title: Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses.
abstract: Formation of complex inorganic structures is widespread in nature. Diatoms create intricately patterned cell walls of inorganic silicon that are a biomimetic model for design and generation of three-dimensional silica nanostructures. To date, only relatively simple silica structures can be generated in vitro through manipulation of known diatom phosphoproteins (silaffins) and long-chain polyamines. Here, we report the use of genome-wide transcriptome analyses of the marine diatom Thalassiosira pseudonana to identify additional candidate gene products involved in the biological manipulation of silicon. Whole-genome oligonucleotide tiling arrays and tandem mass spectrometry identified transcripts for >8,000 genes, approximately 3,000 of which were not previously described and included noncoding and antisense RNAs. Gene-specific expression profiles detected a set of 75 genes induced only under low concentrations of silicon but not under low concentrations of nitrogen or iron, alkaline pH, or low temperatures. Most of these induced gene products were predicted to contain secretory signals and/or transmembrane domains but displayed no homology to known proteins. Over half of these genes were newly discovered, identified only through the use of tiling arrays. Unexpectedly, a common set of 84 genes were induced by both silicon and iron limitations, suggesting that biological manipulation of silicon may share pathways in common with iron or, alternatively, that iron may serve as a required cofactor for silicon processes. These results provide insights into the transcriptional and translational basis for the biological generation of elaborate silicon nanostructures by these ecologically important microbes.
authors.affiliation: School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Mock
authors.forename: Manoj Pratim
authors.initials: MP
authors.lastname: Samanta
authors.forename: Vaughn
authors.initials: V
authors.lastname: Iverson
authors.forename: Chris
authors.initials: C
authors.lastname: Berthiaume
authors.forename: Matthew
authors.initials: M
authors.lastname: Robison
authors.forename: Karie
authors.initials: K
authors.lastname: Holtermann
authors.forename: Colleen
authors.initials: C
authors.lastname: Durkin
authors.forename: Sandra Splinter
authors.initials: SS
authors.lastname: Bondurant
authors.forename: Kathryn
authors.initials: K
authors.lastname: Richmond
authors.forename: Matthew
authors.initials: M
authors.lastname: Rodesch
authors.forename: Toivo
authors.initials: T
authors.lastname: Kallas
authors.forename: Edward L
authors.initials: EL
authors.lastname: Huttlin
authors.forename: Francesco
authors.initials: F
authors.lastname: Cerrina
authors.forename: Michael R
authors.initials: MR
authors.lastname: Sussman
authors.forename: E Virginia
authors.initials: EV
authors.lastname: Armbrust
mesh_terms: D017377:Diatoms / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome / Q000235:genetics; D007501:Iron / Q000378:metabolism; D000090463:Iron Deficiencies; D008386:Marine Biology; D049329:Nanostructures; D036103:Nanotechnology; D020411:Oligonucleotide Array Sequence Analysis; D012825:Silicon / Q000172:deficiency / Q000378:metabolism*
chemical_list: D007501:Iron; D012825:Silicon