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Molecular Cloning, Transcriptome Profiling, and Characterization of Histone Genes in the Dinoflagellate Alexandrium pacificum

  • Riaz, Sadaf (Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education) ;
  • Sui, Zhenghong (Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education)
  • Received : 2018.02.09
  • Accepted : 2018.04.28
  • Published : 2018.07.28

Abstract

The nucleosomal organization of chromatin using histone proteins is a fundamental and ubiquitous feature of eukaryotic nuclei, with the major exception of dinoflagellates. Although a number of recent genomic and transcriptomic analyses have detected numerous histone genes in dinoflagellates, little is known about their expression. Here in, we aimed to investigate the expression pattern of histone genes under nutritional stress, and an attempt was made to detect histone expression at the protein level in Alexandrium pacificum. The presence of histones at the mRNA level was confirmed in this study by the amplification, cloning, and sequencing of 10 different genes. Relative expression profiling of these genes under different growth conditions was determined with real-time PCR and revealed considerable levels of histone transcription in nutritionally stressed cells. We were unable to detect the expression of histones at the protein level even after immunodetection and analysis using mass spectrometry, although a histone-like protein was detected as a major nuclear component. A. pacificum expresses multiple variants of histone, and protein sequences revealed both conservation and divergence with respect to other eukaryotes. We concluded that A. pacificum maintained an active transcription of histone genes within the cell, and enhanced expression of histone genes in nutritional stress strongly suggest that histones have functional significance in dinoflagellates, although expression at the protein level was below our current detection limits, which suggests a limited role of histones in DNA packaging. Finally, the plausible regulation of histone expression at the gene and protein levels in A. pacificum is discussed.

Keywords

References

  1. Over RS, Michaels SD. 2014. Open and closed: the roles of linker histones in plants and animals. Mol. Plant 7: 481-491. https://doi.org/10.1093/mp/sst164
  2. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at $2.8\;{\AA}$ resolution. Nature 389: 251-260. https://doi.org/10.1038/38444
  3. Lyons SM, Cunningham CH, Welch JD, Groh B, Guo AY, Wei B, et al. 2016. A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Nucleic Acids Res. 44: 9190-9205
  4. Sournia A. 1995. Red tide and toxic marine phytoplankton of the world ocean: an inquiry into biodiversity, pp. 103-112. In: Proceedings of the 6th International Conference on Toxic Marine Phytoplankton, Harmful Marine Algal Blooms, 1993, Nantes, France. Lavoisier Publising/Intercept, Paris, France.
  5. John U, Litaker RW, Montresor M, Murray S, Brosnahan ML, Anderson DM. 2014. Formal revision of the Alexandrium tamarense species complex (Dinophyceae) taxonomy: the introduction of five species with emphasis on molecularbased (rDNA) classification. Protist 165: 779-804. https://doi.org/10.1016/j.protis.2014.10.001
  6. Wang L, Zhuang Y, Zhang H, Lin X, Lin S. 2014. DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species. Harmful Algae 31: 100-113. https://doi.org/10.1016/j.hal.2013.10.013
  7. Imai I, Yamaguchi M, Hori Y. 2006. Eutrophication and occurrences of harmful algal blooms in the Seto Inland Sea, Japan. Plankton Benthos Res. 1: 71-84. https://doi.org/10.3800/pbr.1.71
  8. Waller RF, Jackson CJ. 2009. Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology. Bioessays 31: 237-245. https://doi.org/10.1002/bies.200800164
  9. Barbrook A, Howe C. 2000. Minicircular plastid DNA in the dinoflagellate Amphidinium operculatum. Mol. Gen. Genet. 263: 152-158. https://doi.org/10.1007/s004380050042
  10. Dodge J. 1971. A dinoflagellate with both a mesocaryotic and a eucaryotic nucleus I. Fine structure of the nuclei. Protoplasma 73: 145-157. https://doi.org/10.1007/BF01275591
  11. Costas E, Goyanes V. 2005. Architecture and evolution of dinoflagellate chromosomes: an enigmatic origin. Cytogenet. Genome Res. 109: 268-275. https://doi.org/10.1159/000082409
  12. Shupe K, Rizzo PJ. 1983. Nuclease digestion of chromatin from the eukaryotic algae Olisthodiscus luteus, Peridinium balticum, and Crypthecodinium cohnii. J. Protozool. 30: 599-606. https://doi.org/10.1111/j.1550-7408.1983.tb01429.x
  13. Herzog M, Soyer M. 1981. Distinctive features of dinoflagellate chromatin. Absence of nucleosomes in a primitive species Prorocentrum micans E. Eur. J. Cell Biol. 23: 295-302.
  14. Rill RL, Livolant F, Aldrich HC, Davidson MW. 1989. Electron microscopy of liquid crystalline DNA: direct evidence for cholesteric-like organization of DNA in dinoflagellate chromosomes. Chromosoma 98: 280-286. https://doi.org/10.1007/BF00327314
  15. Chan Y-H, Wong JT. 2007. Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3. Nucleic Acids Res. 35: 2573-2583. https://doi.org/10.1093/nar/gkm165
  16. Chan Y, Kwok A, Tsang JS, Wong JT. 2006. Alveolata histone?like proteins have different evolutionary origins. J. Evolutionary Biol. 19: 1717-1721. https://doi.org/10.1111/j.1420-9101.2006.01089.x
  17. Chudnovsky Y, Li JF, Rizzo PJ, Hastings J, Fagan TF. 2002. Cloning, expression, and characterization of a histone-like protein from the marine dinoflagellate Lingulodinium polyedrum. J. Phycol. 38: 543-550. https://doi.org/10.1046/j.1529-8817.2002.01186.x
  18. Wargo MJ, Rizzo PJ. 2000. Characterization of Gymnodinium mikimotoi (Dinophyceae) nuclei and identification of the major histone-like protein, HGm. J. Phycol. 36: 584-589. https://doi.org/10.1046/j.1529-8817.2000.99122.x
  19. Kohli GS, John U, Figueroa RI, Rhodes LL, Harwood DT, Groth M, et al. 2015. Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae). BMC Genomics 16: 410. https://doi.org/10.1186/s12864-015-1625-y
  20. Zhang S, Sui Z, Chang L, Kang K, Ma J, Kong F, et al. 2014. Transcriptome de novo assembly sequencing and analysis of the toxic dinoflagellate Alexandrium catenella using the Illumina platform. Gene 537: 285-293. https://doi.org/10.1016/j.gene.2013.12.041
  21. Shoguchi E, Shinzato C, Kawashima T, Gyoja F, Mungpakdee S, Koyanagi R, et al. 2013. Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Curr. Biol. 23: 1399-1408. https://doi.org/10.1016/j.cub.2013.05.062
  22. Roy S, Morse D. 2012. A full suite of histone and histone modifying genes are transcribed in the dinoflagellate Lingulodinium. PLoS One 7: e34340. https://doi.org/10.1371/journal.pone.0034340
  23. B ayer T , Aranda M , Sunagawa S, Y um L K, D eSalvo M K, Lindquist E, et al. 2012. Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reefbuilding corals. PLoS One 7: e35269. https://doi.org/10.1371/journal.pone.0035269
  24. Lin S, Zhang H, Zhuang Y, Tran B, Gill J. 2010. Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates. Proc. Natl. Acad. Sci. USA 107: 20033-20038. https://doi.org/10.1073/pnas.1007246107
  25. Guillard RR. 1975. Culture of phytoplankton for feeding marine invertebrates, pp. 29-60. In Smith WL, Chanley MH (eds.), Culture of Marine Invertebrate Animals. Plenum Press, New York.
  26. Geng H, Sui Z, Zhang S, Du Q, Ren Y, Liu Y, et al. 2015. Identification of microRNAs in the toxigenic dinoflagellate Alexandrium catenella by high-throughput Illumina sequencing and bioinformatic analysis. PLoS One 10: e0138709. https://doi.org/10.1371/journal.pone.0138709
  27. Galleron C. 1976. Synchronization of the marine dinoflagellate Amphydinium carteri in dense cultures. J. Phycol. 12: 69-73.
  28. Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the $2-{\Delta}{\Delta}CT$ method. Methods 25: 402-408. https://doi.org/10.1006/meth.2001.1262
  29. Lupke M, Frahm J, Lantow M, Maercker C, Remondini D, Bersani F, et al. 2006. Gene expression analysis of ELF-MF exposed human monocytes indicating the involvement of the alternative activation pathway. Biochim. Biophys. Acta 1763: 402-412. https://doi.org/10.1016/j.bbamcr.2006.03.003
  30. Kruger NJ. 1994. The Bradford method for protein quantitation. Methods Mol. Biol. 32: 9-15.
  31. Shechter D, Dormann HL, Allis CD, Hake SB. 2007. Extraction, purification and analysis of histones. Nat. Protoc. 2: 1445-1457. https://doi.org/10.1038/nprot.2007.202
  32. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797. https://doi.org/10.1093/nar/gkh340
  33. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. 2009. Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189-1191. https://doi.org/10.1093/bioinformatics/btp033
  34. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, et al. 2005. Protein identification and analysis tools on the ExPASy server, pp. 571-607. In Walker JM (ed.), The Proteomics Protocols Handbook. Humana Press, New York.
  35. Mitchell A, Chang H-Y, Daugherty L, Fraser M, Hunter S, Lopez R, et al. 2014. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43(Database Issue): D213-D221.
  36. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44: D279-D285. https://doi.org/10.1093/nar/gkv1344
  37. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. 2015. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10: 845-858. https://doi.org/10.1038/nprot.2015.053
  38. Mariadason JM. 2008. HDACs and HDAC inhibitors in colon cancer. Epigenetics 3: 28-37. https://doi.org/10.4161/epi.3.1.5736
  39. Orphanides G, LeRoy G, Chang C-H, Luse DS, Reinberg D. 1998. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92: 105-116. https://doi.org/10.1016/S0092-8674(00)80903-4
  40. Gornik SG, Ford KL, Mulhern TD, Bacic A, McFadden GI, Waller RF. 2012. Loss of nucleosomal DNA condensation coincides with appearance of a novel nuclear protein in dinoflagellates. Curr. Biol. 22: 2303-2312. https://doi.org/10.1016/j.cub.2012.10.036
  41. de la Espina SMD, Alverca E, Cuadrado A, Franca S. 2005. Organization of the genome and gene expression in a nuclear environment lacking histones and nucleosomes: the amazing dinoflagellates. Eur. J. Cell Biol. 84: 137-149. https://doi.org/10.1016/j.ejcb.2005.01.002
  42. Rizzo PJ, Nooden LD. 1972. Chromosomal proteins in the dinoflagellate alga Gyrodinium cohnii. Science 176: 796-797. https://doi.org/10.1126/science.176.4036.796
  43. Tomas RN, Cox ER, Steidinger KA. 1973. Peridinium balticum (Levander) Lemmermann, an unusual dinoflagellate with a mesocaryotic and an eucaryotic nucleus. J. Phycol. 9: 91-98.
  44. Azevedo C. 1989. Fine structure of Perkinsus atlanticus n. sp. (Apicomplexa, Perkinsea) parasite of the clam Ruditapes decussatus from Portugal. J. Parasitol. 627-635.
  45. Marinov GK, Lynch M. 2016. Diversity and divergence of dinoflagellate histone proteins. G3 (Bethesda) 6: 397-422.
  46. Figueroa RI, Bravo I, Fraga S, Garcés E, Llaveria G. 2009. The life history and cell cycle of Kryptoperidinium foliaceum, a dinoflagellate with two eukaryotic nuclei. Protist 160: 285-300. https://doi.org/10.1016/j.protis.2008.12.003
  47. Suganuma T, Workman JL. 2011. Signals and combinatorial functions of histone modifications. Annu. Rev. Biochem. 80: 473-499. https://doi.org/10.1146/annurev-biochem-061809-175347
  48. Marzluff WF, Wagner EJ, Duronio RJ. 2008. Metabolism and regulation of canonical histone mRNAs: life without a poly (A) tail. Nat. Rev. Genet. 9: 843-854. https://doi.org/10.1038/nrg2438
  49. Ehinger A, Denison SH, May GS. 1990. Sequence, organization and expression of the core histone genes of Aspergillus nidulans. Mol. Gen. Genet. 222: 416-424. https://doi.org/10.1007/BF00633848
  50. Wu RS, Bonner WM. 1981. Separation of basal histone synthesis from S-phase histone synthesis in dividing cells. Cell 27: 321-330. https://doi.org/10.1016/0092-8674(81)90415-3
  51. Smith AP, Jain A, Deal RB, Nagarajan VK, Poling MD, Raghothama KG, et al. 2010. Histone H2A.Z regulates the expression of several classes of phosphate starvation response genes but not as a transcriptional activator. Plant Physiol. 152: 217-225. https://doi.org/10.1104/pp.109.145532
  52. Sura W, Kabza M, Karlowski WM, Bieluszewski T, Kus-Slowinska M, Paweloszek L, et al. 2017. Dual role of the histone variant H2A.Z in transcriptional regulation of stressresponse genes. Plant Cell 29: 791-807. https://doi.org/10.1105/tpc.16.00573
  53. Li M, Shi X, Guo C, Lin S. 2016. Phosphorus deficiency inhibits cell division but not growth in the dinoflagellate Amphidinium carterae. Front. Microbiol. 7: 826.
  54. Williams AS, Marzluff WF. 1995. The sequence of the stem and flanking sequences at the 3' end of histone mRNA are critical determinants for the binding of the stem-loop binding protein. Nucleic Acids Res. 23: 654-662. https://doi.org/10.1093/nar/23.4.654
  55. Yang L, Duff MO, Graveley BR, Carmichael GG, Chen L-L. 2011. Genomewide characterization of non-polyadenylated RNAs. Genome Biol. 12: 1. https://doi.org/10.1186/gb-2011-12-S1-P1
  56. Lai E C, B urks C, Posakony JW. 1998. The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development 125: 4077-4088.
  57. Singh RK, Paik J, Gunjan A. 2008. Generation and management of excess histones during the cell cycle. Front. Biosci. (Landmark Ed.) 14: 3145-3158.
  58. Nelson DM, Ye X, Hall C, Santos H, Ma T, Kao GD, et al. 2002. Coupling of DNA synthesis and histone synthesis in S phase independent of cyclin/cdk2 activity. Mol. Cell. Biol. 22: 7459-7472. https://doi.org/10.1128/MCB.22.21.7459-7472.2002
  59. Morillo-Huesca M, Munoz-Centeno M, Singh R, Reddy G, Oreal V, Liang D, et al. 2010. Accumulation of transcriptionevicted histones induces a CLN3-dependent cell cycle delay in G1. PLoS Genet. 6: e1000964. https://doi.org/10.1371/journal.pgen.1000964
  60. Singh RK, Gonzalez M, Kabbaj M-HM, Gunjan A. 2012. Novel E3 ubiquitin ligases that regulate histone protein levels in the budding yeast Saccharomyces cerevisiae. PLoS One 7: e36295. https://doi.org/10.1371/journal.pone.0036295
  61. Commerford S, Carsten A, Cronkite E. 1982. Histone turnover within nonproliferating cells. Proc. Natl. Acad. Sci. USA 79: 1163-1165. https://doi.org/10.1073/pnas.79.4.1163
  62. Gunjan A, Verreault A. 2003. A Rad53 kinase-dependent surveillance mechanism that regulates histone protein levels in S. cerevisiae. Cell 115: 537-549. https://doi.org/10.1016/S0092-8674(03)00896-1
  63. Lubec G, Afjehi-Sadat L. 2007. Limitations and pitfalls in protein identification by mass spectrometry. Chem. Rev. 107: 3568-3584. https://doi.org/10.1021/cr068213f
  64. Sterner DE, Berger SL. 2000. Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev. 64: 435-459. https://doi.org/10.1128/MMBR.64.2.435-459.2000
  65. Vaquero A. 2009. The conserved role of sirtuins in chromatin regulation. Int. J. Dev. Biol. 53: 303-322. https://doi.org/10.1387/ijdb.082675av
  66. Wood A, Shilatifard A. 2004. Posttranslational modifications of histones by methylation. Adv. Protein Chem. 67: 201-222.
  67. Guerra-Calderas L, Gonzalez-Barrios R, Herrera LA, de Leon DC, Soto-Reyes E. 2015. The role of the histone demethylase KDM4A in cancer. Cancer Genet. 208: 215-224. https://doi.org/10.1016/j.cancergen.2014.11.001
  68. Musselman CA, Lalonde M-E, Cote J, Kutateladze TG. 2012. Perceiving the epigenetic landscape through histone readers. Nat. Struct. Mol. Biol. 19: 1218-1227. https://doi.org/10.1038/nsmb.2436
  69. Teif VB, Rippe K. 2009. Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Res. 37: 5641-5655. https://doi.org/10.1093/nar/gkp610
  70. Reinberg D, Sims RJ. 2006. de FACTo nucleosome dynamics. J. Biol. Chem. 281: 23297-23301. https://doi.org/10.1074/jbc.R600007200
  71. Burgess RJ, Zhang Z. 2013. Histone chaperones in nucleosome assembly and human disease. Nat. Struct. Mol. Biol. 20: 14-22. https://doi.org/10.1038/nsmb.2461

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