Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies

Brumm, Phillip J.; De Maayer, Pieter; Mead, David A.; Cowan, Don A.

doi:10.3389/fmicb.2015.00430

Title: Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies

Journal Article · Tue May 12 00:00:00 EDT 2015 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2015.00430· OSTI ID:1628133

Brumm, Phillip J. ^[1]; De Maayer, Pieter ^[2]; Mead, David A. ^[3]; Cowan, Don A. ^[4]

C5-6 Technologies, Middleton, WI (United States); Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center
Univ. of Pretoria (South Africa). Centre for Microbial Ecology and Genomics, Genomics Research Inst. and Dept. of Microbiology and Plant Pathology
C5-6 Technologies, Middleton, WI (United States); Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center; Lucigen Corp., Middleton, WI (United States)
Univ. of Pretoria (South Africa). Centre for Microbial Ecology and Genomics, Genomics Research Inst.

In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.

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Research Organization:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FC02-07ER64494

OSTI ID:: 1628133

Journal Information:: Frontiers in Microbiology, Vol. 6; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 20 works

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Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment Caspers, M. P. M.; Boekhorst, J.; Abee, T. Genome Announcements, Vol. 1, Issue 1 https://doi.org/10.1128/genomea.00010-13	journal	January 2013
Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium Wiegand, S.; Rabausch, U.; Chow, J. Genome Announcements, Vol. 1, Issue 2 https://doi.org/10.1128/genomea.00092-13	journal	February 2013
Draft Genome Sequence of Lignocellulose-Degrading Thermophilic Bacterium Geobacillus sp. Strain WSUCF1 Bhalla, A.; Kainth, A. S.; Sani, R. K. Genome Announcements, Vol. 1, Issue 4 https://doi.org/10.1128/genomea.00595-13	journal	June 2013
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Complete Genome Sequence of Paenibacillus polymyxa CR1, a Plant Growth-Promoting Bacterium Isolated from the Corn Rhizosphere Exhibiting Potential for Biocontrol, Biomass Degradation, and Biofuel Production Eastman, A. W.; Weselowski, B.; Nathoo, N. Genome Announcements, Vol. 2, Issue 1 https://doi.org/10.1128/genomea.01218-13	journal	January 2014
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In silico characterization of the global Geobacillus and Parageobacillus secretome Lebre, Pedro H.; Aliyu, Habibu; De Maayer, Pieter Microbial Cell Factories, Vol. 17, Issue 1 https://doi.org/10.1186/s12934-018-1005-9	journal	October 2018
Engineering Geobacillus thermoglucosidasius for direct utilisation of holocellulose from wheat straw Bashir, Zeenat; Sheng, Lili; Anil, Annamma Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1540-6	journal	August 2019
Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost Brumm, Phillip J.; Land, Miriam L.; Mead, David A. Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0153-y	journal	April 2016
Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. Pogrebnyakov, Ivan; Jendresen, Christian Bille; Nielsen, Alex Toftgaard PLOS ONE, Vol. 12, Issue 2 https://doi.org/10.1371/journal.pone.0171313	journal	February 2017
Current Status of the Degradation of Aliphatic and Aromatic Petroleum Hydrocarbons by Thermophilic Microbes and Future Perspectives Nzila, Alexis International Journal of Environmental Research and Public Health, Vol. 15, Issue 12 https://doi.org/10.3390/ijerph15122782	journal	December 2018
Current Status of the Degradation of Aliphatic and Aromatic Petroleum Hydrocarbons by Thermophilic Microbes and Future Perspectives Nzila, Alexis Preprints.org https://doi.org/10.20944/preprints201811.0166.v1	posted_content	November 2018
In silico characterization of the global Geobacillus and Parageobacillus secretome Lebre, Pedro H.; Aliyu, Habibu; De Maayer, Pieter Karlsruhe https://doi.org/10.5445/ir/1000086679	text	January 2018
Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications Daas, Martinus J. A.; Vriesendorp, Bastienne; van de Weijer, Antonius H. P. Current Microbiology, Vol. 75, Issue 1 https://doi.org/10.1007/s00284-017-1349-0	journal	September 2017
Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity Warda, Alicja K.; Siezen, Roland J.; Boekhorst, Jos PLOS ONE, Vol. 11, Issue 6 https://doi.org/10.1371/journal.pone.0156796	journal	June 2016
The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor Brumm, Phillip J.; Gowda, Krishne; Robb, Frank T. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01979	journal	December 2016
Not All That Glitters Is Gold: The Paradox of CO-dependent Hydrogenogenesis in Parageobacillus thermoglucosidasius Aliyu, Habibu; Maayer, Pieter De; Neumann, Anke Frontiers Media https://doi.org/10.5445/ir/1000141719	text	January 2021

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