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Huang T, Ma Y. Advances in biosynthesis of higher alcohols in Escherichia coli. World J Microbiol Biotechnol 2023; 39:125. [PMID: 36941474 DOI: 10.1007/s11274-023-03580-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 03/23/2023]
Abstract
In recent years, the development of green energy to replace fossil fuels has been the focus of research. Higher alcohols are important biofuels and chemicals. The production of higher alcohols in microbes has gained attention due to its environmentally friendly character. Higher alcohols have been synthesized in model microorganism Escherichia coli, and the production has reached the gram level through enhancement of metabolic flow, the balance of reducing power and the optimization of fermentation processes. Sustainable bio-higher alcohols production is expected to replace fossil fuels as a green and renewable energy source. Therefore, this review summarizes the latest developments in producing higher alcohols (C3-C6) by E. coli, elucidate the main bottlenecks limiting the biosynthesis of higher alcohols, and proposes potential engineering strategies of improving the production of biological higher alcohols. This review would provide a theoretical basis for further research on higher alcohols production by E. coli.
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Affiliation(s)
- Tong Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Yuanyuan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- School of Marin Science and Technology, Tianjin University, Tianjin, 300072, China.
- R&D Center for Petrochemical Technology, Tianjin University, Tianjin, 300072, China.
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2
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A Critical Review on the Economically Feasible and Sustainable Poly(3-Hydroxybutyrate- co-3-hydroxyvalerate) Production from Alkyl Alcohols. Polymers (Basel) 2022; 14:polym14040670. [PMID: 35215584 PMCID: PMC8876610 DOI: 10.3390/polym14040670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 01/14/2023] Open
Abstract
Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (P(3HB-co-3HV)) is the most studied short-chain-length polyhydroxyalkanoates (PHA) with high application importance in various fields. The domination of high-cost propionate and valerate over other 3-hydroxyvalerate (3HV) precursors owing to their wide preference among PHA-producing bacteria has hindered the development of diverse production processes. As alkyl alcohols are mainly produced from inexpensive starting materials through oxo synthesis, they contribute a cost-effective advantage over propionate and valerate. Moreover, alkyl alcohols can be biosynthesized from natural substrates and organic wastes. Despite their great potential, their toxicity to most PHA-producing bacteria has been the major drawback for their wide implementation as 3HV precursors for decades. Although the standard PHA-producing bacteria Cupriavidus necator showed promising alcohol tolerance, the 3HV yield was discouraging. Continuous discovery of alkyl alcohols-utilizing PHA-producing bacteria has enabled broader choices in 3HV precursor selection for diverse P(3HB-co-3HV) production processes with higher economic feasibility. Besides continuous effort in searching for promising wild-type strains, genetic engineering to construct promising recombinant strains based on the understanding of the mechanisms involved in alkyl alcohols toxicity and tolerance is an alternative approach. However, more studies are required for techno-economic assessment to analyze the economic performance of alkyl alcohol-based production compared to that of organic acids.
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3
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Biocatalytic Conversion of Short-Chain Fatty Acids to Corresponding Alcohols in Escherichia coli. Processes (Basel) 2021. [DOI: 10.3390/pr9060973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Advanced biofuels possess superior characteristics to serve for gasoline substitutes. In this study, a whole cell biocatalysis system was employed for production of short-chain alcohols from corresponding fatty acids. To do so, Escherichia coli strain was equipped with a biocatalytic pathway consisting of endogenous atoDA and Clostridium acetobutylicum adhE2. The strain was further reprogrammed to improve its biocatalytic activity by direction the glycolytic flux to acetyl-CoA and recycling acetate. The production of 1-propanol and n-pentanol were exemplified with the engineered strain. By substrate (glucose and propionate) feeding, the strain enabled production of 5.4 g/L 1-propanol with productivity reaching 0.15 g/L/h. In addition, the strain with a heavy inoculum was implemented for the n-pentanol production from n-pentanoic acid. The production titer and productivity finally attained 4.3 g/L and 0.86 g/L/h, respectively. Overall, the result indicates that this developed system is useful and effective for biocatalytic production of short-chain alcohols.
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Fan HY, Tung YT, Yang YCSH, Hsu JB, Lee CY, Chang TH, Su ECY, Hsieh RH, Chen YC. Maternal Vegetable and Fruit Consumption during Pregnancy and Its Effects on Infant Gut Microbiome. Nutrients 2021; 13:1559. [PMID: 34063157 PMCID: PMC8148194 DOI: 10.3390/nu13051559] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/20/2022] Open
Abstract
Maternal nutrition intake during pregnancy may affect the mother-to-child transmission of bacteria, resulting in gut microflora changes in the offspring, with long-term health consequences in later life. Longitudinal human studies are lacking, as only a small amount of studies showing the effect of nutrition intake during pregnancy on the gut microbiome of infants have been performed, and these studies have been mainly conducted on animals. This pilot study explores the effects of high or low fruit and vegetable gestational intake on the infant microbiome. We enrolled pregnant women with a complete 3-day dietary record and received postpartum follow-up. The 16S rRNA gene sequence was used to characterize the infant gut microbiome at 2 months (n = 39). Principal coordinate analysis ordination revealed that the infant gut microbiome clustered differently for high and low maternal fruit and vegetable consumption (p < 0.001). The linear discriminant analysis effect size and feature selection identified 6 and 17 taxa from both the high and low fruit and vegetable consumption groups. Among the 23 abundant taxa, we observed that six maternal intake nutrients were associated with nine taxa (e.g., Erysipelatoclostridium, Isobaculum, Lachnospiraceae, Betaproteobacteria, Burkholderiaceae, Sutterella, Clostridia, Clostridiales, and Lachnoclostridium). The amount of gestational fruit and vegetable consumption is associated with distinct changes in the infant gut microbiome at 2 months of age. Therefore, strategies involving increased fruit and vegetable consumption during pregnancy should be employed for modifying the gut microbiome early in life.
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Affiliation(s)
- Hsien-Yu Fan
- Department of Family Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan;
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yu-Tang Tung
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Yu-Chen S. H. Yang
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei 110, Taiwan;
| | - Justin BoKai Hsu
- Department of Medical Research, Taipei Medical University Hospital, Taipei 110, Taiwan;
| | - Cheng-Yang Lee
- Office of Information Technology, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.L.); (T.-H.C.)
| | - Tzu-Hao Chang
- Office of Information Technology, Taipei Medical University, Taipei 110, Taiwan; (C.-Y.L.); (T.-H.C.)
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan;
| | - Emily Chia-Yu Su
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan;
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Rong-Hong Hsieh
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
| | - Yang-Ching Chen
- Department of Family Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan;
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
- School of Nutrition and Health Sciences, College of Nutrition, Taipei Medical University, Taipei 110, Taiwan;
- Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
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Scully SM, Orlygsson J. Biotransformation of Carboxylic Acids to Alcohols: Characterization of Thermoanaerobacter Strain AK152 and 1-Propanol Production via Propionate Reduction. Microorganisms 2020; 8:microorganisms8060945. [PMID: 32586016 PMCID: PMC7356315 DOI: 10.3390/microorganisms8060945] [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: 05/25/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 11/22/2022] Open
Abstract
Thermoanaerobacter strains have recently gained interest because of their ability to convert short chain fatty acids to alcohols using actively growing cells. Thermoanaerobacter thermohydrosulfuricus strain AK152 was physiologically investigated for its ethanol and other alcohol formation. The temperature and pH optimum of the strain was 70 °C and pH 7.0 and the strain degraded a variety of compounds present in lignocellulosic biomass like monosaccharides, disaccharides, and starch. The strain is highly ethanologenic, producing up to 86% of the theoretical ethanol yield form hexoses. Strain AK152 was inhibited by relatively low initial substrate (30 mM) concentration, leading to inefficient degradation of glucose and levelling up of all end-product formation. The present study shows that the strain produces alcohols from most of the tested carboxylic acids, with the highest yields for propionate conversion to propanol (40.7%) with kinetic studies demonstrating that the maximum conversion happens within the first 48 h of fermentation. Various physiological tests were performed to maximize the acid conversion to the alcohol which reveals that the optimum pH for propionate conversion is pH 6.7 which affords a 57.3% conversion. Kinetic studies reveal that propionate conversion is rapid, achieving a maximum conversion within the first 48 h of fermentation. Finally, by using 13C NMR, it was shown that the addition of propionate indeed converted to propanol.
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Rocha Martin VN, Schwab C, Krych L, Voney E, Geirnaert A, Braegger C, Lacroix C. Colonization of Cutibacterium avidum during infant gut microbiota establishment. FEMS Microbiol Ecol 2019; 95:5154911. [PMID: 30388209 DOI: 10.1093/femsec/fiy215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023] Open
Abstract
Establishment of the infant gut microbiota affects gut maturation and influences long-term health. Cutibacterium (formerly Propionibacterium) have been identified as early colonizers, but little is known about their function. Using a cultivation-dependent and -independent approach, we determined Cutibacterium prevalence, diversity and functional potential. In feces from a Swiss infant cohort (n = 38), prevalence of Propionibacterium/Cutibacterium decreased from 84% at 2 weeks, to 65% at 4 weeks, 47% at 8 weeks and 41% at 12 weeks of age. Abundance varied among individuals, and persistence depended on the colonization levels at 2 weeks. Cutibacterium isolates (n = 87) were obtained from 10 infants from a smaller cohort (n = 12); restriction fragment length polymorphism clustered isolates in four groups, and all identified as Cutibacterium avidum. Colonization potential and metabolic effects of C. avidum addition were tested in an in vitro continuous intestinal fermentation model mimicking infant proximal colon conditions. Cutibacterium avidum spiked daily at 108 or 109 cells mL-1 colonized, decreased formate and persisted during the washout period. Significant correlations were observed between Propionibacterium/Cutibacterium and lactate-producers and protein-degraders in both reactors and infant feces. Our findings highlight the natural presence of C. avidum and its role as a lactate-consumer and propionate-producer in infants younger than 3 months.
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Affiliation(s)
- Vanesa Natalin Rocha Martin
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland.,Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| | - Lukasz Krych
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen 1958, Denmark
| | - Evelyn Voney
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| | - Christian Braegger
- Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
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Rocha Martin VN, Lacroix C, Killer J, Bunesova V, Voney E, Braegger C, Schwab C. Cutibacterium avidum is phylogenetically diverse with a subpopulation being adapted to the infant gut. Syst Appl Microbiol 2019; 42:506-516. [PMID: 31128887 DOI: 10.1016/j.syapm.2019.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/18/2022]
Abstract
The infant gut harbors a diverse microbial community consisting of several taxa whose persistence depends on adaptation to the ecosystem. In healthy breast-fed infants, the gut microbiota is dominated by Bifidobacterium spp.. Cutibacterium avidum is among the initial colonizers, however, the phylogenetic relationship of infant fecal isolates to isolates from other body sites, and C. avidum carbon utilization related to the infant gut ecosystem have been little investigated. In this study, we investigated the phylogenetic and phenotypic diversity of 28 C. avidum strains, including 16 strains isolated from feces of healthy infants. We investigated the in vitro capacity of C. avidum infant isolates to degrade and consume carbon sources present in the infant gut, and metabolic interactions of C. avidum with infant associated Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum. Isolates of C. avidum showed genetic heterogeneity. C. avidum consumed d- and l-lactate, glycerol, glucose, galactose, N-acetyl-d-glucosamine and maltodextrins. Alpha-galactosidase- and β-glucuronidase activity were a trait of a group of non-hemolytic strains, which were mostly isolated from infant feces. Beta-glucuronidase activity correlated with the ability to ferment glucuronic acid. Co-cultivation with B. infantis and B. bifidum enhanced C. avidum growth and production of propionate, confirming metabolic cross-feeding. This study highlights the phylogenetic and functional diversity of C. avidum, their role as secondary glycan degraders and propionate producers, and suggests adaptation of a subpopulation to the infant gut.
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Affiliation(s)
- Vanesa Natalin Rocha Martin
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland; Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| | - Jiri Killer
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Czech Republic
| | - Vera Bunesova
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, Suchdol 165 00, Czech Republic
| | - Evelyn Voney
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland
| | - Christian Braegger
- Division of Gastroenterology and Nutrition, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH-Zurich, 8092 Zurich, Switzerland.
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Cheng L, Marinelli LJ, Grosset N, Fitz-Gibbon ST, Bowman CA, Dang BQ, Russell DA, Jacobs-Sera D, Shi B, Pellegrini M, Miller JF, Gautier M, Hatfull GF, Modlin RL. Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages. BMC Microbiol 2018; 18:19. [PMID: 29490612 PMCID: PMC5831693 DOI: 10.1186/s12866-018-1159-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 02/15/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND A remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is also a member of the Propionibacteriaceae family, Propionibacterium freudenreichii, a bacterium used in production of Swiss-type cheeses, have also been described and are common contaminants of the cheese manufacturing process. However, little is known about their genetic composition and diversity. RESULTS We obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-type cheese samples, and determined their complete genome sequences. These data revealed that all seven phage isolates are of similar genomic length and GC% content, but their genomes are highly diverse, including genes encoding the capsid, tape measure, and tail proteins. In contrast to C. acnes phages, all P. freudenreichii phage genomes encode a putative integrase protein, suggesting they are capable of lysogenic growth. This is supported by the finding of related prophages in some P. freudenreichii strains. The seven phages could further be distinguished as belonging to two distinct genomic types, or 'clusters', based on nucleotide sequences, and host range analyses conducted on a collection of P. freudenreichii strains show a higher degree of host specificity than is observed for the C. acnes phages. CONCLUSIONS Overall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.
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Affiliation(s)
- Lucy Cheng
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Laura J. Marinelli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Noël Grosset
- Equipe Microbiologie de l’œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l’Œuf, Rennes, France
| | - Sorel T. Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Charles A. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Brian Q. Dang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Baochen Shi
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Jeff F. Miller
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Michel Gautier
- Equipe Microbiologie de l’œuf et des Ovoproduits (MICOV), Agrocampus Ouest, INRA, (UMR1253) Science et Technologie du Lait et de l’Œuf, Rennes, France
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Robert L. Modlin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095 CA USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095 USA
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Deptula P, Laine PK, Roberts RJ, Smolander OP, Vihinen H, Piironen V, Paulin L, Jokitalo E, Savijoki K, Auvinen P, Varmanen P. De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii. BMC Genomics 2017; 18:790. [PMID: 29037147 PMCID: PMC5644110 DOI: 10.1186/s12864-017-4165-9] [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: 06/07/2017] [Accepted: 10/05/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species. RESULTS We used the PacBio RS II sequencing platform to generate complete genomes of 20 P. freudenreichii strains and compared them in detail. Comparative analyses revealed both sequence conservation and genome organisational diversity among the strains. Assembly from long reads resulted in the discovery of additional circular elements: two putative conjugative plasmids and three active, lysogenic bacteriophages. It also permitted characterisation of the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed identification of DNA modifications, which in turn allowed characterisation of the restriction-modification systems together with their recognition motifs. The observed genomic differences suggested strain variation in surface piliation and specific mucus binding, which were validated by experimental studies. The phenotypic characterisation displayed large diversity between the strains in ability to utilise a range of carbohydrates, to grow at unfavourable conditions and to form a biofilm. CONCLUSION The complete genome sequencing allowed detailed characterisation of the industrially important species, P. freudenreichii by facilitating the discovery of previously unknown features. The results presented here lay a solid foundation for future genetic and functional genomic investigations of this actinobacterial species.
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Affiliation(s)
- Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Pia K. Laine
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Helena Vihinen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
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Gonzalez-Garcia RA, McCubbin T, Wille A, Plan M, Nielsen LK, Marcellin E. Awakening sleeping beauty: production of propionic acid in Escherichia coli through the sbm operon requires the activity of a methylmalonyl-CoA epimerase. Microb Cell Fact 2017; 16:121. [PMID: 28716098 PMCID: PMC5512728 DOI: 10.1186/s12934-017-0735-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/05/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Propionic acid is used primarily as a food preservative with smaller applications as a chemical building block for the production of many products including fabrics, cosmetics, drugs, and plastics. Biological production using propionibacteria would be competitive against chemical production through hydrocarboxylation of ethylene if native producers could be engineered to reach near-theoretical yield and good productivity. Unfortunately, engineering propionibacteria has proven very challenging. It has been suggested that activation of the sleeping beauty operon in Escherichia coli is sufficient to achieve propionic acid production. Optimising E. coli production should be much easier than engineering propionibacteria if tolerance issues can be addressed. RESULTS Propionic acid is produced in E. coli via the sleeping beauty mutase operon under anaerobic conditions in rich medium via amino acid degradation. We observed that the sbm operon enhances amino acids degradation to propionic acid and allows E. coli to degrade isoleucine. However, we show here that the operon lacks an epimerase reaction that enables propionic acid production in minimal medium containing glucose as the sole carbon source. Production from glucose can be restored by engineering the system with a methylmalonyl-CoA epimerase from Propionibacterium acidipropionici (0.23 ± 0.02 mM). 1-Propanol production was also detected from the promiscuous activity of the native alcohol dehydrogenase (AdhE). We also show that aerobic conditions are favourable for propionic acid production. Finally, we increase titre 65 times using a combination of promoter engineering and process optimisation. CONCLUSIONS The native sbm operon encodes an incomplete pathway. Production of propionic acid from glucose as sole carbon source is possible when the pathway is complemented with a methylmalonyl-CoA epimerase. Although propionic acid via the restored succinate dissimilation pathway is considered a fermentative process, the engineered pathway was shown to be functional under anaerobic and aerobic conditions.
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Affiliation(s)
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Annalena Wille
- Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
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Walther T, François JM. Microbial production of propanol. Biotechnol Adv 2016; 34:984-996. [PMID: 27262999 DOI: 10.1016/j.biotechadv.2016.05.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/08/2016] [Accepted: 05/31/2016] [Indexed: 11/19/2022]
Abstract
Both, n-propanol and isopropanol are industrially attractive value-added molecules that can be produced by microbes from renewable resources. The development of cost-effective fermentation processes may allow using these alcohols as a biofuel component, or as a precursor for the chemical synthesis of propylene. This review reports and discusses the recent progress which has been made in the biochemical production of propanol. Several synthetic propanol-producing pathways were developed that vary with respect to stoichiometry and metabolic entry point. These pathways were expressed in different host organisms and enabled propanol production from various renewable feedstocks. Furthermore, it was shown that the optimization of fermentation conditions greatly improved process performance, in particular, when continuous product removal prevented accumulation of toxic propanol levels. Although these advanced metabolic engineering and fermentation strategies have facilitated significant progress in the biochemical production of propanol, the currently achieved propanol yields and productivities appear to be insufficient to compete with chemical propanol synthesis. The development of biosynthetic pathways with improved propanol yields, the breeding or identification of microorganisms with higher propanol tolerance, and the engineering of propanol producer strains that efficiently utilize low-cost feedstocks are the major challenges on the way to industrially relevant microbial propanol production processes.
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Affiliation(s)
- Thomas Walther
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France; CNRS, UMR5504, 31400 Toulouse, France; Toulouse White Biotechnology (TWB) Center, 3 rue Ariane, Canal Biotech Building 2, 31520 Ramonville - St. Agne, France.
| | - Jean Marie François
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, 31077 Toulouse, France; INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, 31400 Toulouse, France; CNRS, UMR5504, 31400 Toulouse, France
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12
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Zhang A, Sun J, Wang Z, Yang ST, Zhou H. Effects of carbon dioxide on cell growth and propionic acid production from glycerol and glucose by Propionibacterium acidipropionici. BIORESOURCE TECHNOLOGY 2015; 175:374-381. [PMID: 25459845 DOI: 10.1016/j.biortech.2014.10.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/04/2014] [Accepted: 10/09/2014] [Indexed: 06/04/2023]
Abstract
The effects of CO2 on propionic acid production and cell growth in glycerol or glucose fermentation were investigated in this study. In glycerol fermentation, the volumetric productivity of propionic acid with CO2 supplementation reached 2.94g/L/day, compared to 1.56g/L/day without CO2. The cell growth using glycerol was also significantly enhanced with CO2. In addition, the yield and productivity of succinate, the main intermediate in Wood-Werkman cycle, increased 81% and 280%, respectively; consistent with the increased activities of pyruvate carboxylase and propionyl CoA transferase, two key enzymes in the Wood-Werkman cycle. However, in glucose fermentation CO2 had minimal effect on propionic acid production and cell growth. The carbon flux distributions using glycerol or glucose were also analyzed using a stoichiometric metabolic model. The calculated maintenance coefficient (mATP) increased 100%, which may explain the increase in the productivity of propionic acid in glycerol fermentation with CO2 supplement.
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Affiliation(s)
- An Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH 43210, USA
| | - Jianxin Sun
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH 43210, USA
| | - Zhongqiang Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH 43210, USA
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 140 West 19th Avenue, Columbus, OH 43210, USA
| | - Haiying Zhou
- Elixir Bioscience LLC, 1119 Jewel Creek Dr., Cary, NC 27519, USA.
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13
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Engineering propionibacteria as versatile cell factories for the production of industrially important chemicals: advances, challenges, and prospects. Appl Microbiol Biotechnol 2014; 99:585-600. [PMID: 25431012 DOI: 10.1007/s00253-014-6228-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/11/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
Propionibacteria are actinobacteria consisting of two principal groups: cutaneous and dairy. Cutaneous propionibacteria are considered primary pathogens to humans, whereas dairy propionibacteria are widely used in the food and pharmaceutical industries. Increasing attention has been focused on improving the performance of dairy propionibacteria for the production of industrially important chemicals, and significant advances have been made through strain engineering and process optimization in the production of flavor compounds, nutraceuticals, and antimicrobial compounds. In addition, genome sequencing of several propionibacteria species has been completed, deepening understanding of the metabolic and physiological features of these organisms. However, the metabolic engineering of propionibacteria still faces several challenges owing to the lack of efficient genome manipulation tools and the existence of various types of strong restriction-modification systems. The emergence of systems and synthetic biology provides new opportunities to overcome these bottlenecks. In this review, we first introduce the major species of propionibacteria and their properties and provide an overview of their functions and applications. We then discuss advances in the genome sequencing and metabolic engineering of these bacteria. Finally, we discuss systems and synthetic biology approaches for engineering propionibacteria as efficient and robust cell factories for the production of industrially important chemicals.
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14
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Poonam, Pophaly SD, Tomar SK, De S, Singh R. Multifaceted attributes of dairy propionibacteria: a review. World J Microbiol Biotechnol 2012; 28:3081-95. [PMID: 22806746 DOI: 10.1007/s11274-012-1117-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/21/2012] [Indexed: 12/31/2022]
Abstract
Dairy propionibacteria are Generally Recognized as Safe (GRAS) status microorganisms which have been traditionally used for the manufacture of Swiss type cheeses. In the last two decades various added features and functionalities have been discovered and developed from these bacteria. Propionibacteria are robust organisms with remarkable adaptability to technological and physiological stress conditions. Besides, they also display a multitude of health promoting properties like modulation of gut microbiota, improved gut physiology and immunomodulation suggesting their promising probiotic potential. Propionibacteria produce an interestingly wide range of functional biomolecules like B group vitamins, trehalose, conjugated linoleic acid, propionic acid, bacteriocins, bifidogenic factors etc. These bacteria are thus now being explored for designing novel functional foods as well as for industrial production of nutraceuticals. Growing interest in these bacteria is fueled by the first whole genome sequencing of a Propionibacterium freudenreichii strain providing a platform for better understanding of various pathways and further improvement in related process technologies.
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Affiliation(s)
- Poonam
- Dairy Microbiology Division, National Dairy Research Institute, Karnal, Haryana 132001, India
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15
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Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET. Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol 2012; 23:364-81. [DOI: 10.1016/j.copbio.2011.10.008] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/06/2011] [Accepted: 10/20/2011] [Indexed: 12/19/2022]
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16
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Liu L, Zhu Y, Li J, Wang M, Lee P, Du G, Chen J. Microbial production of propionic acid from propionibacteria: current state, challenges and perspectives. Crit Rev Biotechnol 2012; 32:374-81. [PMID: 22299651 DOI: 10.3109/07388551.2011.651428] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Propionic acid (PA) is an important building block chemical and finds a variety of applications in organic synthesis, food, feeding stuffs, perfume, paint and pharmaceutical industries. Presently, PA is mainly produced by petrochemical route. With the continuous increase in oil prices, public concern about environmental pollution, and the consumers' desire for bio-based natural and green ingredients in foods and pharmaceuticals, PA production from propionibacteria has attracted considerable attention, and substantial progresses have been made on microbial PA production. However, production of PA by propionibacteria is facing challenges such as severe inhibition of end-products during cell growth and the formation of by-products (acetic acid and succinic acid). The integration of reverse metabolic engineering and systematic metabolic engineering provides an opportunity to significantly improve the acid tolerance of propionibacteria and reduce the formation of by-products, and makes it feasible to strengthen the commercial competition of biotechnological PA production from propionibacteria to be comparable to the petrochemical route.
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Affiliation(s)
- Long Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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17
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Thierry A, Deutsch SM, Falentin H, Dalmasso M, Cousin FJ, Jan G. New insights into physiology and metabolism of Propionibacterium freudenreichii. Int J Food Microbiol 2011; 149:19-27. [DOI: 10.1016/j.ijfoodmicro.2011.04.026] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 04/14/2011] [Accepted: 04/29/2011] [Indexed: 01/25/2023]
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18
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Brzuszkiewicz E, Weiner J, Wollherr A, Thürmer A, Hüpeden J, Lomholt HB, Kilian M, Gottschalk G, Daniel R, Mollenkopf HJ, Meyer TF, Brüggemann H. Comparative genomics and transcriptomics of Propionibacterium acnes. PLoS One 2011; 6:e21581. [PMID: 21738717 PMCID: PMC3124536 DOI: 10.1371/journal.pone.0021581] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 06/03/2011] [Indexed: 11/19/2022] Open
Abstract
The anaerobic gram-positive bacterium Propionibacterium acnes is a human skin commensal that is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with maintenance of skin homeostasis. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits differ between phylotypes, as judged from PCR analysis of a collection of P. acnes strains. Comparative transcriptome analysis of strains KPA171202 (type I-2) and 266 during exponential growth revealed inter-strain differences in gene expression of transport systems and metabolic pathways. In addition, transcript levels of genes encoding possible virulence factors such as dermatan-sulphate adhesin, polyunsaturated fatty acid isomerase, iron acquisition protein HtaA and lipase GehA were upregulated in strain 266. We investigated differential gene expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by upregulation of genes involved in stress responses and amino acid metabolism. Our data highlight the genomic basis for strain diversity and identify, for the first time, the actively transcribed part of the genome, underlining the important role growth status plays in the inflammation-inducing activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by the phylotype-specific genome content but also by variable gene expression.
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Affiliation(s)
- Elzbieta Brzuszkiewicz
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Antje Wollherr
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Jennifer Hüpeden
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Hans B. Lomholt
- Department of Medical Microbiology and Immunology, Aarhus University, Aarhus, Denmark
| | - Mogens Kilian
- Department of Medical Microbiology and Immunology, Aarhus University, Aarhus, Denmark
| | - Gerhard Gottschalk
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | | | - Thomas F. Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Holger Brüggemann
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
- * E-mail:
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19
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Cousin FJ, Mater DD, Foligne B, Jan G. Dairy propionibacteria as human probiotics: A review of recent evidence. ACTA ACUST UNITED AC 2010. [DOI: 10.1051/dst/2010032] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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20
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Falentin H, Deutsch SM, Jan G, Loux V, Thierry A, Parayre S, Maillard MB, Dherbécourt J, Cousin FJ, Jardin J, Siguier P, Couloux A, Barbe V, Vacherie B, Wincker P, Gibrat JF, Gaillardin C, Lortal S. The complete genome of Propionibacterium freudenreichii CIRM-BIA1, a hardy actinobacterium with food and probiotic applications. PLoS One 2010; 5:e11748. [PMID: 20668525 PMCID: PMC2909200 DOI: 10.1371/journal.pone.0011748] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 06/29/2010] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use. This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats. It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P. acnes. The genome of the type strain, P. freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027(T)), was sequenced with an 11-fold coverage. METHODOLOGY/PRINCIPAL FINDINGS The circular chromosome of 2.7 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (3.5% of the genome in base pairs). Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed. The annotation revealed the genetic basis for the hardiness of P. freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage. The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria. By comparative genomics, no pathogenicity factors found in P. acnes or in other pathogenic microbial species were identified in P. freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P. freudenreichii. Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters. CONCLUSIONS/SIGNIFICANCE With the exception of its ability to degrade lactose, P. freudenreichii seems poorly adapted to dairy niches. This genome annotation opens up new prospects for the understanding of the P. freudenreichii probiotic activity.
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Affiliation(s)
- Hélène Falentin
- INRA, UMR 1253, Science et Technologie du Lait et de l'OEuf, Rennes, France.
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21
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Crow VL. Metabolism of Aspartate by Propionibacterium freudenreichii subsp. shermanii: Effect on Lactate Fermentation. Appl Environ Microbiol 2010; 52:359-65. [PMID: 16347135 PMCID: PMC203530 DOI: 10.1128/aem.52.2.359-365.1986] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
More than 90% of the aspartate in a defined medium was metabolized after lactate exhaustion such that 3 mol of aspartate and 1 mol of propionate were converted to 3 mol of succinate, 3 mol of ammonia, 1 mol of acetate, and 1 mol of CO(2). This pathway was also evident when propionate and aspartate were the substrates in complex medium in the absence of lactate. In complex medium with lactate present, about 70% of the aspartate was metabolized to succinate and ammonia during lactate fermentation, and as a consequence of aspartate metabolism, more lactate was fermented to acetate and CO(2) than was fermented to propionate. The conversion of aspartate to fumarate and ammonia by the enzyme aspartase and subsequent reduction of fumarate to succinate occurred in the five strains of Propionibacterium freudenreichii subsp. shermanii studied. The ability to metabolize aspartate in the presence of lactate appeared to be related to aspartase activity. The specific activity of aspartase increased during and after lactate utilization, and the levels of this enzyme were lower in cells grown in defined medium than levels in those cells grown in complex medium. Under the conditions used, no other amino acids were readily metabolized in the presence of lactate. The possibility that aspartate metabolism by propionibacteria in Swiss cheese has an influence on CO(2) production is discussed.
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Affiliation(s)
- V L Crow
- New Zealand Dairy Research Institute, Palmerston North, New Zealand
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22
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Crow VL. Utilization of Lactate Isomers by Propionibacterium freudenreichii subsp. shermanii: Regulatory Role for Intracellular Pyruvate. Appl Environ Microbiol 2010; 52:352-8. [PMID: 16347134 PMCID: PMC203529 DOI: 10.1128/aem.52.2.352-358.1986] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five strains of Propionibacterium freudenreichii subsp. shermanii utilized the l-(+) isomer of lactate at a faster rate than they did the d-(-) isomer when grown with a mixture of lactate isomers under a variety of conditions. ATCC 9614, grown anaerobically in defined medium containing 160 mM dl-lactate, utilized only 4 and 15% of the d-(-)-lactate by the time 50 and 90%, respectively, of the l-(+)-lactate was used. The intracellular pyruvate concentration was high (>100 mM) in the initial stages of lactate utilization, when either dl-lactate or the l-(+) isomer was the starting substrate. The concentration of this intermediate dropped during dl-lactate fermentation such that when only d-(-)-lactate remained, the concentration was <20 mM. When only the d-(-) isomer was initially present, a similar relatively low concentration of intracellular pyruvate was present, even at the start of lactate utilization. The NAD-independent lactate dehydrogenase activities in extracts showed different kinetic properties with regard to pyruvate inhibition, depending upon the lactate isomer present. Pyruvate gave a competitive inhibitor pattern with l-(+)-lactate and a mixed-type inhibitor pattern with d-(-)-lactate. It is suggested that these properties of the lactate dehydrogenases and the intracellular pyruvate concentrations explain the preferential use of the l-(+) isomer.
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Affiliation(s)
- V L Crow
- New Zealand Dairy Research Institute, Palmerston North, New Zealand
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23
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Boumba VA, Ziavrou KS, Vougiouklakis T. Biochemical pathways generating post-mortem volatile compounds co-detected during forensic ethanol analyses. Forensic Sci Int 2007; 174:133-51. [PMID: 17452087 DOI: 10.1016/j.forsciint.2007.03.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Revised: 03/13/2007] [Accepted: 03/21/2007] [Indexed: 11/23/2022]
Abstract
In this contribution are presented the fermentations of the main substrates present in a decaying corpse, namely carbohydrates, amino acids, glycerol and fatty acids, generating the post-mortem volatile compounds that could be detected along with ethanol during the forensic ethanol analysis. The available literature (preferably reviews) on microbial metabolic pathways (enzymes, substrates, conditions) that are implicated in the formation of these volatiles has been reviewed. The microbial formation of the following volatiles is supported by the presented biochemical data: ethanol, acetaldehyde, acetone, 2-propanol, 1-propanol, 1-butanol, isobutanol, isoamyl alcohol, d-amyl alcohol, acetate, propionate, butyrate, isobutyrate and ethyl esters (mainly ethyl acetate). The extracted information was correlated with the existing forensic literature on the post-mortem detected volatiles. The significance of the microbial produced volatiles on the selection of an appropriate internal standard for the ethanol analysis has been considered. Finally, the possible contribution of the presence of volatiles in the interpretation of ethanol analysis results in post-mortem cases is discussed.
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Affiliation(s)
- Vassiliki A Boumba
- Department of Forensic Medicine and Toxicology, Medical School, University of Ioannina, 45110 Ioannina, Greece.
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Furuichi K, Katakura Y, Ninomiya K, Shioya S. Enhancement of 1,4-dihydroxy-2-naphthoic acid production by Propionibacterium freudenreichii ET-3 fed-batch culture. Appl Environ Microbiol 2007; 73:3137-43. [PMID: 17369348 PMCID: PMC1907098 DOI: 10.1128/aem.01307-06] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The production of 1,4-dihydroxy-2-naphthoic acid (DHNA) was investigated using a fed-batch culture of Propionibacterium freudenreichii ET-3. DHNA is a precursor of menaquinone (MK) and is transformed to MK by combination with an isoprenoid unit. We found that ET-3 stopped MK production and increased DHNA production in an anaerobic fed-batch culture by maintaining the lactose concentration at approximately zero. The maximum DHNA concentration observed in the anaerobic fed-batch culture was markedly higher than the maximum DHNA concentration observed in an anaerobic batch culture. Moreover, MK or DHNA production was affected by the lactose feeding rate; this suggests that lactose metabolism participates in the syntheses of these products. On the other hand, accumulation of propionate was found to inhibit DHNA production in the fed-batch culture. Based on the fact that ET-3 increases DHNA production in an aerobic culture by consuming propionate, we carried out a cultivation experiment in which an anaerobic fed-batch culture was switched to an anaerobic batch culture and found that the DHNA production was increased to a greater extent than the DHNA production in an anaerobic fed-batch culture. These results suggest that DHNA production by ET-3 is markedly influenced by carbon source limitation and the oxygen supply.
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Affiliation(s)
- Keisuke Furuichi
- Food Technology Research Institute, Meiji Dairies Corporation, 540 Naruda, Odawara, Kanagawa 250-0862, Japan.
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25
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Hervé C, Fondrevez M, Chéron A, Barloy-Hubler F, Jan G. Transcarboxylase mRNA: A marker which evidences P. freudenreichii survival and metabolic activity during its transit in the human gut. Int J Food Microbiol 2007; 113:303-14. [PMID: 17156879 DOI: 10.1016/j.ijfoodmicro.2006.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Accepted: 08/20/2006] [Indexed: 11/17/2022]
Abstract
Dairy propionibacteria have recently been considered as probiotics which may beneficially modulate the intestinal ecosystem. However, appropriate vectors (food matrices containing the probiotic) which preserve their viability and offer good tolerance towards digestive stresses need to be developed. In addition, the development of efficient non-invasive methods which specifically monitor Propionibacterium freudenreichii concentration and activity within the human gut is required. To address this latter need, an enzyme involved in propionic fermentation, transcarboxylase, was evaluated in this study as molecular marker in P. freudenreichii. In vitro, the three transcarboxylase subunits were shown to be encoded by an operon and their expression regulated. It occurred during propionic fermentation, ceased in starved cells and was not affected by digestive stresses. The 5S subunit gene of transcarboxylase allowed specific detection of P. freudenreichii by real time PCR in the complex human faecal microbiota. A dairy vector harbouring P. freudenreichii was developed and afforded elevated probiotic faecal concentrations in humans. In vivo, this PCR method allowed rapid quantification of faecal P. freudenreichii in agreement with the cultural method (cfu counting). Moreover, real time Reverse Transcription (RT) -PCR evidenced transcription of the 5S subunit gene during transit through the human digestive tract. This work constitutes a methodological advance for survival and activity evaluation in human trials of the probiotics belonging to the P. freudenreichii species. It strongly suggests that this bacterium not only survives but remains metabolically active in the human gut.
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Affiliation(s)
- Christophe Hervé
- Laboratoires Standa, UMR-STLO, 65 rue de Saint-Brieuc, 35042 RENNES cedex, France.
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26
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Furuichi K, Hojo KI, Katakura Y, Ninomiya K, Shioya S. Aerobic culture of Propionibacterium freudenreichii ET-3 can increase production ratio of 1,4-dihydroxy-2-naphthoic acid to menaquinone. J Biosci Bioeng 2006; 101:464-70. [PMID: 16935247 DOI: 10.1263/jbb.101.464] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2006] [Accepted: 03/10/2006] [Indexed: 11/17/2022]
Abstract
This is the first report on the production of both 1,4-dihydroxy-2-naphthoic acid (DHNA) and menaquinone by Propionibacterium freudenreichii ET-3. DHNA can be a stimulator of bifidogenic growth, and menaquinone has important roles in blood coagulation and bone metabolism. During anaerobic culture, DHNA and menaquinone concentrations reached 0.18 mM and 0.12 mM, respectively. The molar ratio between these products was approximately 3:2, which was not affected by culture pH and temperature over the ranges of 6.0-7.0 and 31-35 degrees C, respectively. As for organic acid, propionate and acetate accumulated at concentrations of 0.3 M and 0.15 M, respectively, and the propionate accumulation particularly inhibited further production of DHNA. To improve DHNA production, we switched from anaerobic condition to aerobic condition during the culture when lactose was depleted. DHNA concentration continued to increase even after lactose exhaustion, reaching 0.24 mM. In contrast to DHNA production, menaquinone production stopped after the switch to aerobic condition. The total molar production of DHNA and menaquinone was 0.3 mM irrespective of aerobic culture and anaerobic-aerobic switching culture. Therefore, the anaerobic-aerobic switching culture could increase the production ratio of DHNA to menaquinone. The DHNA concentration obtained from the anaerobic-aerobic switching culture was 1.3-fold higher than that in the anaerobic culture, because P. freudenreichii ET-3 utilized propionate accumulated in the medium via the reversed methylmalonyl CoA pathway under aerobic condition. The culture method proposed in this study could be applicable to industrial-scale fermentation using 1000 l of media, by which 0.23 mM DHNA was produced.
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Affiliation(s)
- Keisuke Furuichi
- Food Technology Research Institute, Meiji Dairies Corporation, 540 Naruda, Odawara, Kanagawa 250-0862, Japan
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27
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Benjelloun H, Lebeault JM. Effect of Environmental Factors in Aerobiosis and Anaerobiosis on the Growth and Activity of Propionic Acid Bacteria Evaluated by Pressure Measurement. Eng Life Sci 2005. [DOI: 10.1002/elsc.200520106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Benjelloun H, Rochex A, Lecouturier D, Dechemi S, Lebeault JM. An on-line technique for monitoring propionic acid fermentation. Appl Microbiol Biotechnol 2005; 68:316-21. [PMID: 15682290 DOI: 10.1007/s00253-005-1888-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Revised: 12/16/2004] [Accepted: 12/17/2004] [Indexed: 11/26/2022]
Abstract
An on-line technique, based on measuring the increase in pressure due to CO(2) release in a closed air-tight reactor, was used to evaluate the fermentation of lactate by propionibacteria. The method was applied to batch cultures of Propionibacterium shermanii grown in yeast extract/sodium lactate medium containing lactate as a carbon source under micro-aerophilic conditions. Gas pressure evolution was compared both with substrate consumption and metabolites production and with acidification and growth. Linear relationships were found between gas pressure variation, lactate consumption and propionate and acetate production. The technique also enabled the evaluation of total CO(2) produced, by taking account of pressure, oxygen and pH measurements. These results tend to show that this simple and rapid method could be useful to monitor propionic acid bacteria growth.
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Affiliation(s)
- Houda Benjelloun
- Laboratoire Génie des Procédés Industriels UMR CNRS 6067, Département Génie Chimique, Centre de Recherche de Royallieu, Université de Technologie de Compiègne, France
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Miescher S, Stierli MP, Teuber M, Meile L. Propionicin SM1, a bacteriocin from Propionibacterium jensenii DF1: isolation and characterization of the protein and its gene. Syst Appl Microbiol 2000; 23:174-84. [PMID: 10930068 DOI: 10.1016/s0723-2020(00)80002-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
We purified a bacteriocin from the cell-free supernatant of Propionibacterium jensenii DF1 isolated from Swiss raw milk, and named it propionicin SM1. The heat-stable protein was strongly bactericidal against P. jensenii DSM20274. On the basis of the N-terminal amino acid sequence of the purified protein, a degenerate oligonucleotide probe was designed to locate and clone the corresponding gene of P. jensenii DF1. It hybridized exclusively with the DF1l-resident plasmid pLME106, but not with chromosomal DNA. Sequencing of the 6.9-kb plasmid revealed the targeted amino acid sequence within an open reading frame (ORF4) of 207 amino acids (molecular mass, 22,865 Da). The corresponding gene was named ppnA. It encodes the prepeptide PpnA that is processed to the mature protein (19,942 Da) propionicin SM1. No sequence homology is detectable with known proteins. However, the proposed leader peptide sequence containing 27 amino acids has typical signal peptide features and shows good homology to the leader peptide of Usp45, a protein excreted from Lactococcus lactis (VAN ASSELDONK et al., 1993). Plasmid pLME106 contains at least 9 ORFs, some exhibiting significant homologies to plasmid-encoded functions from other bacteria. The highest identity values were found for ORF1 with the theta replicase (acc. no. U39878) of Brevibacterium linens (58.8%) and ORF6 with the recombinase/invertase (acc. no. AF060871) found in Rhodococcus rhodochrous (46.4%).
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Affiliation(s)
- S Miescher
- Laboratorium für Lebensmittelmikrobiologie, Institut für Lebensmittelwissenschaften, Eidgenössische Technische Hochschule, ETH-Zentrum, Zurich, Switzerland
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Deborde C, Boyaval P. Interactions between pyruvate and lactate metabolism in Propionibacterium freudenreichii subsp. shermanii: in vivo (13)C nuclear magnetic resonance studies. Appl Environ Microbiol 2000; 66:2012-20. [PMID: 10788375 PMCID: PMC101448 DOI: 10.1128/aem.66.5.2012-2020.2000] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In vivo (13)C nuclear magnetic resonance spectroscopy was used to elucidate the pathways and the regulation of pyruvate metabolism and pyruvate-lactate cometabolism noninvasively in living-cell suspensions of Propionibacterium freudenreichii subsp. shermanii. The most important result of this work concerns the modification of fluxes of pyruvate metabolism induced by the presence of lactate. Pyruvate was temporarily converted to lactate and alanine; the flux to acetate synthesis was maintained, but the flux to propionate synthesis was increased; and the reverse flux of the first part of the Wood-Werkman cycle, up to acetate synthesis, was decreased. Pyruvate was consumed at apparent initial rates of 148 and 90 micromol. min(-1). g(-1) (cell dry weight) when it was the sole substrate or cometabolized with lactate, respectively. Lactate was consumed at an apparent initial rate of 157 micromol. min(-1). g(-1) when it was cometabolized with pyruvate. P. shermanii used several pathways, namely, the Wood-Werkman cycle, synthesis of acetate and CO(2), succinate synthesis, gluconeogenesis, the tricarboxylic acid cycle, and alanine synthesis, to manage its pyruvate pool sharply. In both types of experiments, acetate synthesis and the Wood-Werkman cycle were the metabolic pathways used most.
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Affiliation(s)
- C Deborde
- INRA, Laboratoire de Recherche de Technologie Laitière, 35042 Rennes Cedex, France
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31
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Deborde C, Rolin DB, Boyaval P. In vivo 13C NMR study of the bidirectional reactions of the Wood-Werkman cycle and around the pyruvate node in Propionibacterium freudenreichii subsp. shermanii and Propionibacterium acidipropionici. Metab Eng 1999; 1:309-19. [PMID: 10937824 DOI: 10.1006/mben.1999.0124] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study used in vitro 13C NMR spectroscopy to directly examine bidirectional reactions of the Wood-Werkman cycle involved in central carbon metabolic pathways of dairy propionibacteria during pyruvate catabolism. The flow of [2-13C]pyruvate label was monitored on living cell suspensions of Propionibacterium freudenreichii subsp. shermanii and Propionibacterium acidipropionici under acidic conditions. P. shermanii and P. acidipropionici cells consumed pyruvate at apparent initial rates of 161 and 39 micromol min(-1) g(-1) (cell dry weight), respectively. The bidirectionality of reactions in the first part of the Wood-Werkman cycle was evident from the formation of intermediates such as [3-13C]pyruvate and [3-13C]malate and of products like [2-13C]acetate from [2-13C]pyruvate. For the first time alanine labeled on C2 and C3 and aspartate labeled on C2 and C3 were observed during [2-13C]pyruvate metabolism by propionibacteria. The kinetics of aspartate isotopic enrichment was evidence for its production from oxaloacetate via aspartate aminotransferase. Activities of a partial tricarboxylic acid pathway, acetate synthesis, succinate synthesis, gluconeogenesis, aspartate synthesis, and alanine synthesis pathways were evident from the experimental results.
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Affiliation(s)
- C Deborde
- INRA, Laboratoire de Recherches de Technologie Laitière, Rennes, France
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32
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Acetate oxidation through a modified citric acid cycle in Propionibacterium freudenreichii. Arch Microbiol 1995. [DOI: 10.1007/bf00305351] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Woskow SA, Glatz BA. Propionic Acid Production by a Propionic Acid-Tolerant Strain of
Propionibacterium acidipropionici
in Batch and Semicontinuous Fermentation. Appl Environ Microbiol 1991; 57:2821-8. [PMID: 16348561 PMCID: PMC183881 DOI: 10.1128/aem.57.10.2821-2828.1991] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A propionic acid-tolerant derivative of
Propionibacterium acidipropionici
P9 was obtained by serially transferring strain P9 through broth that contained increasing amounts of propionic acid. After 1 year of repeated transfers, a strain (designed P200910) capable of growth at higher propionic acid concentrations than P9 was obtained. An increase in the proportion of cellular straight-chain fatty acids and uncoupling of propionic acid production from growth were observed for strain P200910. Growth rate, sugar utilization, and acid production were monitored during batch and semicontinuous fermentations of semidefined medium and during batch fermentation of whey permeate for both strain P200910 and strain P9. The highest propionic acid concentration (47 g/liter) was produced by P200910 in a semicontinuous fermentation. Strain P200910 produced a higher ratio of propionic acid to acetic acid, utilized sugar more efficiently, and produced more propionic acid per gram of biomass than did its parent in all fermentations.
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Affiliation(s)
- S A Woskow
- Department of Food Science and Human Nutrition, Iowa State University, Ames, Iowa 50011
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Houwen FP, Dijkema C, Stams AJ, Zehnder AJ. Propionate metabolism in anaerobic bacteria; determination of carboxylation reactions with 13C-NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1991. [DOI: 10.1016/s0005-2728(05)80278-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Propionate acts as carboxylic group acceptor in aspartate fermentation by Propionibacterium freudenreichii. Arch Microbiol 1990. [DOI: 10.1007/bf00291273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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Crow VL. Polysaccharide Production by Propionibacteria during Lactose Fermentation. Appl Environ Microbiol 1988; 54:1892-5. [PMID: 16347702 PMCID: PMC202769 DOI: 10.1128/aem.54.7.1892-1895.1988] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fermentation products from 10 strains of propionibacteria accounted for only 72% (average value) of the lactose carbon utilized. The balance of the carbon was accounted for by the production of a polysaccharide containing methylpentose (the major component), glucose, and galactose. The presence of methylpentose explained the low ratios of propionate to acetate (<2:1).
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Affiliation(s)
- V L Crow
- New Zealand Dairy Research Institute, Palmerston North, New Zealand
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37
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Crow VL. Citrate Cycle Intermediates in the Metabolism of Aspartate and Lactate by
Propionibacterium freudenreichii
subsp.
shermanii. Appl Environ Microbiol 1987; 53:2600-2. [PMID: 16347477 PMCID: PMC204154 DOI: 10.1128/aem.53.10.2600-2602.1987] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Propionibacterium freudenreichii
subsp.
shermanii
metabolized 7 mol of aspartate to 6 mol of succinate, 4 mol of CO
2
, and 7 mol of ammonia. When lactate, sparged with 100% CO
2
, was fermented at pH 5.5, unexpectedly high ratios of propionate to acetate were obtained (i.e., 3.2 to 3.8:1). Citrate cycle intermediates may be involved in these fermentations.
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Affiliation(s)
- V L Crow
- New Zealand Dairy Research Institute, Palmerston North, New Zealand
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