Transcriptomic reprogramming of diatom Minutocellus polymorphus grown on urea

References

• Armbrust E.V. 2009. The life of diatoms in the world’s oceans. Nature 459: 185–192.
   PubMed Web of Science ®Google Scholar
• Armbrust E.V., Berges J.A., Bowler C., Green B.R., Martinez D., Putnam N.H., Zhou S., Allen A.E., Apt K. E. & Bechner M. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306: 79–86.
   PubMed Web of Science ®Google Scholar
• Arumugam M., Agarwal A., Arya M.C. & Ahmed Z. 2013. Influence of nitrogen sources on biomass productivity of microalgae Scenedesmus bijugatus. Bioresource Technology 131: 246–249.
   PubMed Web of Science ®Google Scholar
• Badger M.R., Andrews T.J., Whitney S., Ludwig M., Yellowlees D.C., Leggat W. & Price G.D. 1998. The diversity and coevolution of Rubisco, plastids, pyrenoids, and chloroplast-based CO2-concentrating mechanisms in algae. Canadian Journal of Botany 76: 1052–1071.
   Google Scholar
• Bender S.J., Parker M. S. & Armbrust E.V. 2012. Coupled effects of light and nitrogen source on the urea cycle and nitrogen metabolism over a diel cycle in the marine diatom Thalassiosira pseudonana. Protist 163: 232–251.
   PubMedGoogle Scholar
• Bhadra P. & Helms V. 2021. Molecular modeling of signal peptide recognition by eukaryotic Sec complexes. International Journal of Molecular Sciences 22: 10705.
   PubMedGoogle Scholar
• Büchel C. 2020. Light harvesting complexes in chlorophyll c-containing algae. Biochimica et Biophysica Acta (BBA)-Bioenergetics 1861: 148027.
   PubMedGoogle Scholar
• Cassar N., Laws E.A., Popp B.N. & Bidigare R.R. 2002. Sources of inorganic carbon for photosynthesis in a strain of Phaeodactylum tricornutum. Limnology and Oceanography 47: 1192–1197.
   Web of Science ®Google Scholar
• Chen Y., Gao Y., Chen C., Li X., Liang J., Sun L. & Wang Y. 2019. Interactions between the brown tide-causing microalga Aureococcus anophagefferens and the small diatom Minutocellus polymorphus under laboratory culture. Journal of Applied Phycology 31: 1793–1803.
   Google Scholar
• Cira E.K., Paerl H.W. & Wetz M.S. 2016. Effects of nitrogen availability and form on phytoplankton growth in a eutrophied estuary (Neuse River Estuary, NC, USA). PLoS One 11: e0160663.
   PubMed Web of Science ®Google Scholar
• Costa S.S., Miranda A.L., Andrade B.B., de Jesus Assis D., Souza C.O., de Morais M.G., Costa J.A.V. & Druzian J.I. 2018. Influence of nitrogen on growth, biomass composition, production, and properties of polyhydroxyalkanoates (PHAs) by microalgae. International Journal of Biological Macromolecules 116: 552–562.
   PubMedGoogle Scholar
• Curtis B.A., Tanifuji G., Burki F., Gruber A., Irimia M., Maruyama S., Arias M.C., Ball S.G., Gile G.H. & Hirakawa Y. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492: 59–65.
   PubMed Web of Science ®Google Scholar
• Donald D.B., Bogard M.J., Finlay K., Bunting L. & Leavitt P.R. 2013. Phytoplankton-specific response to enrichment of phosphorus-rich surface waters with ammonium, nitrate, and urea. PLoS One 8: e53277.
   PubMed Web of Science ®Google Scholar
• Dyhrman S.T. 2016. Nutrients and their acquisition: phosphorus physiology in microalgae. In: The physiology of microalgae, pp. 155–183. Springer International Publishing, Cham.
   Google Scholar
• El-Sheekh M., Eladel H., Battah M. & Abd-Elal S. 2004. Effect of different nitrogen sources on growth and biochemical composition of the green microalgae Scenedesmus obliquus and Chlorella kessleri. International Conference Biological Sciences 3: 419–432.
   Google Scholar
• Fan C., Glibert P., Alexander J. & Lomas M. 2003. Characterization of urease activity in three marine phytoplankton species, Aureococcus anophagefferens, Prorocentrum minimum, and Thalassiosira weissflogii. Marine Biology 142: 949–958.
   Google Scholar
• Fan J., Xu H. & Li Y. 2016. Transcriptome-based global analysis of gene expression in response to carbon dioxide deprivation in the green algae Chlorella pyrenoidosa. Algal Research 16: 12–19.
   Google Scholar
• Glibert P.M. 2016. Margalef revisited: a new phytoplankton mandala incorporating twelve dimensions, including nutritional physiology. Harmful Algae 55: 25–30.
   PubMedGoogle Scholar
• Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R. & Zeng Q. 2011. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature Biotechnology 29: 644–652.
   PubMed Web of Science ®Google Scholar
• Gruber A., Rocap G., Kroth P.G., Armbrust E.V. & Mock T. 2015. Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. The Plant Journal 81: 519–528.
   PubMedGoogle Scholar
• Gundermann K., Wagner V., Mittag M. & Büchel C. 2019. Fucoxanthin-chlorophyll protein complexes of the centric diatom Cyclotella meneghiniana differ in Lhcx1 and Lhcx6_1 content. Plant Physiology 179: 1779–1795.
   PubMedGoogle Scholar
• Huang K., Feng Q., Zhang Y., Ou L., Cen J., Lu S. & Qi Y. 2020. Comparative uptake and assimilation of nitrate, ammonium, and urea by dinoflagellate Karenia mikimotoi and diatom Skeletonema costatum s.l. in the coastal waters of the East China Sea. Marine Pollution Bulletin 155: 111200.
   PubMedGoogle Scholar
• Jing X., Lin S., Zhang H., Koerting C. & Yu Z. 2017. Utilization of urea and expression profiles of related genes in the dinoflagellate Prorocentrum donghaiense. PLoS One 12: e0187837.
   PubMedGoogle Scholar
• Jing X., Mi T., Zhen Y., Wang H. & Yu Z. 2019. Influence of N, P, Fe nutrients availability on nitrogen metabolism-relevant genes expression in Skeletonema marinoi. Journal of Ocean University of China 18: 239–252.
   Google Scholar
• Keeling P.J. & Palmer J.D. 2008. Horizontal gene transfer in eukaryotic evolution. Nature Reviews Genetics 9: 605–618.
   PubMed Web of Science ®Google Scholar
• Kroon B.M. & Thoms S. 2006. From electron to biomass: a mechanistic model to describe phytoplankton photosynthesis and steady-state growth rates. Journal of Phycology 42: 593–609.
   Web of Science ®Google Scholar
• Levitan O., Dinamarca J., Hochman G. & Falkowski P.G. 2014. Diatoms: a fossil fuel of the future. Trends in Biotechnology 32: 117–124.
   PubMed Web of Science ®Google Scholar
• Li B. & Dewey C.N. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12: 1–16.
   PubMed Web of Science ®Google Scholar
• Li J., Glibert P.M. & Zhou M. 2010. Temporal and spatial variability in nitrogen uptake kinetics during harmful dinoflagellate blooms in the East China Sea. Harmful Algae 9: 531–539.
   Google Scholar
• Li T., Yu L., Song B., Song Y., Li L., Lin X. & Lin S. 2020. Genome improvement and core gene set refinement of Fugacium kawagutii. Microorganisms 8: 102.
   PubMedGoogle Scholar
• Li Y., Mi T., Qiao L. & Zhen Y. 2019. NItrogen metabolism pathway of Minutocellus polymorphus under two nitrogen nutrition conditions based on transcriptome. Oceanologia et Limnologia Sinica 50: 1241–1251.
   Google Scholar
• Lindqvist L.M., Tandoc K., Topisirovic I. & Furic L. 2018. Cross-talk between protein synthesis, energy metabolism and autophagy in cancer. Current Opinion in Genetics & Development 48: 104–111.
   PubMed Web of Science ®Google Scholar
• Lomas M. 2004. Nitrate reductase and urease enzyme activity in the marine diatom Thalassiosira weissflogii (Bacillariophyceae): interactions among nitrogen substrates. Marine Biology 144: 37–44.
   Google Scholar
• Lourenco S.O., Barbarino E., Mancini-Filho J., Schinke K.P. & Aidar E. 2002. Effects of different nitrogen sources on the growth and biochemical profile of 10 marine microalgae in batch culture: an evaluation for aquaculture. Phycologia 41: 158–168.
   Web of Science ®Google Scholar
• Love M.I., Huber W. & Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15: 1–21.
   Web of Science ®Google Scholar
• Malviya S., Scalco E., Audic S., Vincent F., Veluchamy A., Poulain J., Wincker P., Iudicone D., de Vargas C. & Bittner L. 2016. Insights into global diatom distribution and diversity in the world’s ocean. Proceedings of the National Academy of Sciences 113: E1516–E1525.
   PubMedGoogle Scholar
• Mao X., Cai T., Olyarchuk J.G. & Wei L. 2005. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21: 3787–3793.
   PubMed Web of Science ®Google Scholar
• Martino A.D., Meichenin A., Shi J., Pan K. & Bowler C. 2007. Genetic and phenotypic characterization of Phaeodactylum tricornutum (Bacillariophyceae) accessions. Journal of Phycology 43: 992–1009.
   Google Scholar
• Pahl S.L., Lewis D.M., King K.D. & Chen F. 2012. Heterotrophic growth and nutritional aspects of the diatom Cyclotella cryptica (Bacillariophyceae): effect of nitrogen source and concentration. Journal of Applied Phycology 24: 301–307.
   Google Scholar
• Pan X., Ma J., Su X., Cao P., Chang W., Liu Z., Zhang X. & Li M. 2018. Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II. Science 360: 1109–1113.
   PubMedGoogle Scholar
• Qiao L., Chen Y., Mi T., Zhen Y., Gao Y. & Yu Z. 2017. Quantitative PCR analysis of the spatiotemporal dynamics of Aureococcus anophagefferens and Minutocellus polymorphus and the relationship between brown tides and nutrients in the coastal waters of Qinhuangdao, China. Journal of Applied Phycology 29: 297–308.
   Google Scholar
• Rastogi A., Vieira F.R.J., Deton-Cabanillas A.-F., Veluchamy A., Cantrel C., Wang G., Vanormelingen P., Bowler C., Piganeau G. & Hu H. 2020. A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum. The ISME Journal 14: 347–363.
   PubMed Web of Science ®Google Scholar
• Rausch C. & Bucher M. 2002. Molecular mechanisms of phosphate transport in plants. Planta 216: 23–37.
   PubMed Web of Science ®Google Scholar
• Reinfelder J.R., Milligan A.J. & Morel F.M. 2004. The role of the C4 pathway in carbon accumulation and fixation in a marine diatom. Plant Physiology 135: 2106–2111.
   PubMed Web of Science ®Google Scholar
• Reiskind J.B. & Bowes G. 1991. The role of phosphoenolpyruvate carboxykinase in a marine macroalga with C4-like photosynthetic characteristics. Proceedings of the National Academy of Sciences 88: 2883–2887.
   PubMed Web of Science ®Google Scholar
• Ren L.-J., Sun X.-M., Ji X.-J., Chen S.-L., Guo D.-S. & Huang H. 2017. Enhancement of docosahexaenoic acid synthesis by manipulation of antioxidant capacity and prevention of oxidative damage in Schizochytrium sp. Bioresource Technology 223: 141–148.
   PubMedGoogle Scholar
• Singh D., Nedbal L. & Ebenhöh O. 2018. Modelling phosphorus uptake in microalgae. Biochemical Society Transactions 46: 483–490.
   PubMed Web of Science ®Google Scholar
• Subramanian S., Barry A.N., Pieris S. & Sayre R.T. 2013. Comparative energetics and kinetics of autotrophic lipid and starch metabolism in chlorophytic microalgae: implications for biomass and biofuel production. Biotechnology for Biofuels 6: 1–12.
   PubMedGoogle Scholar
• Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A. & Speleman F. 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 3: research0034.1.
   PubMed Web of Science ®Google Scholar
• Versaw W.K. & Harrison M.J. 2002. A chloroplast phosphate transporter, PHT2; 1, influences allocation of phosphate within the plant and phosphate-starvation responses. The Plant Cell 14: 1751–1766.
   PubMed Web of Science ®Google Scholar
• Walsh G.E., McLaughlin L.L., Yoder M.J., Moody P.H., Lores E.M., Forester J. & Wessinger-Duvall P.B. 1988. Minutocellus polymorphus: a new marine diatom for use in algal toxicity tests. Environmental Toxicology and Chemistry: An International Journal 7: 925–929.
   Web of Science ®Google Scholar
• Wang M., Shi S., Lin F., Hao Z., Jiang P. & Dai G. 2012. Effects of soil water and nitrogen on growth and photosynthetic response of Manchurian ash (Fraxinus mandshurica) seedlings in northeastern China. PLoS One 7: e30754.
   PubMed Web of Science ®Google Scholar
• Wilhelm C. & Jakob T. 2011. From photons to biomass and biofuels: evaluation of different strategies for the improvement of algal biotechnology based on comparative energy balances. Applied Microbiology and Biotechnology 92: 909–919.
   PubMed Web of Science ®Google Scholar
• Wu Y., Jeans J., Suggett D.J., Finkel Z.V. & Campbell D.A. 2014. Large centric diatoms allocate more cellular nitrogen to photosynthesis to counter slower RUBISCO turnover rates. Frontiers in Marine Science 1: 68.
   Google Scholar
• Wunder T., Oh Z.G. & Mueller-Cajar O. 2019. CO2-fixing liquid droplets: towards a dissection of the microalgal pyrenoid. Traffic 20: 380–389.
   PubMedGoogle Scholar
• Yi Z., Xu M., Di X., Brynjolfsson S. & Fu W. 2017. Exploring valuable lipids in diatoms. Frontiers in Marine Science 4: 17.
   Google Scholar
• Young M.D., Wakefield M.J., Smyth G.K. & Oshlack A. 2010. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11: 1–12.
   Web of Science ®Google Scholar
• Zhang H., He Y., Wu P., Zhang S., Xie Z., Li D., Lin L., Chen F. & Wang D. 2019. Comparative metaproteomics reveals functional differences in the blooming phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense. Applied and Environmental Microbiology 85: e01425-19.
   PubMedGoogle Scholar
• Zhang M., Wang H. & Chen F. 2022. Time-resolved transcriptome analysis of Scenedesmus obliquus HTB1 under 10% CO2 condition. Microbial Biotechnology: 1–15.
   Google Scholar
• Zhang M., Zhen Y., Mi T. & Lin S. 2021. Integrated transcriptome sequencing (RNA-seq) and proteomic studies reveal resource reallocation towards energy metabolism and defense in Skeletonema marinoi in response to CO2 increase. Applied and Environmental Microbiology 87: e02614-20.
   Google Scholar
• Zulu N. N., Zienkiewicz K., Vollheyde K. & Feussner I. 2018. Current trends to comprehend lipid metabolism in diatoms. Progress in Lipid Research 70: 1–16.
   PubMed Web of Science ®Google Scholar