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Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant.

ABSTRACT: We report on the nearly complete genome sequence of Clostridium beijerinckii strain Br21, formerly isolated from a sugarcarne vinasse wastewater treatment plant. The resulting genome is ca. 5.9 Mbp in length and resembles the size of previously published C. beijerinckii genomes. We annotated the genome sequence and predicted a total of 5323 genes. Strain Br21 has a genetic toolkit that allows it to exploit diverse sugars that are often found after lignocellulosic biomass pretreatment to yield products of commercial interest. Besides the whole set of genes encoding for enzymes underlying hydrogen production, the genome of the new strain includes genes that enable carbon sources conversion into butanol, ethanol, acetic acid, butyric acid, and the chemical block 1,3-propanediol, which is used to obtain polymers. Moreover, the genome of strain Br21 has a higher number of ORFs with predicted beta-glucosidase activity as compared to other C. beijerinckii strains described in the KEGG database. These characteristics make C. beijerinckii strain Br21 a remarkable candidate for direct use in biotechnological processes and attest that it is a potential biocatalyst supplier.

SUBMITTER: Fonseca BC

PROVIDER: S-EPMC6428130 | biostudies-literature | 2019 Jan-Mar

REPOSITORIES: biostudies-literature

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Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant.

Fonseca Bruna Constante BC Riaño-Pachón Diego Mauricio DM Guazzaroni María-Eugenia ME Reginatto Valeria V

Genetics and molecular biology 20190131 1

We report on the nearly complete genome sequence of Clostridium beijerinckii strain Br21, formerly isolated from a sugarcarne vinasse wastewater treatment plant. The resulting genome is ca. 5.9 Mbp in length and resembles the size of previously published C. beijerinckii genomes. We annotated the genome sequence and predicted a total of 5323 genes. Strain Br21 has a genetic toolkit that allows it to exploit diverse sugars that are often found after lignocellulosic biomass pretreatment to yield pr ...[more]

PMID: 30730526

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Project description:BackgroundSolventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications.ResultsWe present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the hydrogenase reaction was found to have a strong effect on butanol formation--as experimentally observed.ConclusionsMicrobial production of butanol by C. beijerinckii offers a promising, sustainable, method for generation of this important chemical and potential biofuel. iCM925 is a predictive model that can accurately reproduce physiological behavior and provide insight into the underlying mechanisms of microbial butanol production. As such, the model will be instrumental in efforts to better understand, and metabolically engineer, this microorganism for improved butanol production.

Project description:Macroalgae (or seaweeds) are considered potential biomass feedstocks for the production of renewable fuels and chemicals. Their sugar composition is different from that of lignocellulosic biomasses, and in green species, including Ulva lactuca, the major sugars are l-rhamnose and d-glucose. C. beijerinckii DSM 6423 utilized these sugars in a U. lactuca hydrolysate to produce acetic acid, butyric acid, isopropanol, butanol, and ethanol (IBE), and 1,2-propanediol. d-Glucose was almost completely consumed in diluted hydrolysates, while l-rhamnose or d-xylose was only partially utilized. In this study, the metabolism of l-rhamnose by C. beijerinckii DSM 6423 was investigated to improve its utilization from natural resources. Fermentations on d-glucose, l-rhamnose, and a mixture of d-glucose and l-rhamnose were performed. On l-rhamnose, the cultures showed low growth and sugar consumption and produced 1,2-propanediol, propionic acid, and n-propanol in addition to acetic and butyric acids, whereas on d-glucose, IBE was the major product. On a d-glucose-l-rhamnose mixture, both sugars were converted simultaneously and l-rhamnose consumption was higher, leading to high levels of 1,2-propanediol (78.4 mM), in addition to 59.4 mM butanol and 31.9 mM isopropanol. Genome and transcriptomics analysis of d-glucose- and l-rhamnose-grown cells revealed the presence and transcription of genes involved in l-rhamnose utilization and in bacterial microcompartment (BMC) formation. These data provide useful insights into the metabolic pathways involved in l-rhamnose utilization and the effects on the general metabolism (glycolysis, early sporulation, and stress response) induced by growth on l-rhamnose.IMPORTANCE A prerequisite for a successful biobased economy is the efficient conversion of biomass resources into useful products, such as biofuels and bulk and specialty chemicals. In contrast to other industrial microorganisms, natural solvent-producing clostridia utilize a wide range of sugars, including C5, C6, and deoxy-sugars, for production of long-chain alcohols (butanol and 2,3-butanediol), isopropanol, acetone, n-propanol, and organic acids. Butanol production by clostridia from first-generation sugars is already a commercial process, but for the expansion and diversification of the acetone, butanol, and ethanol (ABE)/IBE process to other substrates, more knowledge is needed on the regulation and physiology of fermentation of sugar mixtures. Green macroalgae, produced in aquaculture systems, harvested from the sea or from tides, can be processed into hydrolysates containing mixtures of d-glucose and l-rhamnose, which can be fermented. The knowledge generated in this study will contribute to the development of more efficient processes for macroalga fermentation and of mixed-sugar fermentation in general.

Dataset Information

Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant.

Publications

Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant.

Similar Datasets

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