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BMC Syst Biol. 2015 Jun 26;9:30. doi: 10.1186/s12918-015-0159-x.

Genome-scale resources for Thermoanaerobacterium saccharolyticum.

Author information

1
Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. Devin.H.Currie.GR@dartmouth.edu.
2
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. raman.babu@gmail.com.
3
Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA. raman.babu@gmail.com.
4
Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843028, Richmond, Virginia, 23284, USA. chris.gowen@utoronto.ca.
5
Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada. chris.gowen@utoronto.ca.
6
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. tschaplinstj@ornl.gov.
7
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. landml@ornl.gov.
8
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. brownsd@ornl.gov.
9
Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. scovalla@mascoma.com.
10
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. klingemandm@ornl.gov.
11
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. yangz@ornl.gov.
12
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. englenl@ornl.gov.
13
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. Courtney.Johnson10@fsis.usda.gov.
14
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. rodriguezmjr@ornl.gov.
15
Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. joeshawiv@gmail.com.
16
Novogy Inc, Cambridge, MA, 02138, USA. joeshawiv@gmail.com.
17
Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. wkenealy@mascoma.com.
18
Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. lee.r.lynd@dartmouth.edu.
19
Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA. lee.r.lynd@dartmouth.edu.
20
Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843028, Richmond, Virginia, 23284, USA. ssfong@vcu.edu.
21
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. mielenzjr@ornl.gov.
22
BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. davisonbh@ornl.gov.
23
Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. dhogsett@opxbio.com.
24
Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. chrisherringfish@gmail.com.
25
Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA. chrisherringfish@gmail.com.

Abstract

BACKGROUND:

Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation.

RESULTS:

Here we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid. An active prophage was also detected, and the expression levels of CRISPR genes were observed to increase in association with those of the phage. Hemicellulose hydrolysate elicited a response of carbohydrate transport and catabolism genes, as well as poorly characterized genes suggesting a redox challenge. In some conditions, a time series of combined transcription and metabolite measurements were made to allow careful study of microbial physiology under process conditions. As a demonstration of the potential utility of the metabolic reconstruction, the OptKnock algorithm was used to predict a set of gene knockouts that maximize growth-coupled ethanol production. The predictions validated intuitive strain designs and matched previous experimental results.

CONCLUSION:

These data will be a useful asset for efforts to develop T. saccharolyticum for efficient industrial production of biofuels. The resources presented herein may also be useful on a comparative basis for development of other lignocellulose degrading microbes, such as Clostridium thermocellum.

PMID:
26111937
PMCID:
PMC4518999
DOI:
10.1186/s12918-015-0159-x
[Indexed for MEDLINE]
Free PMC Article

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