Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423

Hadrien Máté de Gérando, François Wasels, Angélique Bisson, Benjamin Clement, Frédérique Bidard, Etienne Jourdier, Ana María López-Contreras, Nicolas Lopes Ferreira*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Scopus)

Abstract

Background: There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isopropanol, Butanol and Ethanol (IBE) by anaerobic fermentation has already a long industrial history. Isopropanol has recently received a specific interest and the best studied natural isopropanol producer is C. beijerinckii DSM 6423 (NRRL B-593). This strain metabolizes sugars into a mix of IBE with only low concentrations of ethanol produced (< 1 g/L). However, despite its relative ancient discovery, few genomic details have been described for this strain. Research efforts including omics and genetic engineering approaches are therefore needed to enable the use of C. beijerinckii as a microbial cell factory for production of isopropanol. Results: The complete genome sequence and a first transcriptome analysis of C. beijerinckii DSM 6423 are described in this manuscript. The combination of MiSeq and de novo PacBio sequencing revealed a 6.38 Mbp chromosome containing 6254 genomic objects. Three Mobile Genetic Elements (MGE) were also detected: a linear double stranded DNA bacteriophage (ϕ6423) and two plasmids (pNF1 and pNF2) highlighting the genomic complexity of this strain. A first RNA-seq transcriptomic study was then performed on 3 independent glucose fermentations. Clustering analysis allowed us to detect some key gene clusters involved in the main life cycle steps (acidogenesis, solvantogenesis and sporulation) and differentially regulated among the fermentation. These putative clusters included some putative metabolic operons comparable to those found in other reference strains such as C. beijerinckii NCIMB 8052 or C. acetobutylicum ATCC 824. Interestingly, only one gene was encoding for an alcohol dehydrogenase converting acetone into isopropanol, suggesting a single genomic event occurred on this strain to produce isopropanol. Conclusions: We present the full genome sequence of Clostridium beijerinckii DSM 6423, providing a complete genetic background of this strain. This offer a great opportunity for the development of dedicated genetic tools currently lacking for this strain. Moreover, a first RNA-seq analysis allow us to better understand the global metabolism of this natural isopropanol producer, opening the door to future targeted engineering approaches.
Original languageEnglish
Article number242
JournalBMC Genomics
Volume19
DOIs
Publication statusPublished - 10 Apr 2018

Fingerprint

Clostridium beijerinckii
2-Propanol
Transcriptome
Genome
Butanols
Ethanol
Fermentation
Acetone
RNA
Interspersed Repetitive Sequences
Genetic Engineering
Alcohol Dehydrogenase
Gene Expression Profiling
Operon
Multigene Family
Life Cycle Stages
Bacteriophages
Cluster Analysis
Plasmids
Chromosomes

Keywords

  • Clostridium beijerinckii
  • Clustering
  • DSM6423
  • Genome
  • IBE fermentation
  • Isopropanol
  • RNA-seq transcriptome

Cite this

Máté de Gérando, H., Wasels, F., Bisson, A., Clement, B., Bidard, F., Jourdier, E., ... Lopes Ferreira, N. (2018). Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423. BMC Genomics, 19, [242]. https://doi.org/10.1186/s12864-018-4636-7
Máté de Gérando, Hadrien ; Wasels, François ; Bisson, Angélique ; Clement, Benjamin ; Bidard, Frédérique ; Jourdier, Etienne ; López-Contreras, Ana María ; Lopes Ferreira, Nicolas. / Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423. In: BMC Genomics. 2018 ; Vol. 19.
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Máté de Gérando, H, Wasels, F, Bisson, A, Clement, B, Bidard, F, Jourdier, E, López-Contreras, AM & Lopes Ferreira, N 2018, 'Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423', BMC Genomics, vol. 19, 242. https://doi.org/10.1186/s12864-018-4636-7

Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423. / Máté de Gérando, Hadrien; Wasels, François; Bisson, Angélique; Clement, Benjamin; Bidard, Frédérique; Jourdier, Etienne; López-Contreras, Ana María; Lopes Ferreira, Nicolas.

In: BMC Genomics, Vol. 19, 242, 10.04.2018.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423

AU - Máté de Gérando, Hadrien

AU - Wasels, François

AU - Bisson, Angélique

AU - Clement, Benjamin

AU - Bidard, Frédérique

AU - Jourdier, Etienne

AU - López-Contreras, Ana María

AU - Lopes Ferreira, Nicolas

PY - 2018/4/10

Y1 - 2018/4/10

N2 - Background: There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isopropanol, Butanol and Ethanol (IBE) by anaerobic fermentation has already a long industrial history. Isopropanol has recently received a specific interest and the best studied natural isopropanol producer is C. beijerinckii DSM 6423 (NRRL B-593). This strain metabolizes sugars into a mix of IBE with only low concentrations of ethanol produced (< 1 g/L). However, despite its relative ancient discovery, few genomic details have been described for this strain. Research efforts including omics and genetic engineering approaches are therefore needed to enable the use of C. beijerinckii as a microbial cell factory for production of isopropanol. Results: The complete genome sequence and a first transcriptome analysis of C. beijerinckii DSM 6423 are described in this manuscript. The combination of MiSeq and de novo PacBio sequencing revealed a 6.38 Mbp chromosome containing 6254 genomic objects. Three Mobile Genetic Elements (MGE) were also detected: a linear double stranded DNA bacteriophage (ϕ6423) and two plasmids (pNF1 and pNF2) highlighting the genomic complexity of this strain. A first RNA-seq transcriptomic study was then performed on 3 independent glucose fermentations. Clustering analysis allowed us to detect some key gene clusters involved in the main life cycle steps (acidogenesis, solvantogenesis and sporulation) and differentially regulated among the fermentation. These putative clusters included some putative metabolic operons comparable to those found in other reference strains such as C. beijerinckii NCIMB 8052 or C. acetobutylicum ATCC 824. Interestingly, only one gene was encoding for an alcohol dehydrogenase converting acetone into isopropanol, suggesting a single genomic event occurred on this strain to produce isopropanol. Conclusions: We present the full genome sequence of Clostridium beijerinckii DSM 6423, providing a complete genetic background of this strain. This offer a great opportunity for the development of dedicated genetic tools currently lacking for this strain. Moreover, a first RNA-seq analysis allow us to better understand the global metabolism of this natural isopropanol producer, opening the door to future targeted engineering approaches.

AB - Background: There is a worldwide interest for sustainable and environmentally-friendly ways to produce fuels and chemicals from renewable resources. Among them, the production of acetone, butanol and ethanol (ABE) or Isopropanol, Butanol and Ethanol (IBE) by anaerobic fermentation has already a long industrial history. Isopropanol has recently received a specific interest and the best studied natural isopropanol producer is C. beijerinckii DSM 6423 (NRRL B-593). This strain metabolizes sugars into a mix of IBE with only low concentrations of ethanol produced (< 1 g/L). However, despite its relative ancient discovery, few genomic details have been described for this strain. Research efforts including omics and genetic engineering approaches are therefore needed to enable the use of C. beijerinckii as a microbial cell factory for production of isopropanol. Results: The complete genome sequence and a first transcriptome analysis of C. beijerinckii DSM 6423 are described in this manuscript. The combination of MiSeq and de novo PacBio sequencing revealed a 6.38 Mbp chromosome containing 6254 genomic objects. Three Mobile Genetic Elements (MGE) were also detected: a linear double stranded DNA bacteriophage (ϕ6423) and two plasmids (pNF1 and pNF2) highlighting the genomic complexity of this strain. A first RNA-seq transcriptomic study was then performed on 3 independent glucose fermentations. Clustering analysis allowed us to detect some key gene clusters involved in the main life cycle steps (acidogenesis, solvantogenesis and sporulation) and differentially regulated among the fermentation. These putative clusters included some putative metabolic operons comparable to those found in other reference strains such as C. beijerinckii NCIMB 8052 or C. acetobutylicum ATCC 824. Interestingly, only one gene was encoding for an alcohol dehydrogenase converting acetone into isopropanol, suggesting a single genomic event occurred on this strain to produce isopropanol. Conclusions: We present the full genome sequence of Clostridium beijerinckii DSM 6423, providing a complete genetic background of this strain. This offer a great opportunity for the development of dedicated genetic tools currently lacking for this strain. Moreover, a first RNA-seq analysis allow us to better understand the global metabolism of this natural isopropanol producer, opening the door to future targeted engineering approaches.

KW - Clostridium beijerinckii

KW - Clustering

KW - DSM6423

KW - Genome

KW - IBE fermentation

KW - Isopropanol

KW - RNA-seq transcriptome

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Máté de Gérando H, Wasels F, Bisson A, Clement B, Bidard F, Jourdier E et al. Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423. BMC Genomics. 2018 Apr 10;19. 242. https://doi.org/10.1186/s12864-018-4636-7