community proteomics of Biofil

Originally published in Science Express on 5 May 2005
Science, Vol 308, Issue 5730, 1915-1920, 24 June 2005

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[DOI: 10.1126/science. 1109070]

Reports

Community Proteomics of a Natural Microbial Biofilm

Rachna J. Ram,¹ Nathan C. VerBerkmoes,^3,4 Michael P. Thelen,^1,6 Gene W. Tyson,¹ Brett J. Baker,² Robert C. Blake, II,⁷ Manesh Shah,⁵ Robert L. Hettich,⁴ Jillian F. Banfield^1,2*

Using genomic and mass spectrometry–based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.

¹ Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA 94720, USA.
² Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA 94720, USA.
³ Graduate School of Genome Science and Technology University of Tennessee–Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830, USA.
⁴ Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
⁵ Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
⁶ Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.
⁷ College of Pharmacy, Xavier University, New Orleans, LA, 70125, USA.

^* To whom correspondence should be addressed. E-mail: [e-mail]

[genevalley]

Enough funding, we can do environmental genomics & proteomics! See what they have done on this field!!