Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum

BMC Genomics

Gad Shaulsky¹  Blaz Zupan²  William F Loomis³  Mariko Katoh-Kurasawa⁴  Danny Fuller³  Balaji Santhanam¹  Rafael David Rosengarten⁴ 

[1] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston 77030, TX, USA;Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, Ljubljana SI-1001, Slovenia;Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla 92093, CA, USA;Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston 77030, TX, USA

关键词: Slime mold;    Dictyostelium discoideum;    Differential expression;    Principal component analysis;    Synchrony;    Development;    Time course;    Transcriptome;   

Others  :  1172201
DOI  :  10.1186/s12864-015-1491-7

 received in 2014-10-09, accepted in 2015-03-26,  发布年份 2015

【 摘 要 】

Background

Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental program are often studied in cells starved in suspension while cAMP is provided exogenously. Previous studies revealed massive shifts in the transcriptome under both developmental conditions and a close relationship between gene expression and morphogenesis, but were limited by the sampling frequency and the resolution of the methods.

Results

Here, we combine the superior depth and specificity of RNA-seq-based analysis of mRNA abundance with high frequency sampling during filter development and cAMP pulsing in suspension. We found that the developmental transcriptome exhibits mostly gradual changes interspersed by a few instances of large shifts. For each time point we treated the entire transcriptome as single phenotype, and were able to characterize development as groups of similar time points separated by gaps. The grouped time points represented gradual changes in mRNA abundance, or molecular phenotype, and the gaps represented times during which many genes are differentially expressed rapidly, and thus the phenotype changes dramatically. Comparing developmental experiments revealed that gene expression in filter developed cells lagged behind those treated with exogenous cAMP in suspension. The high sampling frequency revealed many genes whose regulation is reproducibly more complex than indicated by previous studies. Gene Ontology enrichment analysis suggested that the transition to multicellularity coincided with rapid accumulation of transcripts associated with DNA processes and mitosis. Later development included the up-regulation of organic signaling molecules and co-factor biosynthesis. Our analysis also demonstrated a high level of synchrony among the developing structures throughout development.

Conclusions

Our data describe D. discoideum development as a series of coordinated cellular and multicellular activities. Coordination occurred within fields of aggregating cells and among multicellular bodies, such as mounds or migratory slugs that experience both cell-cell contact and various soluble signaling regimes. These time courses, sampled at the highest temporal resolution to date in this system, provide a comprehensive resource for studies of developmental gene expression.

【 授权许可】

   
2015 Rosengarten et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

【 参考文献 】

• [1]Raper K: Pseudoplasmodium formation and organization in Dictyostelium discoideum. J Elisha Mitchell Sci Soc 1940, 56:241-282.
• [2]Williams JG: Dictyostelium finds new roles to model. Genetics 2010, 185:717-726.
• [3]Kessin RH: Dictyostelium: evolution, cell biology, and development of multicellularity. Cambridge University Press, Cambridge, UK; 2001.
• [4]Van Driessche N, Shaw C, Katoh M, Morio T, Sucgang R, Ibarra M, et al.: A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 2002, 129:1543-1552.
• [5]Sussman R, Sussman M: Cultivation of Dictyostelium discoideum in axenic medium. Biochem Biophys Res Commun 1967, 29:53-55.
• [6]Watts DJ, Ashworth JM: Growth of myxameobae of the cellular slime mould Dictyostelium discoideum in axenic culture. Biochem J 1970, 119:171-174.
• [7]Bonner JT: Evidence for the formation of cell aggregates by chemotaxis in the development of the slime mold Dictyostelium discoideum. J Exp Zool 1947, 106:1-26.
• [8]Loomis WF: Cell signaling during development of Dictyostelium. Dev Biol 2014, 391:1-16.
• [9]Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, et al.: Functional discovery via a compendium of expression profiles. Cell 2000, 102:109-126.
• [10]Ringnér M: What is principal component analysis? Nat Biotechnol 2008, 26:303-304.
• [11]Steuer R, Morgenthal K, Weckwerth W, Selbig J: A gentle guide to the analysis of metabolomic data. Methods Mol Biol Clifton NJ 2007, 358:105-126.
• [12]Iranfar N, Fuller D, Loomis WF: Genome-wide expression analyses of gene regulation during early development of Dictyostelium discoideum. Eukaryot Cell 2003, 2:664-670.
• [13]Tyson JJ, Murray JD: Cyclic AMP waves during aggregation of Dictyostelium amoebae. Development 1989, 106:421-426.
• [14]Li Y, Goldbeter A: Pulsatile signaling in intercellular communication. Periodic stimuli are more efficient than random or chaotic signals in a model based on receptor desensitization. Biophys J 1992, 61:161-171.
• [15]Laub MT, Loomis WF: A molecular network that produces spontaneous oscillations in excitable cells of Dictyostelium. Mol Biol Cell 1998, 9:3521-3532.
• [16]Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, et al.: Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol 2010, 11:R35. BioMed Central Full Text
• [17]Loomis WF, Shaulsky G: Developmental changes in transcriptional profiles. Dev Growth Differ 2011, 53:567-575.
• [18]Miranda ER, Zhuchenko O, Toplak M, Santhanam B, Zupan B, Kuspa A, et al.: ABC transporters in Dictyostelium discoideum development. PLoS One 2013, 8:e70040.
• [19]Williams JG: Transcriptional regulation of Dictyostelium pattern formation. EMBO Rep 2006, 7:694-698.
• [20]Rosengarten RD, Santhanam B, Katoh-Kurasawa M: Transcriptional regulators: dynamic drivers of multicellular formation, cell differentiation and development. In Dictyostelids. Edited by Romeralo M, Baldauf S, Escalante R. Springer, Heidelberg, Germany; 2013:89-108.
• [21]Gerisch G: Cell aggregation and differentiation in Dictyostelium. Curr Top Dev Biol 1968, 3:157-197.
• [22]Ponte E, Rivero F, Fechheimer M, Noegel A, Bozzaro S: Severe developmental defects in Dictyostelium null mutants for actin-binding proteins. Mech Dev 2000, 91:153-161.
• [23]Funamoto S, Milan K, Meili R, Firtel RA: Role of phosphatidylinositol 3’ kinase and a downstream pleckstrin homology domain-containing protein in controlling chemotaxis in Dictyostelium. J Cell Biol 2001, 153:795-810.
• [24]Veeranki S, Kim B, Kim L: The GPI-anchored superoxide dismutase SodC is essential for regulating basal Ras activity and for chemotaxis of Dictyostelium discoideum. J Cell Sci 2008, 121(Pt 18):3099-3108.
• [25]Wang Y, Chen C-L, Iijima M: Signaling mechanisms for chemotaxis. Dev Growth Differ 2011, 53:495-502.
• [26]Zatulovskiy E, Tyson R, Bretschneider T, Kay RR: Bleb-driven chemotaxis of Dictyostelium cells. J Cell Biol 2014, 204:1027-1044.
• [27]Benabentos R, Hirose S, Sucgang R, Curk T, Katoh M, Ostrowski EA, et al.: Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium. Curr Biol 2009, 19:567-572.
• [28]Hirose S, Benabentos R, Ho H-I, Kuspa A, Shaulsky G: Self-recognition in social amoebae is mediated by allelic pairs of tiger genes. Science 2011, 333:467-470.
• [29]Kibler K, Nguyen T-L, Svetz J, Van Driessche N, Ibarra M, Thompson C, et al.: A novel developmental mechanism in Dictyostelium revealed in a screen for communication mutants. Dev Biol 2003, 259:193-208.
• [30]Iranfar N, Fuller D, Loomis WF: Transcriptional regulation of post-aggregation genes in Dictyostelium by a feed-forward loop involving GBF and LagC. Dev Biol 2006, 290:460-469.
• [31]Iranfar N, Fuller D, Sasik R, Hwa T, Laub M, Loomis WF: Expression patterns of cell-type–specific genes in Dictyostelium. Mol Biol Cell 2001, 12:2590.
• [32]Escalante R, Sastre L: Regulated expression of the MADS-box transcription factor SrfA mediates activation of gene expression by protein kinase A during Dictyostelium sporulation. Mech Dev 2002, 117:201-208.
• [33]West CM, Zhang P, McGlynn AC, Kaplan L: Outside-in signaling of cellulose synthesis by a spore coat protein in Dictyostelium. Eukaryot Cell 2002, 1:281-292.
• [34]Cabral M, Anjard C, Loomis WF, Kuspa A: Genetic evidence that the acyl coenzyme A binding protein AcbA and the serine protease/ABC transporter TagA function together in Dictyostelium discoideum cell differentiation. Eukaryot Cell 2006, 5:2024-2032.
• [35]Cabral M, Anjard C, Malhotra V, Loomis WF, Kuspa A: Unconventional secretion of AcbA in Dictyostelium discoideum through a vesicular intermediate. Eukaryot Cell 2010, 9:1009-1017.
• [36]Fukuzawa M: Control of prestalk-cell differentiation by transcription factors. Dev Growth Differ 2011, 53:538-547.
• [37]Yamada Y, Kay RR, Bloomfield G, Ross S, Ivens A, Williams JG: A new Dictyostelium prestalk cell sub-type. Dev Biol 2010, 339:390-397.
• [38]Chen G, Kuspa A: Prespore cell fate bias in G1 phase of the cell cycle in Dictyostelium discoideum. Eukaryot Cell 2005, 4:1755-1764.
• [39]Chen G, Shaulsky G, Kuspa A: Tissue-specific G1-phase cell-cycle arrest prior to terminal differentiation in Dictyostelium. Development 2004, 131:2619-2630.
• [40]Bonner JT, Frascella EB: Mitotic activity in relation to differentiation in the slime mold Dictyostelium discoideum. J Exp Zool 1952, 121:561-571.
• [41]Van Driessche N, Demsar J, Booth EO, Hill P, Juvan P, Zupan B, et al.: Epistasis analysis with global transcriptional phenotypes. Nat Genet 2005, 37:471-477.
• [42]Kay RR, Berks M, Traynor D, Taylor GW, Masento MS, Morris HR: Signals controlling cell differentiation and pattern formation in Dictyostelium. Dev Genet 1988, 9:579-587.
• [43]Wilkinson DG, Wilson J, Hames BD: Spore coat protein synthesis during development of Dictyostelium discoideum requires a low-molecular-weight inducer and continued multicellularity. Dev Biol 1985, 107:38-46.
• [44]Devine KM, Morrissey JH, Loomis WF: Differential synthesis of spore coat proteins in prespore and prestalk cells of Dictyostelium. Proc Natl Acad Sci U S A 1982, 79:7361-7365.
• [45]Ramagopal S: The Dictyostelium ribosome: biochemistry, molecular biology, and developmental regulation. Biochem Cell Biol 1992, 70:738-750.
• [46]Singleton CK, Manning SS, Ken R: Primary structure and regulation of vegetative specific genes of Dictyostelium discoideum. Nucleic Acids Res 1989, 17:9679-9692.
• [47]Tanaka Y, Itakura R, Amagai A, Maeda Y: The signals for starvation response are transduced through elevated [Ca2+] i in Dictyostelium cells. Exp Cell Res 1998, 240:340-348.
• [48]Souza GM, da Silva AM, Kuspa A: Starvation promotes Dictyostelium development by relieving PufA inhibition of PKA translation through the YakA kinase pathway. Development 1999, 126:3263-3274.
• [49]Levine H, Aranson I, Tsimring L, Truong TV: Positive genetic feedback governs cAMP spiral wave formation in Dictyostelium. Proc Natl Acad Sci U S A 1996, 93:6382-6386.
• [50]Shaulsky G, Loomis WF: Mitochondrial DNA replication but no nuclear DNA replication during development of Dictyostelium. Proc Natl Acad Sci U S A 1995, 92:5660-5663.
• [51]Muramoto T, Chubb JR: Live imaging of the Dictyostelium cell cycle reveals widespread S phase during development, a G2 bias in spore differentiation and a premitotic checkpoint. Development 2008, 135:1647-1657.
• [52]Hames BD, Ashworth JM: The metabolism of macromolecules during the differentiation of Myxamoebae of the cellular slime mould Dictyostelium discoideum containing different amounts of glycogen. Biochem J 1974, 142:301-315.
• [53]Lardy B, Bof M, Aubry L, Paclet MH, Morel F, Satre M, et al.: NADPH oxidase homologs are required for normal cell differentiation and morphogenesis in Dictyostelium discoideum. Biochim Biophys Acta 2005, 1774:199-212.
• [54]Stuchell RN, Weinstein BI, Beattie DS: Effects of ethidium bromide on various segments of the respiratory chain in the cellular slime mold, Dictyostelium discoideum. FEBS Lett 1973, 37:23-26.
• [55]McMahon D, Miller M, Long S: The involvement of the plasma membrane in the development of Dictyostelium discoideum. I. Purification of the plasma membrane. Biochim Biophys Acta 1977, 465:224-241.
• [56]Ogawa S, Yoshino R, Angata K, Iwamoto M, Pi M, Kuroe K, et al.: The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization. Mol Gen Genet 2000, 263:514-519.
• [57]Maeda Y, Chida J: Control of cell differentiation by mitochondria, typically evidenced in Dictyostelium development. Biomolecules 2013, 3:943-966.
• [58]Covarrubias L, Hernández-García D, Schnabel D, Salas-Vidal E, Castro-Obregón S: Function of reactive oxygen species during animal development: passive or active? Dev Biol 2008, 320:1-11.
• [59]Hamanaka RB, Chandel NS: Mitochondrial metabolism as a regulator of keratinocyte differentiation. Cell Logist 2013, 3:e25456.
• [60]Hamanaka RB, Glasauer A, Hoover P, Yang S, Blatt H, Mullen AR, et al.: Mitochondrial reactive oxygen species promote epidermal differentiation and hair follicle development. Sci Signal 2013, 6:ra8.
• [61]Bloomfield G, Pears C: Superoxide signalling required for multicellular development of Dictyostelium. J Cell Sci 2003, 116:3387-3397.
• [62]Garcia MXU, Alexander H, Mahadeo D, Cotter DA, Alexander S: The Dictyostelium discoideum prespore-specific catalase B functions to control late development and to protect spore viability. Biochim Biophys Acta 2003, 1641:55-64.
• [63]Escalante R, Yamada Y, Cotter D, Sastre L, Sameshima M: The MADS-box transcription factor SrfA is required for actin cytoskeleton organization and spore coat stability during Dictyostelium sporulation. Mech Dev 2004, 121:51-56.
• [64]Allen RG, Tresini M: Oxidative stress and gene regulation. Free Radic Biol Med 2000, 28:463-499.
• [65]Sussman M: Cultivation and synchronous morphogenesis of Dictyostelium under controlled experimental conditions. Methods Cell Biol 1987, 28:9-29.
• [66]Kay RR, Jermyn KA: A possible morphogen controlling differentiation in Dictyostelium. Nature 1983, 303:242-244.
• [67]Anjard C, Chang WT, Gross J, Nellen W: Production and activity of spore differentiation factors (SDFs) in Dictyostelium. Development 1998, 125:4067-4075.
• [68]Anjard C, Su Y, Loomis WF: Steroids initiate a signaling cascade that triggers rapid sporulation in Dictyostelium. Development 2009, 136:803-812.
• [69]Anjard C, Loomis WF: Cytokinins induce sporulation in Dictyostelium. Development 2008, 135:819-827.
• [70]Anjard C, Loomis WF: GABA induces terminal differentiation of Dictyostelium through a GABAB receptor. Development 2006, 133:2253-2261.
• [71]Bonner JT, Chiang A, Lee J, Suthers HB: The possible role of ammonia in phototaxis of migrating slugs of Dictyostelium discoideum. Proc Natl Acad Sci U S A 1988, 85:3885-3887.
• [72]Bonner JT, Har D, Suthers HB: Ammonia and thermotaxis: further evidence for a central role of ammonia in the directed cell mass movements of Dictyostelium discoideum. Proc Natl Acad Sci U S A 1989, 86:2733-2736.
• [73]Newell PC, Telser A, Sussman M: Alternative developmental pathways determined by environmental conditions in the cellular slime mold Dictyostelium discoideum. J Bacteriol 1969, 100:763-768.
• [74]Schindler J, Sussman M: Ammonia determines the choice of morphogenetic pathways in Dictyostelium discoideum. J Mol Biol 1977, 116:161-169.
• [75]Lake JA, Quick WP, Beerling DJ, Woodward FI: Plant development. Signals from mature to new leaves. Nature 2001, 411:154.
• [76]Eichinger L, Pachebat JA, Glöckner G, Rajandream M-A, Sucgang R, Berriman M, et al.: The genome of the social amoeba Dictyostelium discoideum. Nature 2005, 435:43-57.
• [77]Sucgang R, Kuo A, Tian X, Salerno W, Parikh A, Feasley CL, et al.: Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol 2011, 12:R20. BioMed Central Full Text
• [78]Cai H, Katoh-Kurasawa M, Muramoto T, Santhanam B, Long Y, Li L, et al.: Nucleocytoplasmic shuttling of a GATA transcription factor functions as a development timer. Science 2014, 343:1249531.
• [79]Santhanam B, Cai H, Devreotes PN, Shaulsky G, Katoh-Kurasawa M. The GtaC transcription factor is a master regulator of gene expression dynamics during early Dictyostelium development. In press.
• [80]Miranda ER, Rot G, Toplak M, Santhanam B, Curk T, Shaulsky G, et al.: Transcriptional profiling of Dictyostelium with RNA sequencing. Methods Mol Biol Clifton NJ 2013, 983:139-171.
• [81]Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. BioMed Central Full Text
• [82]Demšar J, Curk T, Erjavec A, Gorup Č, Hočevar T, Milutinovič M, et al.: Orange: data mining toolbox in Python. J Mach Learn Res 2013, 14:2349-2353.
• [83]Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, et al.: Scikit-learn: machine learning in Python. J Mach Learn Res 2011, 12:2825-2830.
• [84]Hardcastle TJ, Kelly KA: baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010, 11:422. BioMed Central Full Text
• [85]Suzuki R, Shimodaira H: Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 2006, 22:1540-1542.