title: Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation.
abstract: Environmental fluctuations affect distribution, growth and abundance of diatoms in nature, with iron (Fe) availability playing a central role. Studies on the response of diatoms to low Fe have either utilized continuous (24 hr) illumination or sampled a single time of day, missing any temporal dynamics. We profiled the physiology, metabolite composition, and global transcripts of the pennate diatom Phaeodactylum tricornutum during steady-state growth at low, intermediate, and high levels of dissolved Fe over light:dark cycles, to better understand fundamental aspects of genetic control of physiological acclimation to growth under Fe-limitation. We greatly expand the catalog of genes involved in the low Fe response, highlighting the importance of intracellular trafficking in Fe-limited diatoms. P. tricornutum exhibited transcriptomic hallmarks of slowed growth leading to prolonged periods of cell division/silica deposition, which could impact biogeochemical carbon sequestration in Fe-limited regions. Light harvesting and ribosome biogenesis transcripts were generally reduced under low Fe while transcript levels for genes putatively involved in the acquisition and recycling of Fe were increased. We also noted shifts in expression towards increased synthesis and catabolism of branched chain amino acids in P. tricornutum grown at low Fe whereas expression of genes involved in central core metabolism were relatively unaffected, indicating that essential cellular function is protected. Beyond the response of P. tricornutum to low Fe, we observed major coordinated shifts in transcript control of primary and intermediate metabolism over light:dark cycles which contribute to a new view of the significance of distinctive diatom pathways, such as mitochondrial glycolysis and the ornithine-urea cycle. This study provides new insight into transcriptional modulation of diatom physiology and metabolism across light:dark cycles in response to Fe availability, providing mechanistic understanding for the ability of diatoms to remain metabolically poised to respond quickly to Fe input and revealing strategies underlying their ecological success.
authors.affiliation: Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, United States of America.|J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Sarah R
authors.identifier: http://orcid.org/0000-0003-1105-3127
authors.initials: SR
authors.lastname: Smith
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.|Department of Biology, CSU Bakersfield, Bakersfield, California, United States of America.
authors.forename: Jeroen T F
authors.initials: JT
authors.lastname: Gillard
authors.affiliation: Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, United States of America.
authors.forename: Adam B
authors.identifier: http://orcid.org/0000-0001-6132-8534
authors.initials: AB
authors.lastname: Kustka
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: John P
authors.initials: JP
authors.lastname: McCrow
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Badger
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Hong
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Department of Earth and Environmental Sciences, Rutgers University, Newark, New Jersey, United States of America.
authors.forename: Ashley M
authors.initials: AM
authors.lastname: New
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Chris L
authors.initials: CL
authors.lastname: Dupont
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany.
authors.forename: Toshihiro
authors.initials: T
authors.lastname: Obata
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany.
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
authors.affiliation: Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, California, United States of America.|J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
mesh_terms: D002453:Cell Cycle / Q000187:drug effects / Q000235:genetics; D002455:Cell Division / Q000187:drug effects / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics; D017377:Diatoms / Q000187:drug effects / Q000254:growth & development / Q000378:metabolism*; D015870:Gene Expression; D007501:Iron / Q000378:metabolism* / Q000494:pharmacology; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008928:Mitochondria / Q000187:drug effects / Q000378:metabolism; D017440:Photoperiod; D014176:Protein Biosynthesis / Q000187:drug effects; D059467:Transcriptome / Q000235:genetics*
chemical_list: D007501:Iron