From the Cover: Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses

@article{citeulike:2339211, 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, {approx}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. 10.1073/pnas.0707946105}, author = {Mock, Thomas and Samanta, Manoj P. and Iverson, Vaughn and Berthiaume, Chris and Robison, Matthew and Holtermann, Karie and Durkin, Colleen and Bondurant, Sandra S. and Richmond, Kathryn and Rodesch, Matthew and Kallas, Toivo and Huttlin, Edward L. and Cerrina, Francesco and Sussman, Michael R. and Armbrust, Virginia E. }, citeulike-article-id = {2339211}, doi = {10.1073/pnas.0707946105}, journal = {Proceedings of the National Academy of Sciences}, keywords = {diatom, genome, pnas}, month = {February}, number = {5}, pages = {1579--1584}, posted-at = {2008-02-06 06:21:19}, priority = {2}, title = {From the Cover: Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses}, url = {http://dx.doi.org/10.1073/pnas.0707946105}, volume = {105}, year = {2008} }

TY - JOUR ID - citeulike:2339211 L3 - citeulike-article-id:2339211 TI - From the Cover: Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses JF - Proceedings of the National Academy of Sciences VL - 105 IS - 5 SP - 1579 EP - 1584 N2 - 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, {approx}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. 10.1073/pnas.0707946105 KW - diatom KW - genome KW - pnas AU - Mock, Thomas AU - Samanta, Manoj AU - Iverson, Vaughn AU - Berthiaume, Chris AU - Robison, Matthew AU - Holtermann, Karie AU - Durkin, Colleen AU - Bondurant, Sandra AU - Richmond, Kathryn AU - Rodesch, Matthew AU - Kallas, Toivo AU - Huttlin, Edward AU - Cerrina, Francesco AU - Sussman, Michael AU - Armbrust, Virginia PY - 2008/02/05/ UR - http://dx.doi.org/10.1073/pnas.0707946105 ER -