Genome Sequence of the Anaerobic, Thermophilic, and Cellulolytic Bacterium “
            <i>Anaerocellum thermophilum</i>
            ” DSM 6725

Kataeva, Irina; Yang, Soo Jin; Dam, Phuongan; Poole, Farris L.; Yin, Yanbin; Zhou, Fengfeng; Chou, Wen Chi; Xu, Ying; Goodwin, Lynne; Sims, David; Detter, John C.; Hauser, Loren; Westpheling, Janet; Adams, Michael W. W.

doi:10.1128/jb.00256-09

Cited by 74 publications

(82 citation statements)

References 10 publications

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“…Their genomes are also AϩT rich, ranging from 35 to 36% GϩC. Similarly to C. bescii (4,12), C. kristjanssonii also possesses an extrachromosomal element, the 15.9-kb plasmid pCALKR01. There are no similarities, however, between pATHE01/ pATHE02 and pCALKR01, suggesting that there are no ubiquitous Caldicellulosiruptor plasmids.…”

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confidence: 99%

“…While 16S rRNA phylogeny indicates a very close relationship within the eight species studied thus far (94.8% to 99.4% identity), microbiological analysis indicated that the genus is more physiologically divergent than previously thought (2). Three complete genome sequences are currently available for this genus, those of C. saccharolyticus (19), C. bescii (12), and C. obsidiansis (5), all of which are capable of crystalline cellulose hydrolysis. To further probe the plant biomass-degrading capacity among Caldicellulosiruptor species, genome sequences of five additional members of this genus, including some hemicellulolytic but less cellulolytic members, were completed: those of C. hydrothermalis, C. kristjanssonii, C. kronotskyensis, C. owensensis, and C. lactoaceticus (draft phase).…”

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confidence: 99%

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Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis , Caldicellulosiruptor kristjanssonii , Caldicellulosiruptor kronotskyensis , Caldicellulosiruptor owensensis , and Caldicellulosiruptor lactoaceticus

et al. 2011

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The genus Caldicellulosiruptor contains the most thermophilic, plant biomass-degrading bacteria isolated to date. Previously, genome sequences from three cellulolytic members of this genus were reported (C. saccharolyticus, C. bescii, and C. obsidiansis). To further explore the physiological and biochemical basis for polysaccharide degradation within this genus, five additional genomes were sequenced: C. hydrothermalis, C. kristjanssonii, C. kronotskyensis, C. lactoaceticus, and C. owensensis. Taken together, the seven completed and one draft-phase Caldicellulosiruptor genomes suggest that, while central metabolism is highly conserved, significant differences in glycoside hydrolase inventories and numbers of carbohydrate transporters exist, a finding which likely relates to variability observed in plant biomass degradation capacity.

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confidence: 99%

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confidence: 99%

Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis , Caldicellulosiruptor kristjanssonii , Caldicellulosiruptor kronotskyensis , Caldicellulosiruptor owensensis , and Caldicellulosiruptor lactoaceticus

et al. 2011

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“…Recently, the complete genome sequencing of a thermophilic cellulose-and xylan-degrading bacterium (59), Caldicellulosiruptor bescii (previously classified as Anaerocellum thermophilum) (58), was accomplished (GenBank accession number CP001393) (12,30). The bacterium has been demonstrated to ferment crystalline cellulose, xylan, and insoluble extracts of the bioenergy feedstock switchgrass (12).…”

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confidence: 99%

Biochemical and Mutational Analyses of a Multidomain Cellulase/Mannanase from Caldicellulosiruptor bescii

Mackie

Cann

2012

Appl Environ Microbiol

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Thermophilic cellulases and hemicellulases are of significant interest to the biofuel industry due to their perceived advantages over their mesophilic counterparts. We describe here biochemical and mutational analyses of Caldicellulosiruptor bescii Cel9B/ Man5A (CbCel9B/Man5A), a highly thermophilic enzyme. As one of the highly secreted proteins of C. bescii, the enzyme is likely to be critical to nutrient acquisition by the bacterium. CbCel9B/Man5A is a modular protein composed of three carbohydratebinding modules flanked at the N terminus and the C terminus by a glycoside hydrolase family 9 (GH9) module and a GH5 module, respectively. Based on truncational analysis of the polypeptide, the cellulase and mannanase activities within CbCel9B/ Man5A were assigned to the N-and C-terminal modules, respectively. CbCel9B/Man5A and its truncational mutants, in general, exhibited a pH optimum of ϳ5.5 and a temperature optimum of 85°C. However, at this temperature, thermostability was very low. After 24 h of incubation at 75°C, the wild-type protein maintained 43% activity, whereas a truncated mutant, TM1, maintained 75% activity. The catalytic efficiency with phosphoric acid swollen cellulose as a substrate for the wild-type protein was 7.2 s ؊1 ml/mg, and deleting the GH5 module led to a mutant (TM1) with a 2-fold increase in this kinetic parameter. Deletion of the GH9 module also increased the apparent k cat of the truncated mutant TM5 on several mannan-based substrates; however, a concomitant increase in the K m led to a decrease in the catalytic efficiencies on all substrates. These observations lead us to postulate that the two catalytic activities are coupled in the polypeptide.

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“…These eight draft genomes were compared to the previously published level 6 finished Sanger/454-based reference genome of wild-type C. bescii DSM 6725 (WT-Ref; accession no. CP001393.1) (21).…”

Section: Resultsmentioning

confidence: 99%

“…The reference genome was that of wild-type C. bescii DSM 6725 (WT-Ref; accession no. CP001393.1) from NCBI's GenBank repository, and the plasmids were removed for consistency in analyses (21). Wholegenome alignments to this reference were created using progressiveMauve (version 20150226 build 10) (40), with the following nondefault settings: default seed weight, false; use seed families, true; match seed weight, 15; and minimum LCB weight, 3,000.…”

Section: Methodsmentioning

confidence: 99%

Genome Stability in Engineered Strains of the Extremely Thermophilic Lignocellulose-Degrading Bacterium Caldicellulosiruptor bescii

Williams-Rhaesa

Poole

Dinsmore

et al. 2017

Appl Environ Microbiol

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Caldicellulosiruptor bescii is the most thermophilic cellulose degrader known and is of great interest because of its ability to degrade nonpretreated plant biomass. For biotechnological applications, an efficient genetic system is required to engineer it to convert plant biomass into desired products. To date, two different genetically tractable lineages of C. bescii strains have been generated. The first (JWCB005) is based on a random deletion within the pyrimidine biosynthesis genes pyrFA, and the second (MACB1018) is based on the targeted deletion of pyrE, making use of a kanamycin resistance marker. Importantly, an active insertion element, ISCbe4, was discovered in C. bescii when it disrupted the gene for lactate dehydrogenase (ldh) in strain JWCB018, constructed in the JWCB005 background. Additional instances of ISCbe4 movement in other strains of this lineage are presented herein. These observations raise concerns about the genetic stability of such strains and their use as metabolic engineering platforms. In order to investigate genome stability in engineered strains of C. bescii from the two lineages, genome sequencing and Southern blot analyses were performed. The evidence presented shows a dramatic increase in the number of single nucleotide polymorphisms, insertions/deletions, and ISCbe4 elements within the genome of JWCB005, leading to massive genome rearrangements in its daughter strain, JWCB018. Such dramatic effects were not evident in the newer MACB1018 lineage, indicating that JWCB005 and its daughter strains are not suitable for metabolic engineering purposes in C. bescii. Furthermore, a facile approach for assessing genomic stability in C. bescii has been established.IMPORTANCE Caldicellulosiruptor bescii is a cellulolytic extremely thermophilic bacterium of great interest for metabolic engineering efforts geared toward lignocellulosic biofuel and bio-based chemical production. Genetic technology in C. bescii has led to the development of two uracil auxotrophic genetic background strains for metabolic engineering. We show that strains derived from the genetic background containing a random deletion in uracil biosynthesis genes (pyrFA) have a dramatic increase in the number of single nucleotide polymorphisms, insertions/deletions, and ISCbe4 insertion elements in their genomes compared to the wild type. At least one daughter strain of this lineage also contains large-scale genome rearrangements that are flanked by these ISCbe4 elements. In contrast, strains developed from the second background strain developed using a targeted deletion strategy of the uracil biosynthetic gene pyrE have a stable genome structure, making them preferable for future metabolic engineering studies.

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Genome Sequence of the Anaerobic, Thermophilic, and Cellulolytic Bacterium “ Anaerocellum thermophilum ” DSM 6725

Cited by 74 publications

References 10 publications

Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis , Caldicellulosiruptor kristjanssonii , Caldicellulosiruptor kronotskyensis , Caldicellulosiruptor owensensis , and Caldicellulosiruptor lactoaceticus

Complete Genome Sequences for the Anaerobic, Extremely Thermophilic Plant Biomass-Degrading Bacteria Caldicellulosiruptor hydrothermalis , Caldicellulosiruptor kristjanssonii , Caldicellulosiruptor kronotskyensis , Caldicellulosiruptor owensensis , and Caldicellulosiruptor lactoaceticus

Biochemical and Mutational Analyses of a Multidomain Cellulase/Mannanase from Caldicellulosiruptor bescii

Genome Stability in Engineered Strains of the Extremely Thermophilic Lignocellulose-Degrading Bacterium Caldicellulosiruptor bescii

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