title: Noncoding and coding transcriptome responses of a marine diatom to phosphate fluctuations.
abstract: Phosphorus (P) is an essential element to all living cells, yet fluctuations in P concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton groups, adapting to and surviving periods of suboptimal conditions and resuming growth as soon as nutrient concentrations permit. A knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete. By strand-specific RNA sequencing, we analyzed the global transcriptome changes of the diatom Phaeodactylum tricornutum in response to P fluctuations over a course of 8 d, defining five distinct physiological states. This study reports previously unidentified genes highly responsive to P stress in P. tricornutum. Our data also uncover the complexity of the P. tricornutum P-responsive sensory and signaling system that combines bacterial two-component systems with more complex pathways reminiscent of metazoans. Finally, we identify a multitude of novel long intergenic nonprotein coding RNAs (lincRNAs) specifically responsive to P depletion, suggesting putative regulatory roles in the regulation of P homeostasis. Our work provides additional molecular insights into the resilience of diatoms and their ecological success, and opens up novel routes to address and explore the function and regulatory roles of P. tricornutum lincRNAs in the context of nutrient stress.
authors.affiliation: Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065, USA.|Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 INSERM U1024, 46 Rue d'Ulm, 75005, Paris, France.
authors.forename: Maria Helena
authors.initials: MH
authors.lastname: Cruz de Carvalho
authors.affiliation: Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065, USA.
authors.forename: Hai-Xi
authors.initials: HX
authors.lastname: Sun
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 INSERM U1024, 46 Rue d'Ulm, 75005, Paris, France.
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
authors.affiliation: Laboratory of Plant Molecular Biology, Rockefeller University, New York, NY, 10065, USA.
authors.forename: Nam-Hai
authors.initials: NH
authors.lastname: Chua
mesh_terms: D059001:Aquatic Organisms / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D017377:Diatoms / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D015536:Down-Regulation / Q000187:drug effects / Q000235:genetics; D063990:Gene Ontology; D016678:Genome; D006706:Homeostasis / Q000187:drug effects; D016366:Open Reading Frames / Q000235:genetics*; D010710:Phosphates / Q000494:pharmacology*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*; D015854:Up-Regulation / Q000187:drug effects / Q000235:genetics
chemical_list: D010710:Phosphates; D012333:RNA, Messenger; D014157:Transcription Factors
keywords: Phaeodactylum tricornutum; diatoms; long noncoding intergenic RNAs; phosphate; signaling; strand-specific RNA-sequencing (ssRNA-Seq); transcription factors (TFs)