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Identification and analysis of two sequences encoding ice-binding proteins obtained from a putative bacterial symbiont of the psychrophilic Antarctic ciliate Euplotes focardii

Published online by Cambridge University Press:  14 February 2014

Sandra Pucciarelli ,
Federica Chiappori ,
Raghul Rajan Devaraj ,
Guang Yang ,
Ting Yu ,
Patrizia Ballarini  and
Cristina Miceli
Sandra Pucciarelli*
Affiliation:
Scuola di Bioscienze e Biotecnologie, Università di Camerino, 62032 Camerino, Macerata, Italy
Federica Chiappori
Affiliation:
Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate, Milan, Italy
Raghul Rajan Devaraj
Affiliation:
Scuola di Bioscienze e Biotecnologie, Università di Camerino, 62032 Camerino, Macerata, Italy
Guang Yang
Affiliation:
Scuola di Bioscienze e Biotecnologie, Università di Camerino, 62032 Camerino, Macerata, Italy
Ting Yu
Affiliation:
National Research Centre for Environmental Toxicology, University of Queensland, QLD 4108, Australia
Patrizia Ballarini
Affiliation:
Scuola di Bioscienze e Biotecnologie, Università di Camerino, 62032 Camerino, Macerata, Italy
Cristina Miceli
Affiliation:
Scuola di Bioscienze e Biotecnologie, Università di Camerino, 62032 Camerino, Macerata, Italy
*
sandra.pucciarelli@unicam.it
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Abstract

We identified two ice-binding protein (IBP) sequences, named EFsymbAFP and EFsymbIBP, from a putative bacterial symbiont of the Antarctic psychrophilic ciliate Euplotes focardii. EFsymbAFP is 57.43% identical to the antifreeze protein (AFP) from the Stigmatella aurantiaca strain DW4/3-1, which was isolated from the Victoria Valley lower glacier. EFsymbIBP is 53.38% identical to the IBP from the Flavobacteriaceae bacterium strain 3519-10, isolated from the glacial ice of Lake Vostok. EFsymbAFP and EFsymbIBP are 31.73% identical at the amino acid level and are organized in tandem on the bacterial chromosome. The relatively low sequence identity and the tandem organization, which appears unique to this symbiont, suggest an occurrence of horizontal gene transfer (HGT). Structurally, EFsymbAFP and EFsymbIBP are similar to the AFPs from the snow mould fungus Typhula ishikariensis and from the Arctic yeast Leucosporidium sp. AY30. A phylogenetic analysis showed that EFsymbAFP and EFsymbIBP cluster principally with the IBP sequences from other Antarctic bacteria, supporting the view that these sequences belong to an Antarctic symbiontic bacterium of E. focardii. These results confirm that IBPs have a complex evolutionary history, which includes HGT events, most probably due to the demands of the environment and the need for rapid adaptation.

Keywords

antifreezebiologycold-adaptationgenomehorizontal gene transferProtozoa
Type
Biological Sciences
Information
Antarctic Science , Volume 26 , Issue 5 , October 2014 , pp. 491 - 501
Copyright
© Antarctic Science Ltd 2014 

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References

Bayer-Giraldi, M., Uhlig, C., John, U., Mock, T. & Valentin, K. 2010. Antifreeze proteins in polar sea ice diatoms: diversity and gene expression in the genus Fragilariopsis . Environmental Microbiology, 12, 1041–1052.Google Scholar
Bowman, J.P., McCammon, S.A., Lewis, T., Skerratt, J.H., Brown, J.L., Nichols, D.S. & McMeekin, T.A. 1998. Psychroflexus torquis gen. nov., sp. nov., a psychrophilic species from Antarctic sea ice, and reclassification of Flavobacterium gondwanense (Dobson et al. 1993) as Psychroflexus gondwanense gen. nov., comb. nov. Microbiology, 144, 1601–1609.Google Scholar
Chiappori, F., Pucciarelli, S., Merelli, I., Ballarini, P., Miceli, C. & Milanesi, L. 2012. Structural thermal adaptation of beta-tubulins from the Antarctic psychrophilic protozoan Euplotes focardii . Proteins, 80, 1154–1166.CrossRefGoogle ScholarPubMed
Clark, M.S., Clarke, A., Cockell, C.S., Convey, P., Detrich, H.W., Fraser, K.P.P., Johnston, I.A., Methe, B.A., Murray, A.E., Peck, L.S., Römisch, K. & Rogers, A.D. 2004. Antarctic genomics. Comparative and Functional Genomics, 5, 230–238.CrossRefGoogle ScholarPubMed
DeVries, A.L. & Wohlschlag, D.E. 1969. Freezing resistance in some Antarctic fishes. Science, 163, 1073–1075.CrossRefGoogle ScholarPubMed
Do, H., Lee, J.H., Lee, S.G. & Kim, H.J. 2012. Crystallization and preliminary X-ray crystallographic analysis of an ice-binding protein (FfIBP) from Flavobacterium frigoris PS1. Acta Crystallographica Section F - Structural Biology and Crystallization Communications, 68, 806–809.Google Scholar
Duman, J.G. 2001. Antifreeze and ice nucleator proteins in terrestrial arthropods. Annual Review of Physiology, 63, 327–357.CrossRefGoogle ScholarPubMed
Ewart, K.V., Rubinsky, B. & Fletcher, G.L. 1992. Structural and functional similarity between fish antifreeze proteins and calcium-dependent lectins. Biochemical and Biophysical Research Communications, 185, 335–340.CrossRefGoogle ScholarPubMed
Eswar, N., Webb, B., Marti-Renom, M.A., Madhusudhan, M.S., Eramian, D., Shen, M.Y., Pieper, U. & Sali, A. 2006. Comparative protein structure modeling with MODELLER. Current Protocols in Bioinformatics, Sup. 15, 5.6.1–5.6.30.CrossRefGoogle ScholarPubMed
Fletcher, G.L., Hew, C.L. & Davies, P.L. 2001. Antifreeze proteins of teleost fishes. Annual Review of Physiology, 63, 359–390.CrossRefGoogle ScholarPubMed
Garnham, C.P., Campbell, R.L. & Davies, P.L. 2011. Anchored clathrate waters bind antifreeze proteins to ice. Proceedings of the National Academy of Sciences of the United States of America, 108, 7363–7367.Google Scholar
Gilbert, J.A., Hill, P.J., Dodd, C.E.R. & Laybourn-Parry, J. 2004. Demonstration of antifreeze protein activity in Antarctic lake bacteria. Microbiology, 150, 171–180.CrossRefGoogle ScholarPubMed
Hoffman, D.C., Anderson, R.C., Dubois, M.L. & Prescott, D.M. 1995. Macronuclear gene-sized molecules of hypotrichs. Nucleic Acids Research, 23, 1279–1283.Google Scholar
Keeling, P.J. & Palmer, J.D. 2008. Horizontal gene transfer in eukaryotic evolution. Nature Reviews Genetics, 9, 605–618.CrossRefGoogle ScholarPubMed
Kelley, J.L., Aagaard, J.E., MacCoss, M.J. & Swanson, W.J. 2010. Functional diversification and evolution of antifreeze proteins in the Antarctic fish Lycodichthys dearborni. Journal of Molecular Evolution, 71, 111–118.Google Scholar
Kondo, H., Hanada, Y., Sugimoto, H., Hoshino, T., Garnham, C.P., Davies, P.L. & Tsuda, S. 2012. Ice-binding site of snow mould fungus antifreeze protein deviates from structural regularity and high conservation. Proceedings of the National Academy of Sciences of the United States of America, 109, 9360–9365.Google Scholar
La Terza, A., Papa, G., Miceli, C. & Luporini, P. 2001. Divergence between two Antarctic species of the ciliate Euplotes, E. focardii and E. nobilii, in the expression of heat-shock protein 70 genes. Molecular Ecology, 10, 1061–1067.Google Scholar
Lee, J.H., Park, A.K., Do, H., Park, K.S., Moh, S.H., Chi, Y.M. & Kim, H.J. 2012. Structural basis for antifreeze activity of ice-binding protein from Arctic yeast. Journal of Biological Chemistry, 287, 11 460–11 468.Google Scholar
Marziale, F., Pucciarelli, S., Ballarini, P., Melki, R., Uzun, A., Ilyin, V.A., Detrich, H.W. & Miceli, C. 2008. Different roles of two gamma-tubulin isotypes in the cytoskeleton of the Antarctic ciliate Euplotes focardii – remodelling of interaction surfaces may enhance microtubule nucleation at low temperature. FEBS Journal, 275, 5367–5382.Google Scholar
Miceli, C., La Terza, A. & Melli, M. 1989. Isolation and structural characterization of cDNA clones encoding the mating pheromone Er-1 secreted by the ciliate Euplotes raikovi. Proceedings of the National Academy of Sciences of the United States of America, 86, 3016–3020.Google Scholar
Morgan-Kiss, R.M., Priscu, J.C., Pocock, T., Gudynaite-Savitch, L. & Huner, N.P.A. 2006. Adaptation and acclimation of photosynthetic microorganisms to permanently cold environments. Microbiology and Molecular Biology Reviews, 70, 222–252.Google Scholar
Pucciarelli, S., Marziale, F., di Giuseppe, G., Barchetta, S. & Miceli, C. 2005. Ribosomal cold-adaptation: characterization of the genes encoding the acidic ribosomal P0 and P2 proteins from the Antarctic ciliate Euplotes focardii. Gene, 360, 103–110.Google Scholar
Pucciarelli, S., La Terza, A., Ballarini, P., Barchetta, S., Yu, T., Marziale, F., Passini, V., Methé, B., Detrich, H.W. & Miceli, C. 2009. Molecular cold-adaptation of protein function and gene regulation: the case for comparative genomic analyses in marine ciliated protozoa. Marine Genomics, 2, 57–66.Google Scholar
Raymond, J.A., Christner, B.C. & Schuster, S.C. 2008. A bacterial ice-binding protein from the Vostok ice core. Extremophiles, 12, 713–717.Google Scholar
Scott, G.K., Hayes, P.H., Fletcher, G.L. & Davies, P.L. 1988. Wolffish antifreeze protein genes are primarily organized as tandem repeats that each contain 2 genes in inverted orientation. Molecular and Cellular Biology, 8, 3670–3675.Google Scholar
Scotter, A.J., Marshall, C.B., Graham, L.A., Gilbert, J.A., Garnham, C.P. & Davies, P.L. 2006. The basis for hyperactivity of antifreeze proteins. Cryobiology, 53, 229–239.Google Scholar
Sidebottom, C., Buckley, S., Pudney, P., Twigg, S., Jarman, C., Holt, C., Telford, J., McArthur, A., Worrall, D., Hubbard, R. & Lillford, P. 2000. Phytochemistry – heat-stable antifreeze protein from grass. Nature, 406, 256.Google Scholar
Sorhannus, U. 2011. Evolution of antifreeze protein genes in the diatom genus fragilariopsis: evidence for horizontal gene transfer, gene duplication and episodic diversifying selection. Evolutionary Bioinformatics, 7, 279–289.CrossRefGoogle ScholarPubMed
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.Google Scholar
Valbonesi, A. & Luporini, P. 1993. Biology of Euplotes focardii, an Antarctic ciliate. Polar Biology, 13, 489–493.Google Scholar
Vannini, C., Schena, A., Verni, F. & Rosati, G. 2004. Euplotes magnicirratus (Ciliophora, Hypotrichia) depends on its bacterial endosymbiont ‘Candidatus Devosia euplotis’ for food digestion. Aquatic Microbial Ecology, 36, 19–28.CrossRefGoogle Scholar
Wang, X., DeVries, A.L. & Cheng, C.H. 1995. Genomic basis for antifreeze peptide heterogeneity and abundance in an Antarctic eel pout – gene structures and organization. Molecular Marine Biology and Biotechnology, 4, 135–147.Google Scholar
Wang, S.Y. & Damodaran, S. 2009. Ice-structuring peptides derived from bovine collagen. Journal of Agricultural and Food Chemistry, 57, 5501–5509.Google Scholar
Yeh, C.M., Kao, B.Y. & Peng, H.J. 2009. Production of a recombinant type 1 antifreeze protein analogue by L. lactis and its applications on frozen meat and frozen dough. Journal of Agricultural and Food Chemistry, 57, 6216–6223.Google Scholar
Yu, T., Barchetta, S., Pucciarelli, S., La Terza, A. & Miceli, C. 2012. A novel robust heat-inducible promoter for heterologous gene expression in Tetrahymena thermophila . Protist, 163, 284–295.CrossRefGoogle ScholarPubMed
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