Skip to main content

Advertisement

SpringerLink
Log in

Transcriptomic identification and expression analysis of cold shock domain protein (CSP) genes in the marine dinoflagellate Prorocentrum minimum

  • Published:
Journal of Applied Phycology Aims and scope Submit manuscript

Abstract

Dinoflagellates are frequently exposed to cold-water temperatures, and some may survive in winter and in polar regions. Cold shock domain proteins (CSPs) seem to function as part of their adaptation to such stressful environments. In this study, we identified two CSP genes (PmCSP1 and PmCSP2) in the marine dinoflagellate Prorocentrum minimum, characterized their structural properties, and investigated their expression patterns in response to cold shock and heavy metal exposure. Putative PmCSP1 (96 aa, 10.1 kDa) and PmCSP2 (91 aa, 9.4 kDa) proteins had two consensus RNA-binding motifs and might be localized in the cytoplasm, due to the absence of a signal peptide. Phylogenetic analyses revealed that PmCSPs clustered with those of other dinoflagellates and had been recycled between genomic DNA and mRNA. Real-time PCR revealed that PmCSPs significantly responded to low temperatures, but not to nickel or cadmium. These genes may allow the organism to adapt to and survive in cold habitats and winter.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Abadie E, Kaci L, Berteaux T, Hess P, Sechet V, Masseret E, Rolland JL, Laabir M (2015) Effect of nitrate, ammonium and urea on growth and pinnatoxin G production of Vulcanodinium rugosum. Mar Drugs 13:5642–5656

    PubMed  PubMed Central  Google Scholar 

  • Abassi S, Wang H, Park BS, Park JW, Ki J-S (2017) A novel cyclophilin B gene in the red tide dinoflagellate Cochlodinium polykrikoides: molecular characterizations and transcriptional responses to environmental stresses. BioMed Res Int 2017:4101580

    PubMed  PubMed Central  Google Scholar 

  • Anderson DM, Alpermann TJ, Cembella AD, Collos Y, Masseret E, Montresor M (2012) The globally distributed genus Alexandrium: multifaceted roles in marine ecosystems and impacts on human health. Harmful Algae 14:10–35

  • Aranda M, Li Y, Liew Y et al (2016) Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Sci Rep 6:39734

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bayer T, Aranda M, Sunagawa S, Yum LK, Desalvo MK, Lindquist E, Coffroth MA, Voolstra CR, Medina M (2012) Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS One 7:e35269

    CAS  PubMed  PubMed Central  Google Scholar 

  • Beauchemin M, Roy S, Daoust P, Dagenais-Bellefeuille S, Bertomeu T, Letourneau L, Lang BF, Morse D (2012) Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic. Proc Natl Acad Sci U S A 109:15793–15798

    CAS  PubMed  PubMed Central  Google Scholar 

  • Beauchemin M, Roy S, Pelletier S, Averback A, Lanthier F, Morse D (2016) Characterization of two dinoflagellate cold shock domain proteins. mSphere 1:e00034-15

  • Blanc G, Agarkova I, Grimwood J et al (2012) The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol 13:R39

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    CAS  PubMed  PubMed Central  Google Scholar 

  • Campanaro S, Treu L, Rodriguez-R LM, Kovalovszki A, Ziels RM, Maus I, Zhu X, Kougias PG, Basile A, Luo G, Schlüter A, Konstantinidis KT, Angelidaki I (2020) New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. Biotechnol Biofuels 13:25

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cerutti H, Ma X, Msanne J, Repas T (2011) RNA-mediated silencing in algae: biological roles and tools for analysis of gene function. Eukaryot Cell 10:1164–1172

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chaikam V, Karlson DT (2010) Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins. BMB Rep 43:1–8

    CAS  PubMed  Google Scholar 

  • Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA (2011) Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol 7:518

    PubMed  PubMed Central  Google Scholar 

  • Chetouhi C, Masseret E, Satta CT, Balliau T, Laabir M, Jean N (2020) Intraspecific variability in membrane proteome, cell growth, and morphometry of the invasive marine neurotoxic dinoflagellate Alexandrium pacificum grown in metal-contaminated conditions. Sci Total Environ 715:136834

    CAS  PubMed  Google Scholar 

  • Cui W, Cao L, Liu J, Ren Z, Zhao B, Dou S (2020) Effects of seawater acidification and cadmium on the antioxidant defense of flounder paralichthys Olivaceus larvae. Sci Total Environ 718:137234

    CAS  PubMed  Google Scholar 

  • Deng Y, Hu ZX, Shang LX, Peng QC, Tang YZ (2017) Transcriptomic analyses of Scrippsiella trochoidea reveals processes regulating encystment and dormancy in the life cycle of a dinoflagellate, with a particular attention to the role of abscisic acid. Front Microbiol 8:2450

    PubMed  PubMed Central  Google Scholar 

  • Deng Y, Hu Z, Chai Z, Tang YZ (2018) Cloning and partial characterization of a cold shock domain-containing protein gene from the dinoflagellate Scrippsiella trochoidea. J Eukaryot Microbiol 66:393–403

    PubMed  Google Scholar 

  • Fertouna-Bellakhal M, Dhib A, Fathalli A, Bellakhal M, Chomérat N, Masseret E, Laabir M, Turki S, Aleya L (2015) Alexandrium pacificum Litaker sp. nov (Group IV): resting cyst distribution and toxin profile of vegetative cells in Bizerte Lagoon (Tunisia, Southern Mediterranean Sea). Harmful Algae 48:69–82

    PubMed  Google Scholar 

  • Giaquinto L, Curmi PM, Siddiqui KS, Poljak A, DeLong E, DasSarma S, Cavicchioli R (2007) Structure and function of cold shock proteins in Archaea. J Bacteriol 189:5738–5748

    CAS  PubMed  PubMed Central  Google Scholar 

  • Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gualerzi CO, Giuliodori AM, Pon CL (2003) Transcriptional and post-transcriptional control of cold-shock genes. J Mol Biol 331:527–539

    CAS  PubMed  Google Scholar 

  • Guo R, Ki J-S (2012) Evaluation and validation of internal control genes for studying gene expression in the dinoflagellate Prorocentrum minimum using real-time PCR. Eur J Protistol 48:199–206

    PubMed  Google Scholar 

  • Guo R, Ebenezer V, Ki J-S (2012) Transcriptional responses of heat shock protein 70 (Hsp70) to thermal, bisphenol A, and copper stresses in the dinoflagellate Prorocentrum minimum. Chemosphere 89:512–520

    CAS  PubMed  Google Scholar 

  • Guo R, Wang H, Suh YS, Ki J-S (2016) Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate. BMC Genomics 17:29

    PubMed  PubMed Central  Google Scholar 

  • Hadjadji I, Frehi H, Ayada L, Abadie E, Collos Y (2014) A comparative analysis of Alexandrium catenella/tamarense blooms in Annaba Bay (Algeria) and Thau Lagoon (France); phosphorus limitation as a trigger. C R Biol 337:117–122

    PubMed  Google Scholar 

  • Heil CA, Glibert PM, Fan C (2005) Prorocentrum minimum (Pavillard) Schiller: a review of a harmful algal bloom species of growing worldwide importance. Harmful Algae 4:449–470

    CAS  Google Scholar 

  • Herzi F, Jean N, Zhao H, Mounier S, Mabrouk HH, Hlaili AS (2013) Copper and cadmium effects on growth and extracellular exudation of the marine toxic dinoflagellate Alexandrium catenella: 3D-fluorescence spectroscopy approach. Chemosphere 93:1230–1239

    CAS  PubMed  Google Scholar 

  • Jones PG, VanBogelen RA, Neidhardt FC (1987) Induction of proteins in response to low temperature in Escherichia coli. J Bacteriol 169:2092–2095

    CAS  PubMed  PubMed Central  Google Scholar 

  • Karlson D, Imai R (2003) Conservation of the cold shock domain protein family in plants. Plant Physiol 131:12–15

    CAS  PubMed  PubMed Central  Google Scholar 

  • Karlson D, Nakaminami K, Toyomasu T, Imai R (2002) A cold-regulated nucleic acid-binding protein of winter wheat shares a domain with bacterial cold shock proteins. J Biol Chem 277:35248–35256

    CAS  PubMed  Google Scholar 

  • Keto-Timonen R, Hietala N, Palonen E, Hakakorpi A, Lindström M, Korkeala H (2016) Cold shock proteins: a minireview with special emphasis on Csp-family of enteropathogenic Yersinia. Front Microbiol 7:1151

    PubMed  PubMed Central  Google Scholar 

  • Kim JS, Park SJ, Kwak KJ, Kim YO, Kim JY, Song J, Jang B, Jung CH, Kang H (2007) Cold shock domain proteins and glycine-rich RNA binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli. Nucleic Acids Res 35:506–516

    CAS  PubMed  Google Scholar 

  • Kobiyama A, Tanaka S, Kaneko Y, Lim PT, Ogata T (2010) Temperature tolerance and expression of heat shock protein 70 in the toxic dinoflagellate Alexandrium tamarense (Dinophyceae). Harmful Algae 9:180–185

    CAS  Google Scholar 

  • Kremer W, Schuler B, Harrieder S, Geyer M, Gronwald W, Welker C, Jaenicke R, Kalbitzer HR (2001) Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima. Eur J Biochem 268:2527–2539

    CAS  PubMed  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    CAS  PubMed  PubMed Central  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    CAS  PubMed  Google Scholar 

  • Lee R, Lai H, Malik SB et al (2014) Analysis of EST data of the marine protist Oxyrrhis marina, an emerging model for alveolate biology and evolution. BMC Genomics 15:122

    PubMed  PubMed Central  Google Scholar 

  • Lin S, Zhang H (2010) Dinoflagellate meta-transcriptomics enabled by spliced leader. Proceedings of 13th International Conference on Harmful Algae, International Society for The Study of Harmful Algae, Hong Kong, China pp. 166-170

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-∆∆Ct method. Methods 25:402–408

    CAS  PubMed  Google Scholar 

  • Middag R, de Baar HJW, Bruland KW, van Heuven SMAC (2020) The distribution of nickel in the West-Atlantic ocean, its relationship with phosphate and a comparison to cadmium and zinc. Front Mar Sci 7:105

    Google Scholar 

  • Mueller U, Perl D, Schmid FX, Heinemann U (2000) Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein. J Mol Biol 297:975–988

    CAS  PubMed  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4326

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nakaminami K, Karlson D, Imai R (2006) Functional conservation of cold shock domains in bacteria and higher plants. Proc Natl Acad Sci U S A 103:10122–10127

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nymark M, Sharma AK, Sparstad T, Bones AM, Winge P (2016) A CRISPR/Cas9 system adapted for gene editing in marine algae. Sci Rep 6:24951

    CAS  PubMed  PubMed Central  Google Scholar 

  • Okamoto OK, Liu L, Robertsonn DL, Hastings JW (2001) Members of the dinoflagellate luciferase gene family differ in synonymous substitution rates. Biochemistry 40:15862–15868

    CAS  PubMed  Google Scholar 

  • Park SJ, Kwak KJ, Oh TR, KimYO KH (2009) Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions. Plant Cell Physiol 50:869–878

    CAS  PubMed  Google Scholar 

  • Phadtare S, Inouye M (2001) Role of CspC and CspE in regulation of expression of RpoS and UspA, the stress response proteins in Escherichia coli. J Bacteriol 183:1205–1214

    CAS  PubMed  PubMed Central  Google Scholar 

  • Phadtare S, Inouye M (2004) Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli. J Bacteriol 186:7007–7014

    CAS  PubMed  PubMed Central  Google Scholar 

  • Prabhakaran P, Ashraf MA, Aqma WS (2016) Microbial stress response to heavy metals in the environment. RSC Adv 6:109862

    CAS  Google Scholar 

  • Quandt CA, Bushley KE, Spatafora JW (2015) The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics. BMC Genomics 16:553

    PubMed  PubMed Central  Google Scholar 

  • Röder K, Hantzsche FM, Gebühr C, Miene C, Helbig T, Krock B, Hoppenrath M, Luckas B, Gerdts G (2012) Effects of salinity, temperature and nutrients on growth, cellular characteristics and yessotoxin production of Protoceratium reticulatum. Harmful Algae 15:59–70

    Google Scholar 

  • Roy S, Letourneau L, Morse D (2014) Cold-induced cysts of the photosynthetic dinoflagellate Lingulodinium polyedrum have an arrested circadian bioluminescence rhythm and lower levels of protein phosphorylation. Plant Physiol 164:966–977

    CAS  PubMed  Google Scholar 

  • Sasaki K, Imai R (2012) Pleiotropic roles of cold shock domain proteins in plants. Front Plant Sci 2:116

    PubMed  PubMed Central  Google Scholar 

  • Sawyer AL, Landsberg MJ, Ross IL, Kruse O, Mobli M, Hankamer B (2015) Solution structure of the RNA-binding cold-shock domain of the Chlamydomonas reinhardtii NAB1 protein and insights into RNA recognition. Biochem J 469:97–106

    CAS  PubMed  Google Scholar 

  • Schmid B, Klumpp J, Raimann E et al (2009) Role of cold shock proteins in growth of Listeria monocytogenes under cold and osmotic stress conditions. Appl Environ Microbiol 75:1621–1627

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schröder K, Graumann P, Schnuchel A, Holak TA, Marahiel MA (1995) Mutational analysis of the putative nucleic acid-binding surface of the cold-shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single-stranded DNA containing the Y-box motif. Mol Microbiol 16:699–708

  • Sierra-Beltrán AP, Cortés-Altamirano R, Cortés-Lara MC (2005) Occurrences of Prorocentrum minimum (Pavillard) in México. Harmful Algae 4:507–517

    Google Scholar 

  • Slamovits CH, Keeling PJ (2008) Widespread recycling of processed cDNAs in dinoflagellates. Curr Biol 18:R550–R552

    CAS  PubMed  Google Scholar 

  • Song B, Morse D, Song Y, Fu Y, Lin X, Wang W, Cheng S, Chen W, Liu X, Lin S (2017) Comparative genomics reveals two major bouts of gene retroposition coinciding with crucial periods of Symbiodinium evolution. Genome Biol Evol 9:2037–2047

    CAS  PubMed  PubMed Central  Google Scholar 

  • Springer JJ, Burkholder JM, Glibert PM, Reed RE (2005) Use of a real-time remote monitoring network (RTRM) and shipborne sampling to characterize a dinoflagellate bloom in the Neuse Estuary, North Carolina, USA. Harmful Algae 4:533–551

    CAS  Google Scholar 

  • Stein JR (ed) (1973) Handbook of phycological methods: culture methods and growth measurements. Cambridge University Press, London, p 448

    Google Scholar 

  • Tango PJ, Magnien R, Butler W, Luckett C, Luckenbach M, Lacouture R, Poukish C (2005) Impacts and potential effects due to Prorocentrum minimum blooms in Chesapeake Bay. Harmful Algae 4:525–531

    Google Scholar 

  • Taylor FJR, Hoppenrath M, Saldarriaga JF (2008) Dinoflagellate diversity and distribution. Biodivers Conserv 17:407–418

    Google Scholar 

  • Tully BJ, Graham ED, Heidelberg JF (2018) The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci Data 5:170203

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang H, Park BS, Lim WA, Ki J-S (2018) CpMCA, a novel metacaspase gene from the harmful dinoflagellate Cochlodinium polykrikoides and its expression during cell death. Gene 651:70–78

    CAS  PubMed  Google Scholar 

  • Wang H, Abassi S, Ki J-S (2019) Origin and roles of a novel copper-zinc superoxide dismutase gene from the harmful dinoflagellate Prorocentrum minimum. Gene 683:113–122

    CAS  PubMed  Google Scholar 

  • Wang H, Kim H, Ki J-S (2020a) Transcriptome survey and toxin measurements reveal evolutionary modification and loss of saxitoxin biosynthesis genes in the dinoflagellates Amphidinium carterae and Prorocentrum micans. Ecotoxicol Environ Saf 195:110474

    CAS  PubMed  Google Scholar 

  • Wang H, Guo R, Lim W-A, Allen AE, Ki J-S (2020b) Comparative transcriptomics of toxin synthesis genes between the non-toxin producing dinoflagellate Cochlodinium polykrikoides and toxigenic Alexandrium pacificum. Harmful Algae 93:101777

    CAS  PubMed  Google Scholar 

  • Wisecaver JH, Hackett JD (2011) Dinoflagellate genome evolution. Annu Rev Microbiol 65:369–387

    CAS  PubMed  Google Scholar 

  • Yamanaka K, Inouye M (1997) Growth phase dependent expression of CspD, encoding a member of the CspA family in Escherichia coli. J Bacteriol 179:5126–5130

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yamanaka K, Zheng W, Crooke E, Wang YH, Inouye M (2001) CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli. Mol Microbiol 39:1572–1584

    CAS  PubMed  Google Scholar 

  • Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S (2007) Spliced leader RNA trans-splicing in dinoflagellates. Proc Nat Acad Sci U.S.A. 104:4618–4623

    CAS  Google Scholar 

  • Zhou W, Juneau P, Qiu B (2006) Growth and photosynthetic responses of the bloom-forming cyanobacterium Microcystis aeruginosa to elevated levels of cadmium. Chemosphere 65:1738–1746

    CAS  PubMed  Google Scholar 

Download references

Funding

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (No. 2020R1A2C2013373), and a part of the project titled “Improvement of management strategies on marine disturbing and harmful organisms (No. 20190518)” funded by the Ministry of Oceans and Fisheries, Korea.

Author information

Authors and Affiliations

  1. Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea

    Hui Wang, Hansol Kim & Jang-Seu Ki

Authors
  1. Hui Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hansol Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jang-Seu Ki
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Hui Wang: Conceptualization, investigation, formal analysis, data curation, and visualization. Hansol Kim: Investigation and data curation. Jang-Seu Ki: Data curation, funding acquisition, conceptualization, supervision, and visualization.

Corresponding author

Correspondence to Jang-Seu Ki.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Table 1

Information of cold-shock domain related proteins identified in Prorocentrum minimum. Some sequences without references were marked as “RNAseq” or “Direct Submission”. (XLSX 27 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, H., Kim, H. & Ki, JS. Transcriptomic identification and expression analysis of cold shock domain protein (CSP) genes in the marine dinoflagellate Prorocentrum minimum. J Appl Phycol 33, 843–854 (2021). https://doi.org/10.1007/s10811-020-02332-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10811-020-02332-9

Keywords

Search

Navigation