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Branska B, Koppova K, Husakova M, Patakova P. Application of fed-batch strategy to fully eliminate the negative effect of lignocellulose-derived inhibitors in ABE fermentation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:87. [PMID: 38915101 PMCID: PMC11197323 DOI: 10.1186/s13068-024-02520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/16/2024] [Indexed: 06/26/2024]
Abstract
BACKGROUND Inhibitors that are released from lignocellulose biomass during its treatment represent one of the major bottlenecks hindering its massive utilization in the biotechnological production of chemicals. This study demonstrates that negative effect of inhibitors can be mitigated by proper feeding strategy. Both, crude undetoxified lignocellulose hydrolysate and complex medium supplemented with corresponding inhibitors were tested in acetone-butanol-ethanol (ABE) fermentation using Clostridium beijerinckii NRRL B-598 as the producer strain. RESULTS First, it was found that the sensitivity of C. beijerinckii to inhibitors varied with different growth stages, being the most significant during the early acidogenic phase and less pronounced during late acidogenesis and early solventogenesis. Thus, a fed-batch regime with three feeding schemes was tested for toxic hydrolysate (no growth in batch mode was observed). The best results were obtained when the feeding of an otherwise toxic hydrolysate was initiated close to the metabolic switch, resulting in stable and high ABE production. Complete utilization of glucose, and up to 88% of xylose, were obtained. The most abundant inhibitors present in the alkaline wheat straw hydrolysate were ferulic and coumaric acids; both phenolic acids were efficiently detoxified by the intrinsic metabolic activity of clostridia during the early stages of cultivation as well as during the feeding period, thus preventing their accumulation. Finally, the best feeding strategy was verified using a TYA culture medium supplemented with both inhibitors, resulting in 500% increase in butanol titer over control batch cultivation in which inhibitors were added prior to inoculation. CONCLUSION Properly timed sequential feeding effectively prevented acid-crash and enabled utilization of otherwise toxic substrate. This study unequivocally demonstrates that an appropriate biotechnological process control strategy can fully eliminate the negative effects of lignocellulose-derived inhibitors.
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Affiliation(s)
- Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 16628, Prague, Czech Republic.
| | - Kamila Koppova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 16628, Prague, Czech Republic
| | - Marketa Husakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 16628, Prague, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technická 5, 16628, Prague, Czech Republic
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Jones DT, Schulz F, Roux S, Brown SD. Solvent-Producing Clostridia Revisited. Microorganisms 2023; 11:2253. [PMID: 37764097 PMCID: PMC10538166 DOI: 10.3390/microorganisms11092253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/09/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
The review provides an overview of the current status of the solvent-producing clostridia. The origin and development of industrial clostridial species, as well as the history of the industrial Acetone Butanol Ethanol fermentation process, is reexamined, and the recent resurgence of interest in the production of biobutanol is reviewed. Over 300 fully sequenced genomes for solvent-producing and closely related clostridial species are currently available in public databases. These include 270 genomes sourced from the David Jones culture collection. These genomes were allocated arbitrary DJ codes, and a conversion table to identify the species and strains has now been provided. The expanded genomic database facilitated new comparative genomic and phylogenetic analysis. A synopsis of the common features, molecular taxonomy, and phylogeny of solvent-producing clostridia and the application of comparative phylogenomics are evaluated. A survey and analysis of resident prophages in solvent-producing clostridia are discussed, and the discovery, occurrence, and role of novel R-type tailocins are reported. Prophage genomes with R-type tailocin-like features were detected in all 12 species investigated. The widespread occurrence of tailocins in Gram-negative species is well documented; this survey has indicated that they may also be widespread in clostridia.
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Affiliation(s)
- David T. Jones
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand
| | - Frederik Schulz
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA; (F.S.); (S.R.)
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA; (F.S.); (S.R.)
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Patakova P, Branska B, Vasylkivska M, Jureckova K, Musilova J, Provaznik I, Sedlar K. Transcriptomic studies of solventogenic clostridia, Clostridium acetobutylicum and Clostridium beijerinckii. Biotechnol Adv 2021; 58:107889. [PMID: 34929313 DOI: 10.1016/j.biotechadv.2021.107889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022]
Abstract
Solventogenic clostridia are not a strictly defined group within the genus Clostridium but its representatives share some common features, i.e. they are anaerobic, non-pathogenic, non-toxinogenic and endospore forming bacteria. Their main metabolite is typically 1-butanol but depending on species and culture conditions, they can form other metabolites such as acetone, isopropanol, ethanol, butyric, lactic and acetic acids, and hydrogen. Although these organisms were previously used for the industrial production of solvents, they later fell into disuse, being replaced by more efficient chemical production. A return to a more biological production of solvents therefore requires a thorough understanding of clostridial metabolism. Transcriptome analysis, which reflects the involvement of individual genes in all cellular processes within a population, at any given (sampling) moment, is a valuable tool for gaining a deeper insight into clostridial life. In this review, we describe techniques to study transcription, summarize the evolution of these techniques and compare methods for data processing and visualization of solventogenic clostridia, particularly the species Clostridium acetobutylicum and Clostridium beijerinckii. Individual approaches for evaluating transcriptomic data are compared and their contributions to advancements in the field are assessed. Moreover, utilization of transcriptomic data for reconstruction of computational clostridial metabolic models is considered and particular models are described. Transcriptional changes in glucose transport, central carbon metabolism, the sporulation cycle, butanol and butyrate stress responses, the influence of lignocellulose-derived inhibitors on growth and solvent production, and other respective topics, are addressed and common trends are highlighted.
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Affiliation(s)
- Petra Patakova
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic.
| | - Barbora Branska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | - Maryna Vasylkivska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | | | - Jana Musilova
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Ivo Provaznik
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Karel Sedlar
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
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Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791T. Processes (Basel) 2021. [DOI: 10.3390/pr9071196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791T, composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.
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5
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Jureckova K, Raschmanova H, Kolek J, Vasylkivska M, Branska B, Patakova P, Provaznik I, Sedlar K. Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data. Front Microbiol 2021; 12:640054. [PMID: 33815328 PMCID: PMC8012504 DOI: 10.3389/fmicb.2021.640054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/17/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology (GO) enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of C. beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however, their validation is required.
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Affiliation(s)
- Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Hana Raschmanova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
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Patakova P, Kolek J, Jureckova K, Branska B, Sedlar K, Vasylkivska M, Provaznik I. Deeper below the surface-transcriptional changes in selected genes of Clostridium beijerinckii in response to butanol shock. Microbiologyopen 2020; 10:e1146. [PMID: 33319506 PMCID: PMC7884928 DOI: 10.1002/mbo3.1146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023] Open
Abstract
The main bottleneck in the return of industrial butanol production from renewable feedstock through acetone–butanol–ethanol (ABE) fermentation by clostridia, such as Clostridium beijerinckii, is the low final butanol concentration. The problem is caused by the high toxicity of butanol to the production cells, and therefore, understanding the mechanisms by which clostridia react to butanol shock is of key importance. Detailed analyses of transcriptome data that were obtained after butanol shock and their comparison with data from standard ABE fermentation have resulted in new findings, while confirmed expected population responses. Although butanol shock resulted in upregulation of heat shock protein genes, their regulation is different than was assumed based on standard ABE fermentation transcriptome data. While glucose uptake, glycolysis, and acidogenesis genes were downregulated after butanol shock, solventogenesis genes were upregulated. Cyclopropanation of fatty acids and formation of plasmalogens seem to be significant processes involved in cell membrane stabilization in the presence of butanol. Surprisingly, one of the three identified Agr quorum‐sensing system genes was upregulated. Upregulation of several putative butanol efflux pumps was described after butanol addition and a large putative polyketide gene cluster was found, the transcription of which seemed to depend on the concentration of butanol.
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Affiliation(s)
- Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Katerina Jureckova
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
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7
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Vasylkivska M, Branska B, Sedlar K, Jureckova K, Provaznik I, Patakova P. Phenotypic and Genomic Analysis of Clostridium beijerinckii NRRL B-598 Mutants With Increased Butanol Tolerance. Front Bioeng Biotechnol 2020; 8:598392. [PMID: 33224939 PMCID: PMC7674653 DOI: 10.3389/fbioe.2020.598392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
N-Butanol, a valuable solvent and potential fuel extender, can be produced via acetone-butanol-ethanol (ABE) fermentation. One of the main drawbacks of ABE fermentation is the high toxicity of butanol to producing cells, leading to cell membrane disruption, low culture viability and, consequently, low produced concentrations of butanol. The goal of this study was to obtain mutant strains of Clostridium beijerinckii NRRL B-598 with improved butanol tolerance using random chemical mutagenesis, describe changes in their phenotypes compared to the wild-type strain and reveal changes in the genome that explain improved tolerance or other phenotypic changes. Nine mutant strains with stable improved features were obtained by three different approaches and, for two of them, ethidium bromide (EB), a known substrate of efflux pumps, was used for either selection or as a mutagenic agent. It is the first utilization of this approach for the development of butanol-tolerant mutants of solventogenic clostridia, for which generally there is a lack of knowledge about butanol efflux or efflux mechanisms and their regulation. Mutant strains exhibited increase in butanol tolerance from 36% up to 127% and the greatest improvement was achieved for the strains for which EB was used as a mutagenic agent. Additionally, increased tolerance to other substrates of efflux pumps, EB and ethanol, was observed in all mutants and higher antibiotic tolerance in some of the strains. The complete genomes of mutant strains were sequenced and revealed that improved butanol tolerance can be attributed to mutations in genes encoding typical stress responses (chemotaxis, autolysis or changes in cell membrane structure), but, also, to mutations in genes X276_07980 and X276_24400, encoding efflux pump regulators. The latter observation confirms the importance of efflux in butanol stress response of the strain and offers new targets for rational strain engineering.
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Affiliation(s)
- Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czechia
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czechia
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czechia
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8
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Sedlar K, Vasylkivska M, Musilova J, Branska B, Provaznik I, Patakova P. Phenotypic and genomic analysis of isopropanol and 1,3-propanediol producer Clostridium diolis DSM 15410. Genomics 2020; 113:1109-1119. [PMID: 33166602 DOI: 10.1016/j.ygeno.2020.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022]
Abstract
Clostridium diolis DSM 15410 is a type strain of solventogenic clostridium capable of conducting isopropanol-butanol-ethanol fermentation. By studying its growth on different carbohydrates, we verified its ability to utilize glycerol and produce 1,3-propanediol and discovered its ability to produced isopropanol. Complete genome sequencing showed that its genome is a single circular chromosome and belongs to the cluster I (sensu scricto) of the genus Clostridium. By cultivation analysis we highlighted its specific behavior in comparison to two selected closely related strains. Despite the fact that several CRISPR loci were found, 16 putative prophages showed the ability to receive foreign DNA. Thus, the strain has the necessary features for future engineering of its 1,3-propanediol biosynthetic pathway and for the possible industrial utilization in the production of biofuels.
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Affiliation(s)
- Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, Brno, Czech Republic.
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Jana Musilova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, Brno, Czech Republic
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Technicka 12, Brno, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
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Vasylkivska M, Jureckova K, Branska B, Sedlar K, Kolek J, Provaznik I, Patakova P. Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598. PLoS One 2019; 14:e0224560. [PMID: 31697692 PMCID: PMC6837493 DOI: 10.1371/journal.pone.0224560] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/16/2019] [Indexed: 11/19/2022] Open
Abstract
In-depth knowledge of cell metabolism and nutrient uptake mechanisms can lead to the development of a tool for improving acetone-butanol-ethanol (ABE) fermentation performance and help to overcome bottlenecks in the process, such as the high cost of substrates and low production rates. Over 300 genes potentially encoding transport of amino acids, metal ions, vitamins and carbohydrates were identified in the genome of the butanol-producing strain Clostridium beijerinckii NRRL B-598, based on similarity searches in protein function databases. Transcriptomic data of the genes were obtained during ABE fermentation by RNA-Seq experiments and covered acidogenesis, solventogenesis and sporulation. The physiological roles of the selected 81 actively expressed transport genes were established on the basis of their expression profiles at particular stages of ABE fermentation. This article describes how genes encoding the uptake of glucose, iron, riboflavin, glutamine, methionine and other nutrients take part in growth, production and stress responses of C. beijerinckii NRRL B-598. These data increase our knowledge of transport mechanisms in solventogenic Clostridium and may be used in the selection of individual genes for further research.
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Affiliation(s)
- Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
- * E-mail:
| | - Katerina Jureckova
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czech Republic
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10
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Russmayer H, Egermeier M, Kalemasi D, Sauer M. Spotlight on biodiversity of microbial cell factories for glycerol conversion. Biotechnol Adv 2019; 37:107395. [DOI: 10.1016/j.biotechadv.2019.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/28/2019] [Accepted: 05/02/2019] [Indexed: 12/28/2022]
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Sedlar K, Kolek J, Gruber M, Jureckova K, Branska B, Csaba G, Vasylkivska M, Zimmer R, Patakova P, Provaznik I. A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:243. [PMID: 31636702 PMCID: PMC6790243 DOI: 10.1186/s13068-019-1584-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND One of the main obstacles preventing solventogenic clostridia from achieving higher yields in biofuel production is the toxicity of produced solvents. Unfortunately, regulatory mechanisms responsible for the shock response are poorly described on the transcriptomic level. Although the strain Clostridium beijerinckii NRRL B-598, a promising butanol producer, has been studied under different conditions in the past, its transcriptional response to a shock caused by butanol in the cultivation medium remains unknown. RESULTS In this paper, we present a transcriptional response of the strain during a butanol challenge, caused by the addition of butanol to the cultivation medium at the very end of the acidogenic phase, using RNA-Seq. We resequenced and reassembled the genome sequence of the strain and prepared novel genome and gene ontology annotation to provide the most accurate results. When compared to samples under standard cultivation conditions, samples gathered during butanol shock represented a well-distinguished group. Using reference samples gathered directly before the addition of butanol, we identified genes that were differentially expressed in butanol challenge samples. We determined clusters of 293 down-regulated and 301 up-regulated genes whose expression was affected by the cultivation conditions. Enriched term "RNA binding" among down-regulated genes corresponded to the downturn of translation and the cluster contained a group of small acid-soluble spore proteins. This explained phenotype of the culture that had not sporulated. On the other hand, up-regulated genes were characterized by the term "protein binding" which corresponded to activation of heat-shock proteins that were identified within this cluster. CONCLUSIONS We provided an overall transcriptional response of the strain C. beijerinckii NRRL B-598 to butanol shock, supplemented by auxiliary technologies, including high-pressure liquid chromatography and flow cytometry, to capture the corresponding phenotypic response. We identified genes whose regulation was affected by the addition of butanol to the cultivation medium and inferred related molecular functions that were significantly influenced. Additionally, using high-quality genome assembly and custom-made gene ontology annotation, we demonstrated that this settled terminology, widely used for the analysis of model organisms, could also be applied to non-model organisms and for research in the field of biofuels.
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Affiliation(s)
- Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Markus Gruber
- Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstraße 17, 80333 Munich, Germany
| | - Katerina Jureckova
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Gergely Csaba
- Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstraße 17, 80333 Munich, Germany
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Ralf Zimmer
- Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstraße 17, 80333 Munich, Germany
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czech Republic
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12
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Deshpande SV, Reed TM, Sullivan RF, Kerkhof LJ, Beigel KM, Wade MM. Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS). Genes (Basel) 2019; 10:genes10080578. [PMID: 31366182 PMCID: PMC6723491 DOI: 10.3390/genes10080578] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies’ (ONT) cloud-based What’s In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT’s framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC’s 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT’s MinION portability, ease-of-use, and identification capability in remote locations.
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Affiliation(s)
- Samir V Deshpande
- Science and Technology Corporation, 111 Bata Blvd, Suite C, Belcamp, MD 21017, USA
| | - Timothy M Reed
- US Army, 20th CBRNE, Aberdeen Proving Ground, MD 21010, USA
| | - Raymond F Sullivan
- US Army, CCDC-Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd, New Brunswick, NJ 08901-8521, USA
| | - Keith M Beigel
- US Army, 20th CBRNE, Aberdeen Proving Ground, MD 21010, USA.
| | - Mary M Wade
- US Army, CCDC-Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
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Yu HY, Meade A, Liu SJ. Phylogeny of Clostridium spp. Based on Conservative Genes and Comparisons with Other Trees. Microbiology (Reading) 2019. [DOI: 10.1134/s002626171904012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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σ 54 (σ L) plays a central role in carbon metabolism in the industrially relevant Clostridium beijerinckii. Sci Rep 2019; 9:7228. [PMID: 31076628 PMCID: PMC6510779 DOI: 10.1038/s41598-019-43822-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/23/2019] [Indexed: 11/09/2022] Open
Abstract
The solventogenic C. beijerinckii DSM 6423, a microorganism that naturally produces isopropanol and butanol, was previously modified by random mutagenesis. In this work, one of the resulting mutants was characterized. This strain, selected with allyl alcohol and designated as the AA mutant, shows a dominant production of acids, a severely diminished butanol synthesis capacity, and produces acetone instead of isopropanol. Interestingly, this solvent-deficient strain was also found to have a limited consumption of two carbohydrates and to be still able to form spores, highlighting its particular phenotype. Sequencing of the AA mutant revealed point mutations in several genes including CIBE_0767 (sigL), which encodes the σ54 sigma factor. Complementation with wild-type sigL fully restored solvent production and sugar assimilation and RT-qPCR analyses revealed its transcriptional control of several genes related to solventogensis, demonstrating the central role of σ54 in C. beijerinckii DSM 6423. Comparative genomics analysis suggested that this function is conserved at the species level, and this hypothesis was further confirmed through the deletion of sigL in the model strain C. beijerinckii NCIMB 8052.
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Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level. Sci Rep 2019; 9:1371. [PMID: 30718562 PMCID: PMC6362236 DOI: 10.1038/s41598-018-37679-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/13/2018] [Indexed: 01/16/2023] Open
Abstract
Clostridium beijerinckii NRRL B-598 is a sporulating, butanol and hydrogen producing strain that utilizes carbohydrates by the acetone-butanol-ethanol (ABE) fermentative pathway. The pathway consists of two metabolic phases, acidogenesis and solventogenesis, from which the latter one can be coupled with sporulation. Thorough transcriptomic profiling during a complete life cycle and both metabolic phases completed with flow cytometry, microscopy and a metabolites analysis helped to find out key genes involved in particular cellular events. The description of genes/operons that are closely involved in metabolism or the cell cycle is a necessary condition for metabolic engineering of the strain and will be valuable for all C. beijerinckii strains and other Clostridial species. The study focused on glucose transport and catabolism, hydrogen formation, metabolic stress response, binary fission, motility/chemotaxis and sporulation, which resulted in the composition of the unique image reflecting clostridial population changes. Surprisingly, the main change in expression of individual genes was coupled with the sporulation start and not with the transition from acidogenic to solventogenic metabolism. As expected, solvents formation started at pH decrease and the accumulation of butyric and acetic acids in the cultivation medium.
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Sedlar K, Koscova P, Vasylkivska M, Branska B, Kolek J, Kupkova K, Patakova P, Provaznik I. Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq. BMC Genomics 2018; 19:415. [PMID: 29843608 PMCID: PMC5975590 DOI: 10.1186/s12864-018-4805-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/18/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data. RESULTS In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabolism of the strain during fermentation. Interestingly, C. beijerinckii NRRL B-598 demonstrated different behavior in comparison with the closely related strain C. beijerinckii NCIMB 8052 in the latter phases of cultivation. CONCLUSIONS We provided a complex analysis of the C. beijerinckii NRRL B-598 fermentation profile using several technologies, including RNA-Seq. We described the changes in the global metabolism of the strain and confirmed the uniqueness of its behavior. The whole experiment demonstrated a good reproducibility. Therefore, we will be able to repeat the experiment under selected conditions in order to investigate particular metabolic changes and signaling pathways suitable for following targeted engineering.
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Affiliation(s)
- Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czechia
| | - Pavlina Koscova
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czechia
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czechia
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czechia
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czechia
- Institute of Aquaculture and Protection of Waters, University of South Bohemia in České Budějovice, Na Sádkách 1780, 370 05 České Budějovice, Czechia
| | - Kristyna Kupkova
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czechia
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908 USA
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czechia
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 616 00 Brno, Czechia
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Patakova P, Kolek J, Sedlar K, Koscova P, Branska B, Kupkova K, Paulova L, Provaznik I. Comparative analysis of high butanol tolerance and production in clostridia. Biotechnol Adv 2018; 36:721-738. [DOI: 10.1016/j.biotechadv.2017.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022]
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Little GT, Willson BJ, Heap JT, Winzer K, Minton NP. The Butanol Producing MicrobeClostridium beijerinckiiNCIMB 14988 Manipulated Using Forward and Reverse Genetic Tools. Biotechnol J 2018; 13:e1700711. [DOI: 10.1002/biot.201700711] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/15/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Gareth T. Little
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Benjamin J. Willson
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - John T. Heap
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), University of Nottingham; University Park, Nottingham NG7 2RD UK
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Branska B, Pechacova Z, Kolek J, Vasylkivska M, Patakova P. Flow cytometry analysis of Clostridium beijerinckii NRRL B-598 populations exhibiting different phenotypes induced by changes in cultivation conditions. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:99. [PMID: 29632557 PMCID: PMC5887253 DOI: 10.1186/s13068-018-1096-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/26/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Biobutanol production by clostridia via the acetone-butanol-ethanol (ABE) pathway is a promising future technology in bioenergetics , but identifying key regulatory mechanisms for this pathway is essential in order to construct industrially relevant strains with high tolerance and productivity. We have applied flow cytometric analysis to C. beijerinckii NRRL B-598 and carried out comparative screening of physiological changes in terms of viability under different cultivation conditions to determine its dependence on particular stages of the life cycle and the concentration of butanol. RESULTS Dual staining by propidium iodide (PI) and carboxyfluorescein diacetate (CFDA) provided separation of cells into four subpopulations with different abilities to take up PI and cleave CFDA, reflecting different physiological states. The development of a staining pattern during ABE fermentation showed an apparent decline in viability, starting at the pH shift and onset of solventogenesis, although an appreciable proportion of cells continued to proliferate. This was observed for sporulating as well as non-sporulating phenotypes at low solvent concentrations, suggesting that the increase in percentage of inactive cells was not a result of solvent toxicity or a transition from vegetative to sporulating stages. Additionally, the sporulating phenotype was challenged with butanol and cultivation with a lower starting pH was performed; in both these experiments similar trends were obtained-viability declined after the pH breakpoint, independent of the actual butanol concentration in the medium. Production characteristics of both sporulating and non-sporulating phenotypes were comparable, showing that in C. beijerinckii NRRL B-598, solventogenesis was not conditional on sporulation. CONCLUSION We have shown that the decline in C. beijerinckii NRRL B-598 culture viability during ABE fermentation was not only the result of accumulated toxic metabolites, but might also be associated with a special survival strategy triggered by pH change.
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Affiliation(s)
- Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Zora Pechacova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
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Chen C, Sun C, Wu YR. The Draft Genome Sequence of a Novel High-Efficient Butanol-Producing Bacterium Clostridium Diolis Strain WST. Curr Microbiol 2018; 75:1011-1015. [PMID: 29564548 DOI: 10.1007/s00284-018-1481-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 03/17/2018] [Indexed: 12/25/2022]
Abstract
A wild-type solventogenic strain Clostridium diolis WST, isolated from mangrove sediments, was characterized to produce high amount of butanol and acetone with negligible level of ethanol and acids from glucose via a unique acetone-butanol (AB) fermentation pathway. Through the genomic sequencing, the assembled draft genome of strain WST is calculated to be 5.85 Mb with a GC content of 29.69% and contains 5263 genes that contribute to the annotation of 5049 protein-coding sequences. Within these annotated genes, the butanol dehydrogenase gene (bdh) was determined to be in a higher amount from strain WST compared to other Clostridial strains, which is positively related to its high-efficient production of butanol. Therefore, we present a draft genome sequence analysis of strain WST in this article that should facilitate to further understand the solventogenic mechanism of this special microorganism.
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Affiliation(s)
- Chaoyang Chen
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, China
| | - Chongran Sun
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, China
| | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, 515063, Guangdong, China. .,STU-UNIVPM Joint Algal Research Center, Shantou University, Shantou, 515063, Guangdong, China. .,Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China.
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Sun C, Zhang S, Xin F, Shanmugam S, Wu YR. Genomic comparison of Clostridium species with the potential of utilizing red algal biomass for biobutanol production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:42. [PMID: 29467820 PMCID: PMC5815214 DOI: 10.1186/s13068-018-1044-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/05/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Sustainable biofuels, which are widely considered as an attractive alternative to fossil fuels, can be generated by utilizing various biomass from the environment. Marine biomass, such as red algal biomass, is regarded as one potential renewable substrate source for biofuels conversion due to its abundance of fermentable sugars (e.g., galactose). Previous studies focused on the enhancement of biofuels production from different Clostridium species; however, there has been limited investigation into their metabolic pathways, especially on the conversion of biofuels from galactose, via whole genomic comparison and evolutionary analysis. RESULTS Two galactose-utilizing Clostridial strains were examined and identified as Clostridium acetobutylicum strain WA and C. beijerinckii strain WB. Via the genomic sequencing of both strains, the comparison of the whole genome together with the relevant protein prediction of 33 other Clostridium species was established to reveal a clear genome profile based upon various genomic features. Among them, five representative strains, including C. beijerinckii NCIMB14988, C. diolis DSM 15410, C. pasteurianum BC1, strain WA and WB, were further discussed to demonstrate the main differences among their respective metabolic pathways, especially in their carbohydrate metabolism. The metabolic pathways involved in the generation of biofuels and other potential products (e.g., riboflavin) were also reconstructed based on the utilization of marine biomass. Finally, a batch fermentation process was performed to verify the fermentative products from strains WA and WB using 60 g/L of galactose, which is the main hydrolysate from algal biomass. It was observed that strain WA and WB could produce up to 16.98 and 12.47 g/L of biobutanol, together with 21,560 and 10,140 mL/L biohydrogen, respectively. CONCLUSIONS The determination of the production of various biofuels by both strains WA and WB and their genomic comparisons with other typical Clostridium species on the analysis of various metabolic pathways was presented. Through the identification of their metabolic pathways, which are involved in the conversion of galactose into various potential products, such as biobutanol, the obtained results extend the current insight into the potential capability of utilizing marine red algal biomass and provide a systematic investigation into the relationship between this genus and the generation of sustainable bioenergy.
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Affiliation(s)
- Chongran Sun
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
| | - Shuangfei Zhang
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
| | - Fengxue Xin
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063 Guangdong China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | | | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, 515063 Guangdong China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063 Guangdong China
- STU-UNIVPM Joint Algal Research Center, Shantou University, Shantou, 515063 Guangdong China
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Kolek J, Diallo M, Vasylkivska M, Branska B, Sedlar K, López-Contreras AM, Patakova P. Comparison of expression of key sporulation, solventogenic and acetogenic genes in C. beijerinckii NRRL B-598 and its mutant strain overexpressing spo0A. Appl Microbiol Biotechnol 2017; 101:8279-8291. [PMID: 28990140 DOI: 10.1007/s00253-017-8555-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/21/2017] [Accepted: 09/26/2017] [Indexed: 01/18/2023]
Abstract
The production of acetone, butanol and ethanol by fermentation of renewable biomass has potential to become a valuable industrial process. Mechanisms of solvent production and sporulation involve some common regulators in some ABE-producing clostridia, although details of the links between the pathways are not clear. In this study, we compare a wild-type (WT) Clostridium beijerinckii NRRL B-598 with its mutant strain OESpo0A, in which the gene encoding Spo0A, an important regulator of both sporulation and solventogenesis, is overexpressed in terms of solvent and acid production. We also compare morphologies during growth on two different media: TYA broth, where the WT culture sporulates, and RCM, where the WT culture does not. In addition, RT-qPCR-based analysis of expression profiles of spo0A, spoIIE, sigG, spoVD, ald and buk1 genes involved in sporulation or solvent production in these strains, were compared. The OESpo0A mutant did not produce spores and butanol titre was lower compared to the WT, but increased amounts of butyric acid and ethanol were produced. The gene spo0A had high levels of expression in the WT under non-sporulating culture conditions while other selected genes for sporulation factors were downregulated significantly. Similar observations were obtained for OESpo0A where spo0A overexpression and downregulation of other sporulation genes were demonstrated. Higher expression of spo0A led to higher expression of buk1 and ald, which could confirm the role of spo0A in activation of the solventogenic pathway, although solvent production was not affected significantly in the WT and was weakened in the OESpo0A mutant.
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Affiliation(s)
- J Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - M Diallo
- Wageningen Food and Biobased Research, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - M Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - B Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic
| | - K Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, 61600, Brno, Czech Republic
| | - A M López-Contreras
- Wageningen Food and Biobased Research, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - P Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28, Prague, Czech Republic.
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