Draft Genome Sequence of Geobacillus icigianus Strain G1w1
            <sup>T</sup>
            Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation)

Bryanskaya, A. V.; Розанов, А. С.; Logacheva, Maria D.; Kotenko, Anastasia V.; Peltek, Sergey E.

doi:10.1128/genomea.01098-14

Cited by 10 publications

(5 citation statements)

References 7 publications

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“…The complete genome of Geobacillus icigianus strain (GenBank assembly accession: GCA_000750005.1) [ 7 ] was used for reannotation by means of the standard RAST (Rapid Annotation Subsystem Technology) annotation scheme [ 11 ]. The KBase web-tool [ 12 ] was employed to generate a draft genome-scale metabolic model of the strain with standard parameters including an in-built gap-filling algorithm [ 13 ].…”

Section: Methodsmentioning

confidence: 99%

“…The Geobacillus icigianus G1w1T is a new thermophilic strain of the genus Geobacillus that was firstly isolated from sludge of the hydrothermal vent located in the Valley of Geysers (Kamchatka, Russia) [ 6 ]. Availability of the annotated bacterium’s genome [ 7 ] enables a systems-level investigation of the Geobacillus icigianus metabolism including whole-genome metabolic reconstruction and flux balance analysis.…”

Section: Introductionmentioning

confidence: 99%

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A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

2020

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The thermophilic strain of the genus Geobacillus, Geobacillus icigianus is a promising bacterial chassis for a wide range of biotechnological applications. In this study, we explored the metabolic potential of Geobacillus icigianus for the production of 2,3-butanediol (2,3-BTD), one of the cost-effective commodity chemicals. Here we present a genome-scale metabolic model iMK1321 for Geobacillus icigianus constructed using an auto-generating pipeline with consequent thorough manual curation. The model contains 1321 genes and includes 1676 reactions and 1589 metabolites, representing the most-complete and publicly available model of the genus Geobacillus. The developed model provides new insights into thermophilic bacterial metabolism and highlights new strategies for biotechnological applications of the strain. Our analysis suggests that Geobacillus icigianus has a potential for 2,3-butanediol production from a variety of utilized carbon sources, including glycerine, a common byproduct of biofuel production. We identified a set of solutions for enhancing 2,3-BTD production, including cultivation under anaerobic or microaerophilic conditions and decreasing the TCA flux to succinate via reducing citrate synthase activity. Both in silico predicted metabolic alternatives have been previously experimentally verified for closely related strains including the genus Bacillus.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

2020

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“… NP NP Esterase 7 WP_043054382 esterase B. paralicheniformis NP NP Esterase 8 WP_020452056 alkaliphilic lipase EstA B. subtilis NP NP Esterase 9 WP_029418313 esterase B. sonorensis Sonoran Desert soil, USA [ 36 ] Lipase 10 ACN79581 thermostable lipase Geobacillus sp. Compost of local area of Taiwan [ 37 ] Lipase 11 KFX34290 lipase G. icigianus Hot Springs in the Valley of Geysers, Kamchatka, Russian Federation [ 38 ] Lipase 12 AFU07645 lipase Geobacillus sp. Botanischer Garten, University of Hamburg, Germany [ 39 ] Abbreviation : NP not published …”

Section: Methodsmentioning

confidence: 99%

Identification and sequence analyses of novel lipase encoding novel thermophillic bacilli isolated from Armenian geothermal springs

et al. 2017

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BackgroundAmong the huge diversity of thermophilic bacteria mainly bacilli have been reported as active thermostable lipase producers. Geothermal springs serve as the main source for isolation of thermostable lipase producing bacilli. Thermostable lipolytic enzymes, functioning in the harsh conditions, have promising applications in processing of organic chemicals, detergent formulation, synthesis of biosurfactants, pharmaceutical processing etc.ResultsIn order to study the distribution of lipase-producing thermophilic bacilli and their specific lipase protein primary structures, three lipase producers from different genera were isolated from mesothermal (27.5–70 °C) springs distributed on the territory of Armenia and Nagorno Karabakh. Based on phenotypic characteristics and 16S rRNA gene sequencing the isolates were identified as Geobacillus sp., Bacillus licheniformis and Anoxibacillus flavithermus strains. The lipase genes of isolates were sequenced by using initially designed primer sets. Multiple alignments generated from primary structures of the lipase proteins and annotated lipase protein sequences, conserved regions analysis and amino acid composition have illustrated the similarity (98–99%) of the lipases with true lipases (family I) and GDSL esterase family (family II). A conserved sequence block that determines the thermostability has been identified in the multiple alignments of the lipase proteins.ConclusionsThe results are spreading light on the lipase producing bacilli distribution in geothermal springs in Armenia and Nagorno Karabakh. Newly isolated bacilli strains could be prospective source for thermostable lipases and their genes.

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“…To correctly identify proteins that change the expression level under the nonthermal action of THz radiation and to determine their functional roles in the G. icigianus genome, we utilized the results of our previously published genome-wide sequencing [ 73 , 74 ].…”

Section: Methodsmentioning

confidence: 99%

Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation

Bannikova

Khlebodarova

Vasilieva

et al. 2022

IJMS

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Studying the effects of terahertz (THz) radiation on the proteome of temperature-sensitive organisms is limited by a number of significant technical difficulties, one of which is maintaining an optimal temperature range to avoid thermal shock as much as possible. In the case of extremophilic species with an increased temperature tolerance, it is easier to isolate the effects of THz radiation directly. We studied the proteomic response to terahertz radiation of the thermophilic Geobacillus icigianus, persisting under wide temperature fluctuations with a 60 °C optimum. The experiments were performed with a terahertz free-electron laser (FEL) from the Siberian Center for Synchrotron and Terahertz Radiation, designed and employed by the Institute of Nuclear Physics of the SB of the RAS. A G. icigianus culture in LB medium was THz-irradiated for 15 min with 0.23 W/cm2 and 130 μm, using a specially designed cuvette. The life cycle of this bacterium proceeds under conditions of wide temperature and osmotic fluctuations, which makes its enzyme systems stress-resistant. The expression of several proteins was shown to change immediately after fifteen minutes of irradiation and after ten minutes of incubation at the end of exposure. The metabolic systems of electron transport, regulation of transcription and translation, cell growth and chemotaxis, synthesis of peptidoglycan, riboflavin, NADH, FAD and pyridoxal phosphate cofactors, Krebs cycle, ATP synthesis, chaperone and protease activity, and DNA repair, including methylated DNA, take part in the fast response to THz radiation. When the response developed after incubation, the systems of the cell’s anti-stress defense, chemotaxis, and, partially, cell growth were restored, but the respiration and energy metabolism, biosynthesis of riboflavin, cofactors, peptidoglycan, and translation system components remained affected and the amino acid metabolism system was involved.

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Draft Genome Sequence of Geobacillus icigianus Strain G1w1 ^T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation)

Cited by 10 publications

References 7 publications

A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

Identification and sequence analyses of novel lipase encoding novel thermophillic bacilli isolated from Armenian geothermal springs

Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation

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Draft Genome Sequence of Geobacillus icigianus Strain G1w1 T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation)

Cited by 10 publications

References 7 publications

A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus

Identification and sequence analyses of novel lipase encoding novel thermophillic bacilli isolated from Armenian geothermal springs

Specific Features of the Proteomic Response of Thermophilic Bacterium Geobacillus icigianus to Terahertz Irradiation

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Draft Genome Sequence of Geobacillus icigianus Strain G1w1 ^T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation)