Research
Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
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* Corresponding authors: Lei Wang wanglei@nankai.edu.cn - Maqsudul Alam alam@hawaii.edu
- † Equal contributors
1 Department of Microbiology, University of Hawai'i, 2538 The Mall, Honolulu, HI 96822, USA
2 GNS Science, Extremophile Research Group, 3352 Taupo, New Zealand
3 TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
4 Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China
5 Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300457, PR China
6 National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
7 Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawai'i, Honolulu, HI 96822, USA
8 School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
9 Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
10 Current address: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
Genome Biology 2008, 9:R161 doi:10.1186/gb-2008-9-11-r161
Published: 17 November 2008Additional files
Additional data file 1:
Figure S1: phylogenetic distribution of the best BLAST hits of A. flavithermus proteins. Figure S2: the tree of the phylum Firmicutes based on similarity of the phyletic patterns in COGs. Figure S3: two-dimensional gels comparing expression of A. flavithermus proteins from cells grown with or without silica. Figure S4: SDS-PAGE analysis of purified recombinant proteins. Figure S5: thin-layer chromatography-based detection of Aflv_0146 and Aflv_1886 reaction products ornithine and agmatine. Figure S6: HPLC chromatographs showing enzymatic activities of expressed Aflv_0024, Aflv_2749, Aflv_1437 and Aflv_2750 proteins. Figure S7: sequence alignment of A. flavithermus agmatinase Aflv_2749 and arginase Aflv_0146 with various agmatinases and arginases. Table S1: examples of paralogous proteins encoded in the genomes of A. flavithermus and five other bacilli. Table S2: presence or absence of certain metabolic pathway genes in the A. flavithermus genome. Table S3: examples of gene gains and losses in Geobacillus/Anoxybacillus lineages. Table S4: A. flavithermus genes that were found to be up- and down-regulated in cells exposed to silica.
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