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| Status |
Public on Nov 29, 2010 |
| Title |
Phylogenetic, microbiological and glycoside hydrolase diversities within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor |
| Platform organism |
Caldicellulosiruptor saccharolyticus |
| Sample organisms |
Caldicellulosiruptor bescii; Caldicellulosiruptor saccharolyticus; Caldicellulosiruptor owensensis; Caldicellulosiruptor acetigenus; Caldicellulosiruptor hydrothermalis; Caldicellulosiruptor kronotskyensis |
| Experiment type |
Genome variation profiling by array
|
| Summary |
Phylogenetic, microbiological and comparative genomic analysis was used to examine the diversity among members of the genus Caldicellulosiruptor with an eye towards the capacity of these extremely thermophilic bacteria for degrading the complex carbohydrate content of plant biomass. Seven species from this genus (C. saccharolyticus, C. bescii (formerly Anaerocellum thermophilum), C. hydrothermalis, C. owensensis, C. kronotskyensis, C. lactoaceticus, and C. kristjanssonii) were compared on the basis of 16S rRNA phylogeny and cross-species DNA-DNA hybridization to a whole genome C. saccharolyticus oligonucleotide microarray. Growth physiology of the seven Caldicellulosiruptor species on a range of carbohydrates showed that, while all could be cultivated on acid pre-treated switchgrass, only C. saccharolyticus, C. besci, C. kronotskyensis, and C. lactoaceticus were capable of hydrolyzing Whatman No. 1 filter paper. Two-dimensional gel electrophoresis of the secretomes from cells grown on microcrystalline cellulose revealed that species capable of crystalline cellulose hydrolysis also had diverse secretome fingerprints. The two-dimensional secretome of C. saccharolyticus revealed a prominent S-layer protein that appears to be also indicative of highly cellulolytic Caldicellulosiruptor species, suggesting a possible role in cell-substrate interaction. These growth physiology results were also linked to glycoside hydrolase and carbohydrate-binding module inventories for the seven bacteria, deduced from draft genome sequence information. These preliminary inventories indicated that the absence of a single glycoside hydrolase family and carbohydrate binding motif family appear to be responsible for some Caldicellulosiruptor species’ diminished cellulolytic capabilities. Overall, the genus Caldicellulosiruptor appears to contain more genomic and physiological diversity than previously reported, and is well suited for biomass deconstruction applications.
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| Overall design |
Six dye-flip experiments were conducted using C. saccharolyticus genomic DNA as the reference in each dye-flip, and one of six different Caldicellulosiruptor spp. as a tester in each dye-flip
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| Contributor(s) |
Blumer-Schuette SE, Lewis DL, Kelly RM |
| Citation(s) |
20971878 |
| |
| Submission date |
Aug 13, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Robert M Kelly |
| Organization name |
North Carolina State University
|
| Department |
Chemical and Biomolecular Engineering
|
| Street address |
Campus Box 7905
|
| City |
Raleigh |
| State/province |
MI |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL6681 |
NCSU_Caldicellulosiruptor saccharolyticus_3K array_version 1 |
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| Samples (6)
|
| GSM578915 |
C. bescii versus C. saccharolyticus |
| GSM578916 |
C. hydrothermalis versus C. saccharolyticus |
| GSM578917 |
C. kristjanssonii versus C. saccharolyticus |
| GSM578918 |
C. kronotskyensis versus C. saccharolyticus |
| GSM578919 |
C. lactoaceticus versus C. saccharolyticus |
| GSM578920 |
C. owensensis versus C. saccharolyticus |
|
| Relations |
| BioProject |
PRJNA129969 |
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