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Genome-scale resources for Thermoanaerobacterium saccharolyticum.

Currie DH, Raman B, Gowen CM, Tschaplinski TJ, Land ML, Brown SD, Covalla SF, Klingeman DM, Yang ZK, Engle NL, Johnson CM, Rodriguez M, Shaw AJ, Kenealy WR, Lynd LR, Fong SS, Mielenz JR, Davison BH, Hogsett DA, Herring CD - BMC Syst Biol (2015)

Bottom Line: The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid.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.

View Article: PubMed Central - PubMed

Affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. Devin.H.Currie.GR@dartmouth.edu.

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.

No MeSH data available.


Related in: MedlinePlus

A comparison between the two versions of the 16 s mRNA found inT. saccharolyticum.A) an alignment and consensus sequence for a heterogeneous segment of the five 16S ribosomal components found in T. saccharolyticum.B) Mfold prediction of the structure of the shorter 16S mRNA [66]. C) Mfold prediction of the structure of the longer 16S mRNA.
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Fig1: A comparison between the two versions of the 16 s mRNA found inT. saccharolyticum.A) an alignment and consensus sequence for a heterogeneous segment of the five 16S ribosomal components found in T. saccharolyticum.B) Mfold prediction of the structure of the shorter 16S mRNA [66]. C) Mfold prediction of the structure of the longer 16S mRNA.

Mentions: The genome contains 5 ribosomal regions, all oriented in the same direction. Remarkably, the ribosomal sequences are not uniform, but rather of two types showing only 95% identity in the “universal” region of the 16 s subunit (Figure 1). Similar, but less pronounced heterogeneity of ribosomal sequences has been noted in other firmicutes [34], but has yet to be explained.Figure 1


Genome-scale resources for Thermoanaerobacterium saccharolyticum.

Currie DH, Raman B, Gowen CM, Tschaplinski TJ, Land ML, Brown SD, Covalla SF, Klingeman DM, Yang ZK, Engle NL, Johnson CM, Rodriguez M, Shaw AJ, Kenealy WR, Lynd LR, Fong SS, Mielenz JR, Davison BH, Hogsett DA, Herring CD - BMC Syst Biol (2015)

A comparison between the two versions of the 16 s mRNA found inT. saccharolyticum.A) an alignment and consensus sequence for a heterogeneous segment of the five 16S ribosomal components found in T. saccharolyticum.B) Mfold prediction of the structure of the shorter 16S mRNA [66]. C) Mfold prediction of the structure of the longer 16S mRNA.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4518999&req=5

Fig1: A comparison between the two versions of the 16 s mRNA found inT. saccharolyticum.A) an alignment and consensus sequence for a heterogeneous segment of the five 16S ribosomal components found in T. saccharolyticum.B) Mfold prediction of the structure of the shorter 16S mRNA [66]. C) Mfold prediction of the structure of the longer 16S mRNA.
Mentions: The genome contains 5 ribosomal regions, all oriented in the same direction. Remarkably, the ribosomal sequences are not uniform, but rather of two types showing only 95% identity in the “universal” region of the 16 s subunit (Figure 1). Similar, but less pronounced heterogeneity of ribosomal sequences has been noted in other firmicutes [34], but has yet to be explained.Figure 1

Bottom Line: The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid.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.

View Article: PubMed Central - PubMed

Affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. Devin.H.Currie.GR@dartmouth.edu.

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.

No MeSH data available.


Related in: MedlinePlus