Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica sol...

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Published inGenome biology Vol. 9; no. 11; pp. R161 - 2023
Main Authors Saw, Jimmy H, Mountain, Bruce W, Feng, Lu, Omelchenko, Marina V, Hou, Shaobin, Saito, Jennifer A, Stott, Matthew B, Li, Dan, Zhao, Guang, Wu, Junli, Galperin, Michael Y, Koonin, Eugene V, Makarova, Kira S, Wolf, Yuri I, Rigden, Daniel J, Dunfield, Peter F, Wang, Lei, Alam, Maqsudul
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 17.11.2008
BioMed Central
Subjects
anaerobes
Anoxybacillus flavithermus
Bacillaceae - chemistry
Bacillaceae - genetics
Bacillaceae - physiology
Bacteria
Bacterial Proteins - analysis
biofilm
biomineralization
chromosomes
drainage water
dried milk
enzymes
Fossils
gelatin
gene deletion
genome
Genome, Bacterial
Geobacillus
geothermal energy
Gram-positive bacteria
habitats
hot springs
Hot Temperature
nanospheres
New Zealand
nucleotide sequences
physiology
polyamines
processed foods
proteome
proteomics
sequence analysis
silica
Silicon Dioxide
thermophilic bacteria
wastewater
Water Microbiology
New Zealand
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Abstract Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.
AbstractList Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation. Background Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. Results We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. Conclusions Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.
BACKGROUND: Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. RESULTS: We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. CONCLUSIONS: Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.
Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.
Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation.
Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life.BACKGROUNDGram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life.We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres.RESULTSWe report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres.Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.CONCLUSIONSMicrobial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.
ArticleNumber R161
Author Omelchenko, Marina V
Li, Dan
Galperin, Michael Y
Koonin, Eugene V
Hou, Shaobin
Zhao, Guang
Feng, Lu
Wolf, Yuri I
Wu, Junli
Alam, Maqsudul
Dunfield, Peter F
Saito, Jennifer A
Stott, Matthew B
Rigden, Daniel J
Wang, Lei
Makarova, Kira S
Saw, Jimmy H
Mountain, Bruce W
AuthorAffiliation 1 Department of Microbiology, University of Hawai'i, 2538 The Mall, Honolulu, HI 96822, USA
4 Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China
6 National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
5 Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300457, PR China
2 GNS Science, Extremophile Research Group, 3352 Taupo, New Zealand
7 Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawai'i, Honolulu, HI 96822, USA
9 Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
8 School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
10 Current address: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
3 TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR Chi
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– name: 10 Current address: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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– name: 9 Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1N4, Canada
– name: 4 Tianjin Research Center for Functional Genomics and Biochip, Tianjin 300457, PR China
– name: 3 TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, PR China
– name: 5 Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin 300457, PR China
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/19014707$$D View this record in MEDLINE/PubMed
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Snippet Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed...
BACKGROUND: Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and...
Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation. Background...
Sequencing of the complete genome of Anoxybacillus flavithermus reveals enzymes that are required for silica adaptation and biofilm formation.
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biomedcentral
proquest
pubmed
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SourceType Open Access Repository
Aggregation Database
Index Database
Enrichment Source
StartPage R161
SubjectTerms anaerobes
Anoxybacillus flavithermus
Bacillaceae - chemistry
Bacillaceae - genetics
Bacillaceae - physiology
Bacteria
Bacterial Proteins - analysis
biofilm
biomineralization
chromosomes
drainage water
dried milk
enzymes
Fossils
gelatin
gene deletion
genome
Genome, Bacterial
Geobacillus
geothermal energy
Gram-positive bacteria
habitats
hot springs
Hot Temperature
nanospheres
New Zealand
nucleotide sequences
physiology
polyamines
processed foods
proteome
proteomics
sequence analysis
silica
Silicon Dioxide
thermophilic bacteria
wastewater
Water Microbiology
Title Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1
URI https://www.ncbi.nlm.nih.gov/pubmed/19014707
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https://www.proquest.com/docview/69939401
http://dx.doi.org/10.1186/gb-2008-9-11-r161
https://pubmed.ncbi.nlm.nih.gov/PMC2614493
Volume 9
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