Acclimation of Antarctic Chlamydomonas to the sea-ice environment: a transcriptomic analysis

Ahmed NU, Park JI, Jung HJ, Kang KK, Hur Y, Lim YP, Nou IS (2012) Molecular characterization of stress resistance-related chitinase genes of Brassica rapa. Plant Physiol Biochem 58:106–115

An M, Mou S, Zhang X, Zheng Z, Ye N, Wang D, Zhang W, Miao J (2013) Expression of fatty acid desaturase genes and fatty acid accumulation in Chlamydomonas sp. ICE-L under salt stress. Bioresour Technol 149:77–83

Andersson JO (2009) Gene transfer and diversification of microbial eukaryotes. Ann Rev Microbiol 63:177–193

Arrigo KR, Mock T, Lizotte MP (2010) Primary production in sea ice. In: Thomas D, Dieckmann G (eds) Sea ice: an introduction to its physics, chemistry, biology and geology. Wiley-Blackwell, Malden, MA, USA, pp 143–183

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[J]. Environ Microbiol 12(4):1041–1052

Bercovich A, Vázquez SC, Yankilevich P, Coria SH, Foti M, Hernández E, Vidal A, Ruberto L, Melo C, Marenssi S, Criscuolo M, Memoli M, Arguelles M, Mac Cormack WP (2008) Bizionia argentinensis sp. nov., isolated from surface marine water in Antarctica. Int J Syst Evol Microbiol 58:2363–2367

Bowman JP, McCammon SA, Lewis T, Skerratt JH, Brown JL, Nichols DS, McMeekin TA (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

Brazelton WJ, Baross JA (2009) Abundant transposases encoded by the metagenome of a hydrothermal chimney biofilm. ISME J 3:1420–1424

Chen Z, He C, Hu H (2012) Temperature responses of growth, photosynthesis, fatty acid and nitrate reductase in Antarctic and temperate Stichococcus. Extremophiles 16:127–133

Chinnusamy V, Gong Z, Zhu JK (2008) Nuclear RNA export and its importance in abiotic stress responses of plants., Nuclear pre-mRNA processing in plantsSpringer, Berlin, pp 235–255

Di Martino Rigano V, Vona V, Lobosco O, Carillo P, Lunn JE, Carfagna S, Esposito S, Caiazzo M, Rigano C (2006) Temperature dependence of nitrate reductase in the psychrophilic unicellular alga Koliella antarctica and the mesophilic alga Chlorella sorokiniana. Plant Cell Environ 29:1400–1409

Dong CH, Hu X, Tang W, Zheng X, Kim YS, Lee BH, Zhu JK (2006) A putative Arabidopsis nucleoporin AtNUP160 is critical for RNA export and required for plant tolerance to cold stress. Mol Cell Biol 26:9533–9543

Feng S, Powell SM, Wilson R, Bowman JP (2014) Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism. Genome Biol Evol 6:133–148

Gupta R, Deswal R (2014) Refolding of β-stranded class I chitinases of Hippophae rhamnoides enhances the antifreeze activity during cold acclimation. PLoS One 9:e91723

Humbert S, Zhong S, Deng Y, Howell SH, Rothstein SJ (2012) Alteration of the bZIP60/IRE1 pathway affects plant response to ER stress in Arabidopsis thaliana. PLoS One 7:e39023–e39023

Hwang YS, Jung G, Jin E (2008) Transcriptome analysis of acclimatory responses to thermal stress in Antarctic algae. Biochem Biophys Res Commun 367:635–641

Janknegt PJ, Van De Poll WH, Visser RJW, Rijstenbil JW, Buma AGJ (2008) Oxidative stress responses in the marine antarctic diatom Chaetoceros brevis (bacillariophyceae) during photoacclimation. J Phycol 44:957–966

Jung G, Lee CG, Kang SH, Jin E (2007) Annotation and expression profile analysis of cDNAs from the Antarctic diatom Chaetoceros neogracile. J Microbiol Biotechnol 17:1330–1337

Kanamori N, Madsen LH, Radutoiu S, Frantescu M, Quistgaard EM, Miwa H, Downie JA, James EK, Felle HH, Haaning LL, Jensen TH, Sato S, Nakamura Y, Tabata S, Sandal N, Stougaard J (2006) A nucleoporin is required for induction of Ca2+ spiking in legume nodule development and essential for rhizobial and fungal symbiosis. Proc Natl Acad Sci USA 103:359–364

Kandror O, Goldberg AL (1997) Trigger factor is induced upon cold shock and enhances viability of Escherichia coli at low temperatures. Proc Natl Acad Sci USA 94:4978–4981

Liu Y, Burne RA (2009) Multiple two-component systems modulate alkali generation in Streptococcus gordonii in response to environmental stresses. J Bacteriol 191:7353–7362

Liu C, Huang X, Wang X, Li G (2006) Phylogenetic studies on two strains of Antarctic ice algae based on morphological and molecular characteristics. Phycologia 45:190–198

Liu S, Zhang P, Cong B, Liu C, Lin X, Shen J, Huang X (2010) Molecular cloning and expression analysis of a cytosolic Hsp70 gene from Antarctic ice algae Chlamydomonas sp. ICE-L. Extremophiles 14:329–337

Liu C, Wu G, Huang X (2012) Validation of housekeeping genes for gene expression studies in an ice alga Chlamydomonas during freezing acclimation. Extremophiles 16:419–425

Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C[T]) method. Methods 25:402–408

Lyon BR, Mock T (2014) Polar microalgae: new approaches towards understanding adaptations to an extreme and changing environment. Biology 3:56–80

Lyon BR, Lee PA, Bennett JM, DiTullio GR, Janech MG (2011) Proteomic analysis of a sea-ice diatom: salinity acclimation provides new insight into the dimethylsulfoniopropionate production pathway. Plant Physiol 157:1926–1941

Lyzenga WJ, Stone SL (2012) Abiotic stress tolerance mediated by protein ubiquitination. J Exp Bot 63:599–616

Ma DK, Li Z, Lu AY, Sun F, Chen S, Rothe M, Menzel R, Sun F, Horvitz HR (2015) Acyl-CoA dehydrogenase drives heat adaptation by sequestering fatty acids. Cell 161:1152–1163

Merchant SS, Prochnik SE, Vallon O (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318:245–250

Mock T, Junge K (2007) Psychrophilic diatoms: mechanisms for survival in freeze–thaw cycles., Algae and cyanobacteria in extreme environmentsSpringer, New York, pp 345–364

Moriya Y, Itoh M, Okuda S, Yoshizawa A, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:182–185

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

Noinaj N, Noinaj N, Guillier M, Barnard TJ, Buchanan SK (2010) TonB-dependent transporters: regulation, structure, and function. Annu Rev Microbiol 64:43

Obertegger U, Camin F, Guella G, Flaim G (2011) Adaptation of a psychrophilic freshwater dinoflagellate to ultraviolet radiation. J Phycol 47:811–820

Osipova S, Dudareva L, Bondarenko N, Nasarova A, Sokolova N, Obolkina L, Glyzina O, Timoshkin O (2009) Temporal variation in fatty acid composition of Ulothrix Zonata (Chlorophyta) from ice and benthic communities of Lake Baikal. Phycologia 48:130–135

Piette F, Leprince P, Feller G (2012) Is there a cold shock response in the Antarctic psychrophile Pseudoalteromonas haloplanktis? Extremophiles 16(4):681–683

Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, Pangilinan J, Kapitonov V, Jurka J, Salamov A, Shapiro H, Schmutz J, Grimwood J, Lindquist E, Lucas S, Grigoriev IV, Schmitt R, Kirk D, Rokhsar DS (2010) Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science 329:223–226

Provasoli L (1968) Media and prospects for the cultivation of marine algae. In: Cultures and collections of algae. Proceedings of the US-Japan conference, Hakone, Japanese Society for Plant Physiology, September 1966, pp 63–75

Raymond JA, Kim HJ (2012) Possible role of horizontal gene transfer in the colonization of sea ice by algae. PLoS One 7:e35968

Rice P, Longden I, Bleasby A (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16:276–277

Ryan KG, McMinn A, Hegseth EN, Davy SK (2012) The effects of ultraviolet-b radiation on Antarctic sea-ice algae. J Phycol 48:74–84

Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber AP (2013) Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science 339:1207–1210

Schönknecht G, Weber APM, Lercher MJ (2014) Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Bioessays 36:9–20

Steege DA (2000) Emerging features of mRNA decay in bacteria. RNA 6:1079–1090

Stock AM, Robinson VL, Goudreau PN (2000) Two-component signal transduction. Annu Rev Biochem 69:183–215

Storey KB, Storey JM (2013) Molecular biology of freezing tolerance. Compr Physiol 3:1283–1308

Takizawa K, Takahashi S, Huner NP, Minagawa J (2009) Salinity affects the photoacclimation of Chlamydomonas raudensis Ettl UWO241. Photosynth Res 99:195–203

Teoh ML, Phang SM, Chu WL (2012) Response of Antarctic, temperate, and tropical microalgae to temperature stress. J Appl Phycol 1:1–13

Thomas DN, Dieckmann GS (2002) Antarctic sea ice: a habitat for extremophiles. Science 295:641–644

Varin T, Lovejoy C, Jungblut AD, Vincent WF, Corbeil J (2012) Metagenomic analysis of stress genes in microbial mat communities from Antarctica and the High Arctic. Appl Environ Microbiol 78:549–559

Vasu S, Shah S, Orjalo A, Park Μ, Fischer WH, Forbes DJ (2001) Novel vertebrate nucleoporins Nup133 and Nup160 play a role in mRNA export. J Cell Biol 155:339–354

Vijay N, Poelstra JW, Künstner A, Wolf JBW (2013) Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Mol Ecol 22:620–634

Vona V, Di Martino Rigano V, Lobosco O, Carfagna S, Esposito S, Rigano C (2004) Temperature responses of growth, photosynthesis, respiration and NADH: nitrate reductase in and mesophilic algae. New Phytol 163:325–331

Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138

Wells LE, Deming JW (2006) Modelled and measured dynamics of viruses in Arctic winter sea-ice brines. Environ Microbiol 8:1115–1121

Welsh DT (2000) Ecological significance of compatible solute accumulation by micro-organisms: from single cells to global climate. FEMS Microbiol Rev 24:263–290

Winkler ME, Hoch JA (2008) Essentiality, bypass, and targeting of the YycFG (VicRK) two-component regulatory system in gram-positive bacteria. J Bacteriol 190:2645–2648

Wu G, Liu C, Liu S, Cong B, Huang X (2010) High-quality RNA preparation for cDNA library construction of the Antarctic sea-ice alga Chlamydomonas sp. ICE-L. J Appl Phycol 22:779–783

Xu XM, Meier I (2008) The nuclear pore comes to the fore. Trends Plant Sci 13:20–27

Zhang P, Liu S, Cong B, Liu C, Lin X, Shen J, Huang X (2011) A novel omega-3 fatty acid desaturase involved in acclimation processes of polar condition from Antarctic ice algae Chlamydomonas sp. ICE-L. Mar Biotechnol 13:393–401

Zhao MG, Chen L, Zhang LL, Zhang WH (2009) Nitric reductase-dependent nitric oxide production is involved in cold acclimation and freezing tolerance in Arabidopsis. Plant Physiol 151:755–767