Genomics and transcriptomics of the hydrogen producing extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus

M.R.A. Verhaart

Research output: Thesisinternal PhD, WU

Abstract

As fossil fuels are depleting, there is a clear need for alternative sustainable fuel sources. One of the interesting alternatives is hydrogen, which can be produced from biomass by bacteria and archaea. To make the application feasible, organisms are needed which have high hydrogen productivities as well as the capacity to handle a wide variety of substrates. Caldicellulosiruptor saccharolyticus has these abilities and this was the reason to select this organism to study hydrogen production at elevated temperatures. The aim of this study was to clarify the pathways involved in hydrogen production as well as studying the regulation of the hydrogen production on different levels. Especially the regulation of the disposal of reducing equivalents (NADH, reduced ferredoxin, NADPH), was an important aspect. The genome sequence was annotated and compared with transcriptome data. This revealed the presence of the Emden-Meyerhof pathway, and the non-oxidative part of the pentose phosphate pathway for the breakdown of glucose and xylose. The genomic data explained the high hydrolyzing capacity of this organism by the presence of a large number of carbohydrate active enzymes as well as a large variety of ABC transporters. With transcriptomics the substrate specificity of several of these transporters was predicted. The absence from the genome of some components involved in classical carbon catabolite repression explained the capacity of C. saccharolyticus to grow simultaneously on C5 and C6 sugars. When C. saccharolyticus was cultured on rhamnose, 1.2 propanediol production was observed. This observation could be explained by the presence of a rhamnose pathway, which could be unraveled using the genome sequence as well as the transcriptome data. As hydrogen pressure seems to be an important factor for hydrogen production by C. saccharolyticus, the effect of a high P(H2) was studied in a continuous culture. This showed a clear shift to lactate and ethanol production at higher P(H2). By comparing the transcriptome for the high and low P(H2) situation, this shift could be explained by the upregulation of the genes encoding an alcohol and a lactate dehydrogenase. This suggested that the electrons of NADH are most likely disposed of via lactate production, while the electrons of reduced ferredoxin might be shuttled via an oxidoreductase to produce ethanol.Overall this study revealed several new insights in the regulation of hydrogen production by thermophilic anaerobic organisms.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • Stams, Fons, Promotor
  • Kengen, Servé, Co-promotor
Award date19 Nov 2010
Place of Publication[S.l.
Publisher
Print ISBNs9789085857969
Publication statusPublished - 2010

Fingerprint

Caldicellulosiruptor saccharolyticus
thermophilic bacteria
hydrogen production
transcriptomics
hydrogen
genomics
transcriptome
ferredoxins
NAD (coenzyme)
rhamnose
organisms
lactates
genome
electrons
propanediols
ABC transporters
pentoses
oxidoreductases
fossil fuels
ethanol production

Keywords

  • thermophilic bacteria
  • hydrogen
  • bioenergy
  • genomics
  • transcriptomics

Cite this

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title = "Genomics and transcriptomics of the hydrogen producing extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus",
abstract = "As fossil fuels are depleting, there is a clear need for alternative sustainable fuel sources. One of the interesting alternatives is hydrogen, which can be produced from biomass by bacteria and archaea. To make the application feasible, organisms are needed which have high hydrogen productivities as well as the capacity to handle a wide variety of substrates. Caldicellulosiruptor saccharolyticus has these abilities and this was the reason to select this organism to study hydrogen production at elevated temperatures. The aim of this study was to clarify the pathways involved in hydrogen production as well as studying the regulation of the hydrogen production on different levels. Especially the regulation of the disposal of reducing equivalents (NADH, reduced ferredoxin, NADPH), was an important aspect. The genome sequence was annotated and compared with transcriptome data. This revealed the presence of the Emden-Meyerhof pathway, and the non-oxidative part of the pentose phosphate pathway for the breakdown of glucose and xylose. The genomic data explained the high hydrolyzing capacity of this organism by the presence of a large number of carbohydrate active enzymes as well as a large variety of ABC transporters. With transcriptomics the substrate specificity of several of these transporters was predicted. The absence from the genome of some components involved in classical carbon catabolite repression explained the capacity of C. saccharolyticus to grow simultaneously on C5 and C6 sugars. When C. saccharolyticus was cultured on rhamnose, 1.2 propanediol production was observed. This observation could be explained by the presence of a rhamnose pathway, which could be unraveled using the genome sequence as well as the transcriptome data. As hydrogen pressure seems to be an important factor for hydrogen production by C. saccharolyticus, the effect of a high P(H2) was studied in a continuous culture. This showed a clear shift to lactate and ethanol production at higher P(H2). By comparing the transcriptome for the high and low P(H2) situation, this shift could be explained by the upregulation of the genes encoding an alcohol and a lactate dehydrogenase. This suggested that the electrons of NADH are most likely disposed of via lactate production, while the electrons of reduced ferredoxin might be shuttled via an oxidoreductase to produce ethanol.Overall this study revealed several new insights in the regulation of hydrogen production by thermophilic anaerobic organisms.",
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Genomics and transcriptomics of the hydrogen producing extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. / Verhaart, M.R.A.

[S.l. : S.n., 2010. 178 p.

Research output: Thesisinternal PhD, WU

TY - THES

T1 - Genomics and transcriptomics of the hydrogen producing extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus

AU - Verhaart, M.R.A.

N1 - WU thesis 4937

PY - 2010

Y1 - 2010

N2 - As fossil fuels are depleting, there is a clear need for alternative sustainable fuel sources. One of the interesting alternatives is hydrogen, which can be produced from biomass by bacteria and archaea. To make the application feasible, organisms are needed which have high hydrogen productivities as well as the capacity to handle a wide variety of substrates. Caldicellulosiruptor saccharolyticus has these abilities and this was the reason to select this organism to study hydrogen production at elevated temperatures. The aim of this study was to clarify the pathways involved in hydrogen production as well as studying the regulation of the hydrogen production on different levels. Especially the regulation of the disposal of reducing equivalents (NADH, reduced ferredoxin, NADPH), was an important aspect. The genome sequence was annotated and compared with transcriptome data. This revealed the presence of the Emden-Meyerhof pathway, and the non-oxidative part of the pentose phosphate pathway for the breakdown of glucose and xylose. The genomic data explained the high hydrolyzing capacity of this organism by the presence of a large number of carbohydrate active enzymes as well as a large variety of ABC transporters. With transcriptomics the substrate specificity of several of these transporters was predicted. The absence from the genome of some components involved in classical carbon catabolite repression explained the capacity of C. saccharolyticus to grow simultaneously on C5 and C6 sugars. When C. saccharolyticus was cultured on rhamnose, 1.2 propanediol production was observed. This observation could be explained by the presence of a rhamnose pathway, which could be unraveled using the genome sequence as well as the transcriptome data. As hydrogen pressure seems to be an important factor for hydrogen production by C. saccharolyticus, the effect of a high P(H2) was studied in a continuous culture. This showed a clear shift to lactate and ethanol production at higher P(H2). By comparing the transcriptome for the high and low P(H2) situation, this shift could be explained by the upregulation of the genes encoding an alcohol and a lactate dehydrogenase. This suggested that the electrons of NADH are most likely disposed of via lactate production, while the electrons of reduced ferredoxin might be shuttled via an oxidoreductase to produce ethanol.Overall this study revealed several new insights in the regulation of hydrogen production by thermophilic anaerobic organisms.

AB - As fossil fuels are depleting, there is a clear need for alternative sustainable fuel sources. One of the interesting alternatives is hydrogen, which can be produced from biomass by bacteria and archaea. To make the application feasible, organisms are needed which have high hydrogen productivities as well as the capacity to handle a wide variety of substrates. Caldicellulosiruptor saccharolyticus has these abilities and this was the reason to select this organism to study hydrogen production at elevated temperatures. The aim of this study was to clarify the pathways involved in hydrogen production as well as studying the regulation of the hydrogen production on different levels. Especially the regulation of the disposal of reducing equivalents (NADH, reduced ferredoxin, NADPH), was an important aspect. The genome sequence was annotated and compared with transcriptome data. This revealed the presence of the Emden-Meyerhof pathway, and the non-oxidative part of the pentose phosphate pathway for the breakdown of glucose and xylose. The genomic data explained the high hydrolyzing capacity of this organism by the presence of a large number of carbohydrate active enzymes as well as a large variety of ABC transporters. With transcriptomics the substrate specificity of several of these transporters was predicted. The absence from the genome of some components involved in classical carbon catabolite repression explained the capacity of C. saccharolyticus to grow simultaneously on C5 and C6 sugars. When C. saccharolyticus was cultured on rhamnose, 1.2 propanediol production was observed. This observation could be explained by the presence of a rhamnose pathway, which could be unraveled using the genome sequence as well as the transcriptome data. As hydrogen pressure seems to be an important factor for hydrogen production by C. saccharolyticus, the effect of a high P(H2) was studied in a continuous culture. This showed a clear shift to lactate and ethanol production at higher P(H2). By comparing the transcriptome for the high and low P(H2) situation, this shift could be explained by the upregulation of the genes encoding an alcohol and a lactate dehydrogenase. This suggested that the electrons of NADH are most likely disposed of via lactate production, while the electrons of reduced ferredoxin might be shuttled via an oxidoreductase to produce ethanol.Overall this study revealed several new insights in the regulation of hydrogen production by thermophilic anaerobic organisms.

KW - thermofiele bacteriën

KW - waterstof

KW - bio-energie

KW - genexpressieanalyse

KW - transcriptomics

KW - thermophilic bacteria

KW - hydrogen

KW - bioenergy

KW - genomics

KW - transcriptomics

M3 - internal PhD, WU

SN - 9789085857969

PB - S.n.

CY - [S.l.

ER -