Previous Article |
Table of Contents
| Next Article 
From the Cover
BIOLOGICAL SCIENCES / ENVIRONMENTAL SCIENCES
Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses
,||,¶,**
*School of Oceanography, University of Washington, Box 357940, Seattle, WA 98195; Systemix Institute, Los Altos, CA 94024; Biotechnology Center, University of Wisconsin, Madison, WI 53706; Department of Biology and Microbiology, University of Wisconsin, Oshkosh, WI 54901; and Departments of ¶Biochemistry and ||Electrical and Computer Engineering, University of Wisconsin, Madison, WI 53706
Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved December 3, 2007 (received for review August 22, 2007)
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, 
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.
silica | transcriptome | iron | nitrogen | temperature
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: Data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE9697).
See Commentary on page 1391.
This article contains supporting information online at www.pnas.org/cgi/content/full/0707946105/DC1.
**To whom correspondence may be addressed. E-mail: msussman{at}wisc.edu or armbrust{at}ocean.washington.edu
© 2008 by The National Academy of Sciences of the USA
CiteULike 
Complore 
Connotea 
Del.icio.us 
Digg What's this?
Related Commentary in PNAS:
This article has been cited by other articles in HighWire Press-hosted journals:
|
|
 |
|
  M. A. Brzezinski Mining the diatom genome for the mechanism of biosilicification PNAS, February 5, 2008; 105(5): 1391 - 1392. [Full Text] [PDF]
|
|
