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Title: The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor

Abstract

In this study we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.

Authors:
 [1];  [2];  [3];  [4]
  1. C5-6 Technologies LLC, Fitchburg, WI (United States); Univ. of Wisconsin, Madison, WI (United States)
  2. Univ. of Wisconsin, Madison, WI (United States); Lucigen Corp., Middleton, WI (United States)
  3. Univ. of Maryland, Baltimore, MD (United States)
  4. Univ. of Wisconsin, Madison, WI (United States); Varigen Biosciences Corp., Madison, WI (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Energy Efficiency and Renewable Energy (EERE)
OSTI Identifier:
1373560
Alternate Identifier(s):
OSTI ID: 1466828
Grant/Contract Number:  
FC02-07ER64494; AC05-76RL01830
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Dictyoglomus turgidum; thermophile; biomass degradation; phage; Dictyoglomi; DNA polymerase; glucanase; reverse gyrase

Citation Formats

Brumm, Phillip J., Gowda, Krishne, Robb, Frank T., and Mead, David A. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. United States: N. p., 2016. Web. doi:10.3389/fmicb.2016.01979.
Brumm, Phillip J., Gowda, Krishne, Robb, Frank T., & Mead, David A. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. United States. doi:10.3389/fmicb.2016.01979.
Brumm, Phillip J., Gowda, Krishne, Robb, Frank T., and Mead, David A. Tue . "The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor". United States. doi:10.3389/fmicb.2016.01979. https://www.osti.gov/servlets/purl/1373560.
@article{osti_1373560,
title = {The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor},
author = {Brumm, Phillip J. and Gowda, Krishne and Robb, Frank T. and Mead, David A.},
abstractNote = {In this study we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.},
doi = {10.3389/fmicb.2016.01979},
journal = {Frontiers in Microbiology},
number = ,
volume = 7,
place = {United States},
year = {Tue Dec 20 00:00:00 EST 2016},
month = {Tue Dec 20 00:00:00 EST 2016}
}

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Works referenced in this record:

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journal, November 2009

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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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