07.010. PubMed DOI
Walters LL. Leishmania differentiation in natural and unnatural sand fly hosts 1. J. Eukaryot. Microbiol. 1993;40:196–206. doi: 10.1111/j.1550-7408.1993.tb04904.x. PubMed DOI
Dostálová A, Volf P. Leishmania development in sand flies: parasite-vector interactions overview. Parasit. Vectors. 2012;5:276. doi: 10.1186/1756-3305-5-276. PubMed DOI PMC
Tsigankov P, Gherardini PF, Helmer-Citterich M, Späth GF, Zilberstein D. Phosphoproteomic analysis of differentiating Leishmania parasites reveals a unique stage-specific phosphorylation motif. J. Proteome Res. 2013;12:3405–3412. doi: 10.1021/pr4002492. PubMed DOI
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. PubMed DOI PMC
Jones NG, et al. Regulators of Trypanosoma brucei cell cycle progression and differentiation identified using a kinome-wide RNAi screen. PLoS Pathog. 2014;10:e1003886. doi: 10.1371/journal.ppat.1003886. PubMed DOI PMC
Ward P, Equinet L, Packer J, Doerig C. Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics. 2004;5:79. doi: 10.1186/1471-2164-5-79. PubMed DOI PMC
Cayla M, et al. Transgenic analysis of the Leishmania MAP kinase MPK10 reveals an auto-inhibitory mechanism crucial for stage-regulated activity and parasite viability. PLoS Pathog. 2014;10:e1004347. doi: 10.1371/journal.ppat.1004347. PubMed DOI PMC
Wiese M, Kuhn D, Grünfelder CG. Protein kinase involved in flagellar-length control. Eukaryot. Cell. 2003;2:769–777. doi: 10.1128/EC.2.4.769-777.2003. PubMed DOI PMC
Erdmann M, Scholz A, Melzer IM, Schmetz C, Wiese M. Interacting protein kinases involved in the regulation of flagellar length. Mol. Biol. Cell. 2006;17:2035–2045. doi: 10.1091/mbc.e05-10-0976. PubMed DOI PMC
Dacher M, et al. Probing druggability and biological function of essential proteins in Leishmania combining facilitated null mutant and plasmid shuffle analyses. Mol. Microbiol. 2014;93:146–166. doi: 10.1111/mmi.12648. PubMed DOI
Martin JL, et al. Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani. PLoS Pathog. 2014;10:e1003938. doi: 10.1371/journal.ppat.1003938. PubMed DOI PMC
Mandal G, et al. Modulation of Leishmania major aquaglyceroporin activity by a mitogen-activated protein kinase. Mol. Microbiol. 2012;85:1204–1218. doi: 10.1111/j.1365-2958.2012.08169.x. PubMed DOI PMC
Goldman-Pinkovich A, et al. An arginine deprivation response pathway is induced in Leishmania during macrophage invasion. PLoS Pathog. 2016;12:e1005494. doi: 10.1371/journal.ppat.1005494. PubMed DOI PMC
Kuhn D, Wiese M. LmxPK4, a mitogen-activated protein kinase kinase homologue of Leishmania mexicana with a potential role in parasite differentiation. Mol. Microbiol. 2005;56:1169–1182. doi: 10.1111/j.1365-2958.2005.04614.x. PubMed DOI
Bengs F, Scholz A, Kuhn D, Wiese M. LmxMPK9, a mitogen-activated protein kinase homologue affects flagellar length in Leishmania mexicana. Mol. Microbiol. 2005;55:1606–1615. doi: 10.1111/j.1365-2958.2005.04498.x. PubMed DOI
Madeira da Silva L, Beverley SM. Expansion of the target of rapamycin (TOR) kinase family and function in Leishmania shows that TOR3 is required for acidocalcisome biogenesis and animal infectivity. Proc. Natl Acad. Sci. USA. 2010;107:11965–11970. doi: 10.1073/pnas.1004599107. PubMed DOI PMC
Bhattacharya A, et al. Coupling chemical mutagenesis to next generation sequencing for the identification of drug resistance mutations in Leishmania. Nat. Commun. 2019;10:5627. doi: 10.1038/s41467-019-13344-6. PubMed DOI PMC
Duncan SM, et al. Conditional gene deletion with DiCre demonstrates an essential role for CRK3 in Leishmania mexicana cell cycle regulation. Mol. Microbiol. 2016;100:931–944. doi: 10.1111/mmi.13375. PubMed DOI PMC
Martel D, Beneke T, Gluenz E, Späth GF, Rachidi N. Characterisation of casein kinase 1.1 in Leishmania donovani using the CRISPR Cas9 toolkit. Biomed. Res. Int. 2017;2017:4635605. doi: 10.1155/2017/4635605. PubMed DOI PMC
Rachidi N, et al. Pharmacological assessment defines Leishmania donovani casein kinase 1 as a drug target and reveals important functions in parasite viability and intracellular infection. Antimicrob. Agents Chemother. 2014;58:1501–1515. doi: 10.1128/AAC.02022-13. PubMed DOI PMC
Agron PG, Reed SL, Engel JN. An essential, putative MEK kinase of Leishmania major. Mol. Biochem. Parasitol. 2005;142:121–125. doi: 10.1016/j.molbiopara.2005.03.007. PubMed DOI
Rocha VPC, et al. Leishmania dual-specificity tyrosine-regulated kinase 1 (DYRK1) is required for sustaining Leishmania stationary phase phenotype. Mol. Microbiol. 2020;113:983–1002. doi: 10.1111/mmi.14464. PubMed DOI
Wang Q, Melzer IM, Kruse M, Sander-Juelch C, Wiese M. LmxMPK4, a mitogen-activated protein (MAP) kinase homologue essential for promastigotes and amastigotes of Leishmania mexicana. Kinetoplastid Biol. Dis. 2005;4:6. doi: 10.1186/1475-9292-4-6. PubMed DOI PMC
Mottram JC, McCready BP, Brown KG, Grant KM. Gene disruptions indicate an essential function for the LmmCRK1 cdc2-related kinase of Leishmania mexicana. Mol. Microbiol. 1996;22:573–583. doi: 10.1046/j.1365-2958.1996.00136.x. PubMed DOI
Beneke T, et al. A CRISPR Cas9 high-throughput genome editing toolkit for kinetoplastids. R. Soc. Open Sci. 2017;4:170095. doi: 10.1098/rsos.170095. PubMed DOI PMC
Cruz A, Coburn CM, Beverley SM. Double targeted gene replacement for creating null mutants. Proc. Natl Acad. Sci. USA. 1991;88:7170–7174. doi: 10.1073/pnas.88.16.7170. PubMed DOI PMC
Damianou A, et al. Essential roles for deubiquitination in Leishmania life cycle progression. PLoS Pathog. 2020;16:e1008455. doi: 10.1371/journal.ppat.1008455. PubMed DOI PMC
Jones NG, Catta-Preta CMC, Lima APCA, Mottram JC. Genetically validated drug targets in Leishmania: current knowledge and future prospects. ACS Infect. Dis. 2018;4:467–477. doi: 10.1021/acsinfecdis.7b00244. PubMed DOI PMC
Carrera AC, Alexandrov K, Roberts TM. The conserved lysine of the catalytic domain of protein kinases is actively involved in the phosphotransfer reaction and not required for anchoring ATP. Proc. Natl Acad. Sci. USA. 1993;90:442–446. doi: 10.1073/pnas.90.2.442. PubMed DOI PMC
Halliday C, et al. Cellular landmarks of Trypanosoma brucei and Leishmania mexicana. Mol. Biochem. Parasitol. 2019;230:24–36. doi: 10.1016/j.molbiopara.2018.12.003. PubMed DOI PMC
Burge RJ, Damianou A, Wilkinson AJ, Rodenko B, Mottram JC. Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex. PLoS Pathog. 2020;16:e1008784. doi: 10.1371/journal.ppat.1008784. PubMed DOI PMC
Wiese M. A mitogen‐activated protein (MAP) kinase homologue of Leishmania mexicana is essential for parasite survival in the infected host. EMBO J. 1998;17:2619–2628. doi: 10.1093/emboj/17.9.2619. PubMed DOI PMC
Bolton RJ, Krzanowski WJ. Projection pursuit clustering for exploratory data analysis. J. Comput. Graph. Stat. 2003;12:121–142. doi: 10.1198/1061860031374. DOI
Fernandez-Cortes F, et al. RNAi screening identifies Trypanosoma brucei stress response protein kinases required for survival in the mouse. Sci. Rep. 2017;7:6156. doi: 10.1038/s41598-017-06501-8. PubMed DOI PMC
Beneke T, et al. Genetic dissection of a Leishmania flagellar proteome demonstrates requirement for directional motility in sand fly infections. PLoS Pathog. 2019;15:e1007828. doi: 10.1371/journal.ppat.1007828. PubMed DOI PMC
Hassan P, Fergusson D, Grant KM, Mottram JC. The CRK3 protein kinase is essential for cell cycle progression of Leishmania mexicana. Mol. Biochem. Parasitol. 2001;113:189–198. doi: 10.1016/S0166-6851(01)00220-1. PubMed DOI
Wyllie S, et al. Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis. Nature. 2018;560:192–197. doi: 10.1038/s41586-018-0356-z. PubMed DOI PMC
Martínez-Calvillo S, Stuart K, Myler PJ. Ploidy changes associated with disruption of two adjacent genes on Leishmania major chromosome 1. Int. J. Parasitol. 2005;35:419–429. doi: 10.1016/j.ijpara.2004.12.014. PubMed DOI
Pearce LR, Komander D, Alessi DR. The nuts and bolts of AGC protein kinases. Nat. Rev. Mol. Cell Biol. 2010;11:9–22. doi: 10.1038/nrm2822. PubMed DOI
Harashima H, Dissmeyer N, Schnittger A. Cell cycle control across the eukaryotic kingdom. Trends Cell Biol. 2013;23:345–356. doi: 10.1016/j.tcb.2013.03.002. PubMed DOI
Akiyoshi B, Gull K. Discovery of unconventional kinetochores in kinetoplastids. Cell. 2014;156:1247–1258. doi: 10.1016/j.cell.2014.01.049. PubMed DOI PMC
Ambit A, Woods KL, Cull B, Coombs GH, Mottram JC. Morphological events during the cell cycle of Leishmania major. Eukaryot. Cell. 2011;10:1429–1438. doi: 10.1128/EC.05118-11. PubMed DOI PMC
Wheeler RJ, Gluenz E, Gull K. The cell cycle of Leishmania: morphogenetic events and their implications for parasite biology. Mol. Microbiol. 2011;79:647–662. doi: 10.1111/j.1365-2958.2010.07479.x. PubMed DOI PMC
Bushell E, et al. Functional profiling of a Plasmodium genome reveals an abundance of essential genes. Cell. 2017;170:260–272.e8. doi: 10.1016/j.cell.2017.06.030. PubMed DOI PMC
Wincott, C. J. et al. The host brain is permissive to colonization by Toxoplasma gondii. Preprint at 10.1101/2020.08.06.239822 (2020).
Behan FM, et al. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature. 2019;568:511–516. doi: 10.1038/s41586-019-1103-9. PubMed DOI
Saldivia M, et al. Targeting the trypanosome kinetochore with CLK1 protein kinase inhibitors. Nat. Microbiol. 2020;5:1207–1216. doi: 10.1038/s41564-020-0745-6. PubMed DOI PMC
Dan-Goor M, Nasereddin A, Jaber H, Jaffe CL. Identification of a secreted casein kinase 1 in Leishmania donovani: effect of protein over expression on parasite growth and virulence. PLoS ONE. 2013;8:e79287. doi: 10.1371/journal.pone.0079287. PubMed DOI PMC
Sádlová J, Volf P. Peritrophic matrix of Phlebotomus duboscqi and its kinetics during Leishmania major development. Cell Tissue Res. 2009;337:313–325. doi: 10.1007/s00441-009-0802-1. PubMed DOI PMC
Zhou Q, Pham KTM, Hu H, Kurasawa Y, Li Z. A kinetochore-based ATM/ATR-independent DNA damage checkpoint maintains genomic integrity in trypanosomes. Nucleic Acids Res. 2019;47:7973–7988. doi: 10.1093/nar/gkz476. PubMed DOI PMC
Varga V, Moreira-Leite F, Portman N, Gull K. Protein diversity in discrete structures at the distal tip of the trypanosome flagellum. Proc. Natl Acad. Sci. USA. 2017;114:E6546–E6555. doi: 10.1073/pnas.1703553114. PubMed DOI PMC
Weischenfeldt J, Porse B. Bone marrow-derived macrophages (BMM): Isolation and applications. CSH Protoc. 2008;3:1–6 db.prot5080. doi: 10.1038/nprot.2007.453. PubMed DOI
Späth GF, Beverley SM. A lipophosphoglycan-independent method for isolation of infective Leishmania metacyclic promastigotes by density gradient centrifugation. Exp. Parasitol. 2001;99:97–103. doi: 10.1006/expr.2001.4656. PubMed DOI
Volf P, Volfova V. Establishment and maintenance of sand fly colonies. J. Vector Ecol. 2011;36(Suppl 1):S1–S9. doi: 10.1111/j.1948-7134.2011.00106.x. PubMed DOI
Pruzinova K, et al. Comparison of bloodmeal digestion and the peritrophic matrix in four sand fly species differing in susceptibility to Leishmania donovani. PLoS ONE. 2015;10:e0128203. doi: 10.1371/journal.pone.0128203. PubMed DOI PMC
Castanys-Muñoz E, Brown E, Coombs GH, Mottram JC. Leishmania mexicana metacaspase is a negative regulator of amastigote proliferation in mammalian cells. Cell Death Dis. 2012;3:e385. doi: 10.1038/cddis.2012.113. PubMed DOI PMC
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10–12. doi: 10.14806/ej.17.1.200. DOI
Beneke T, Gluenz E. Bar-seq strategies for the LeishGEdit toolbox. Mol. Biochem. Parasitol. 2020;239:111295. doi: 10.1016/j.molbiopara.2020.111295. PubMed DOI
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).
Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. 2018;34:867–868. doi: 10.1093/bioinformatics/btx699. PubMed DOI PMC
Tetaud E, Lecuix I, Sheldrake T, Baltz T, Fairlamb AH. A new expression vector for Crithidia fasciculata and Leishmania. Mol. Biochem. Parasitol. 2002;120:195–204. doi: 10.1016/S0166-6851(02)00002-6. PubMed DOI
Kühn MJ, et al. Spatial arrangement of several flagellins within bacterial flagella improves motility in different environments. Nat. Commun. 2018;9:5369. doi: 10.1038/s41467-018-07802-w. PubMed DOI PMC
Martínez de Iturrate P, et al. Towards discovery of new leishmanicidal scaffolds able to inhibit GSK-3. J. Enz. Inhib. Med. Chem. 2020;35:199–210. doi: 10.1080/14756366.2019.1693704. PubMed DOI PMC
Chhajer R, et al. Leishmania donovani Aurora kinase: A promising therapeutic target against visceral leishmaniasis. Biochim. et Biophys. Acta. 2016;1860:1973–1988. doi: 10.1016/j.bbagen.2016.06.005. PubMed DOI
ULK4 and Fused/STK36 interact to mediate assembly of a motile flagellum