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Warrier I, Perry A, Hubbell SM, Eichelman M, van Opijnen T, Meyer MM. RNA cis-regulators are important for Streptococcus pneumoniae in vivo success. PLoS Genet 2024; 20:e1011188. [PMID: 38442125 PMCID: PMC10942264 DOI: 10.1371/journal.pgen.1011188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/15/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4. By evaluating native locus mutants of each regulator that result in constitutively active or repressed expression, we establish that growth defects in planktonic culture are associated with constitutive repression of gene expression, while constitutive activation of gene expression is rarely deleterious. In contrast, in mouse nasal carriage and pneumonia models, strains with either constitutively active and repressed gene expression are significantly less fit than matched control strains. Furthermore, two RNA-regulated pathways, FMN synthesis/transport and pyrimidine synthesis/transport display exceptional sensitivity to mis-regulation or constitutive gene repression in both planktonic culture and in vivo environments. Thus, despite lack of obvious phenotypes associated with constitutive gene expression in vitro, the fitness benefit conferred on bacteria via fine-tuned metabolic regulation through cis-acting regulatory RNAs is substantial in vivo, and therefore easily sufficient to drive the evolution and maintenance of diverse RNA regulatory mechanisms.
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Affiliation(s)
- Indu Warrier
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Ariana Perry
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Sara M. Hubbell
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Matthew Eichelman
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
| | - Tim van Opijnen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Boston Children’s Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michelle M. Meyer
- Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America
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2
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Langa S, Peirotén Á, Rodríguez S, Calzada J, Prieto-Paredes R, Curiel JA, Landete JM. Riboflavin bio-enrichment of soy beverage by selected roseoflavin-resistant and engineered lactic acid bacteria. Int J Food Microbiol 2024; 411:110547. [PMID: 38150774 DOI: 10.1016/j.ijfoodmicro.2023.110547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/27/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
Some lactic acid bacteria (LAB) have the ability to synthesize riboflavin, a trait linked to the presence of ribG, ribB, ribA and ribH genes located in the rib operon. Previous screening of riboflavin producers identified several LAB strains belonging to different species with this ability, but none of them surpassed 0.25 mg/L production of the vitamin. In this study, we explored two strategies to obtain riboflavin-overproducing strains: by roseoflavin selection of mutants, and by the transformation of selected strains with plasmids pNZ:TuR.rib or pNZ:TuB.rib containing the genes ribG, ribB, ribA and ribH from Lactococcus cremoris MG1363. The resulting riboflavin-overproducing strains were able to produce yields between 0.5 and 6 mg/L in culture media and several of them were selected for the fermentation of soy beverages. Riboflavin in bio-enriched soy beverages was evaluated by direct fluorescence measurement and high-performance liquid chromatography-fluorescence analysis. Soy beverages fermented with the recombinant strains Lactococcus cremoris ESI 277 pNZ:TuB.rib and Lactococcus lactis INIA 12 pNZ:TuR.rib showed the highest riboflavin yields (>5 mg/L) after 24 h fermentation. On the other hand, roseoflavin-resistant mutant Limosilactobacillus fermentum INIA P143R2 was able to enrich fermented soy beverages with 1.5 mg/L riboflavin. Riboflavin-overproducing LAB strains constitute a good option for riboflavin enrichment of soy beverages by fermentation and the commercialization of such beverages could be very useful to prevent riboflavin deficiency.
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Affiliation(s)
- Susana Langa
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain.
| | - Ángela Peirotén
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - Susana Rodríguez
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - Javier Calzada
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - Rubén Prieto-Paredes
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - José Antonio Curiel
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
| | - José María Landete
- Departamento de Tecnología de Alimentos, National Institute for Agricultural and Food Research and Technology (INIA-CSIC), Carretera de La Coruña Km 7.5, 28040 Madrid, Spain
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Russo P, Diez-Ozaeta I, Mangieri N, Tamame M, Spano G, Dueñas MT, López P, Mohedano ML. Biotechnological Potential and Safety Evaluation of Dextran- and Riboflavin-Producing Weisella cibaria Strains for Gluten-Free Baking. Foods 2023; 13:69. [PMID: 38201097 PMCID: PMC10778100 DOI: 10.3390/foods13010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Gluten consumption causes several immunological and non-immunological intolerances in susceptible individuals. In this study, the dextran-producing Weissella cibaria BAL3C-5 and its derivative, the riboflavin-overproducing strain BAL3C-5 C120T, together with a commercial bakery yeast, were used to ferment gluten-free (GF)-doughs obtained from corn and rice flours at two different concentrations and supplemented with either quinoa, buckwheat, or chickpea to obtain laboratory-scale GF bread. The levels of dextran, riboflavin, and total flavins were determined in the fermented and breads. Both strains grew in fermented doughs and contributed dextran, especially to those made with corn plus quinoa (~1 g/100 g). The highest riboflavin (350-150 µg/100 g) and total flavin (2.3-1.75 mg/100 g) levels were observed with BAL3C-5 C120T, though some differences were detected between the various doughs or breads, suggesting an impact of the type of flour used. The safety assessment confirmed the lack of pathogenic factors in the bacterial strains, such as hemolysin and gelatinase activity, as well as the genetic determinants for biogenic amine production. Some intrinsic resistance to antibiotics, including vancomycin and kanamycin, was found. These results indicated the microbiological safety of both W. cibaria strains and indicated their potential application in baking to produce GF bread.
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Affiliation(s)
- Pasquale Russo
- Department of Food Environmental and Nutritional Sciences (DeFENS), University of Milan, 20133 Milan, Italy; (P.R.); (N.M.)
| | - Iñaki Diez-Ozaeta
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain; (I.D.-O.); (P.L.)
- Departamento de Química Aplicada, Facultad de Química, Universidad del País Vasco (UPV/EHU), 20018 San Sebastián, Spain;
| | - Nicola Mangieri
- Department of Food Environmental and Nutritional Sciences (DeFENS), University of Milan, 20133 Milan, Italy; (P.R.); (N.M.)
| | - Mercedes Tamame
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Giuseppe Spano
- DAFNE Department, University of Foggia, 71122 Foggia, Italy;
| | - Maria Teresa Dueñas
- Departamento de Química Aplicada, Facultad de Química, Universidad del País Vasco (UPV/EHU), 20018 San Sebastián, Spain;
| | - Paloma López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain; (I.D.-O.); (P.L.)
| | - Mari Luz Mohedano
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain; (I.D.-O.); (P.L.)
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Diez-Ozaeta I, Martín-Loarte L, Mohedano ML, Tamame M, Ruiz-Masó JÁ, del Solar G, Dueñas MT, López P. A methodology for the selection and characterization of riboflavin-overproducing Weissella cibaria strains after treatment with roseoflavin. Front Microbiol 2023; 14:1154130. [PMID: 37089563 PMCID: PMC10116070 DOI: 10.3389/fmicb.2023.1154130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023] Open
Abstract
Fermentative processes by lactic acid bacteria can produce metabolites of interest to the health and food industries. Two examples are the production of B-group vitamins, and of prebiotic and immunomodulatory dextran-type exopolysaccharides. In this study, three riboflavin- and dextran-producing Weissella cibaria strains (BAL3C-5, BAL3C-7 and BAL3C-22) were used to develop a new method for selection and isolation of spontaneous riboflavin-overproducing W. cibaria mutants. This method was based on the selection of strains resistant to roseoflavin. The DNA sequencing of the FMN riboswitch of bacterial cell populations treated with various roseoflavin concentrations, revealed the existence of at least 10 spontaneous and random point mutations at this location. Folding and analysis of the mutated FMN riboswitches with the RNA fold program predicted that these mutations could result in a deregulation of the rib operon expression. When the roseoflavin-treated cultures were plated on medium supporting dextran synthesis, the most promising mutants were identified by the yellow color of their mucous colonies, exhibiting a ropy phenotype. After their isolation and recovery in liquid medium, the evaluation of their riboflavin production revealed that the mutant strains synthesized a wide range of riboflavin levels (from 0.80 to 6.50 mg/L) above the wild-type level (0.15 mg/L). Thus, this was a reliable method to select spontaneous riboflavin-overproducing and dextran-producing strains of W. cibaria. This species has not yet been used as a starter or adjunct culture, but this study reinforces the potential that it has for the food and health industry for the production of functional foods or as a probiotic. Furthermore, analysis of the influence of FMN present in the growth medium, on rib mRNA and riboflavin levels, revealed which mutant strains produce riboflavin without flavin regulation. Moreover, the BAL3C-5 C120T mutant was identified as the highest riboflavin-overproducer. Determination of its chromosomal DNA sequence and that of BAL3C-5, revealed a total identity between the 2 strains except for the C120T mutation at the FMN riboswitch. To our knowledge, this work is the first demonstration that only a single alteration in the genome of a lactic acid bacteria is required for a riboflavin-overproducing phenotype.
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Affiliation(s)
- Iñaki Diez-Ozaeta
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
- Departamento de Química Aplicada, Facultad de Química, Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Lucía Martín-Loarte
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Mari Luz Mohedano
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Mercedes Tamame
- Instituto de Biología Funcional y Genómica, (IBFG) CSIC-Universidad de Salamanca, Salamanca, Spain
| | - José Ángel Ruiz-Masó
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Gloria del Solar
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - María Teresa Dueñas
- Departamento de Química Aplicada, Facultad de Química, Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
- *Correspondence: María Teresa Dueñas,
| | - Paloma López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
- Paloma López,
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5
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Hernández-Alcántara AM, Chiva R, Mohedano ML, Russo P, Ruiz-Masó JÁ, del Solar G, Spano G, Tamame M, López P. Weissella cibaria riboflavin-overproducing and dextran-producing strains useful for the development of functional bread. Front Nutr 2022; 9:978831. [PMID: 36267909 PMCID: PMC9577222 DOI: 10.3389/fnut.2022.978831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
This work describes a method for deriving riboflavin overproducing strains of Weissella cibaria by exposing three strains (BAL3C-5, BAL3C-7, and BAL3C-22) isolated from dough to increasing concentrations of roseoflavin. By this procedure, we selected one mutant overproducing strain from each parental strain (BAL3C-5 B2, BAL3C-7 B2, and BAL3C-22 B2, respectively). Quantification of dextran and riboflavin produced by the parental and mutant strains in a defined medium lacking riboflavin and polysaccharides confirmed that riboflavin was only overproduced by the mutant strains, whereas dextran production was similar in both mutant and parental strains. The molecular basis of the riboflavin overproduction by the mutants was determined by nucleotide sequencing of their rib operons, which encode the enzymes of the riboflavin biosynthetic pathway. We detected a unique mutation in each of the overproducing strains. These mutations, which map in the sensor domain (aptamer) of a regulatory element (the so-called FMN riboswitch) present in the 5’ untranslated region of the rib operon mRNA, appear to be responsible for the riboflavin-overproducing phenotype of the BAL3C-5 B2, BAL3C-7 B2, and BAL3C-22 B2 mutant strains. Furthermore, the molecular basis of dextran production by the six W. cibaria strains has been characterized by (i) the sequencing of their dsr genes encoding dextransucrases, which synthesize dextran using sucrose as substrate, and (ii) the detection of active Dsr proteins by zymograms. Finally, the parental and mutant strains were analyzed for in situ production of riboflavin and dextran during experimental bread making. The results indicate that the mutant strains were able to produce experimental wheat breads biofortified with both riboflavin and dextran and, therefore, may be useful for the manufacture of functional commercial breads.
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Affiliation(s)
- Annel M. Hernández-Alcántara
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Rosana Chiva
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - María Luz Mohedano
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Pasquale Russo
- Department of Agriculture Food Natural Science Engineering, University of Foggia, Foggia, Italy
| | - José Ángel Ruiz-Masó
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Gloria del Solar
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Giuseppe Spano
- Department of Agriculture Food Natural Science Engineering, University of Foggia, Foggia, Italy
| | - Mercedes Tamame
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Paloma López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain,*Correspondence: Paloma López,
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Spacova I, Ahannach S, Breynaert A, Erreygers I, Wittouck S, Bron PA, Van Beeck W, Eilers T, Alloul A, Blansaer N, Vlaeminck SE, Hermans N, Lebeer S. Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods. Front Nutr 2022; 9:916607. [PMID: 35757245 PMCID: PMC9218631 DOI: 10.3389/fnut.2022.916607] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/19/2022] [Indexed: 12/19/2022] Open
Abstract
Riboflavin-producing lactic acid bacteria represent a promising and cost-effective strategy for food biofortification, but production levels are typically insufficient to support daily human requirements. In this study, we describe the novel human isolate Limosilactobacillus reuteri AMBV339 as a strong food biofortification candidate. This strain shows a high natural riboflavin (vitamin B2) overproduction of 18.36 μg/ml, biomass production up to 6 × 1010 colony-forming units/ml (in the typical range of model lactobacilli), and pH-lowering capacities to a pH as low as 4.03 in common plant-based (coconut, soy, and oat) and cow milk beverages when cultured up to 72 h at 37°C. These properties were especially pronounced in coconut beverage and butter milk fermentations, and were sustained in co-culture with the model starter Streptococcus thermophilus. Furthermore, L. reuteri AMBV339 grown in laboratory media or in a coconut beverage survived in gastric juice and in a simulated gastrointestinal dialysis model with colon phase (GIDM-colon system) inoculated with fecal material from a healthy volunteer. Passive transport of L. reuteri AMBV339-produced riboflavin occurred in the small intestinal and colon stage of the GIDM system, and active transport via intestinal epithelial Caco-2 monolayers was also demonstrated. L. reuteri AMBV339 did not cause fecal microbiome perturbations in the GIDM-colon system and inhibited enteric bacterial pathogens in vitro. Taken together, our data suggests that L. reuteri AMBV339 represents a promising candidate to provide riboflavin fortification of plant-based and dairy foods, and has a high application potential in the human gastrointestinal tract.
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Affiliation(s)
- Irina Spacova
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sarah Ahannach
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Annelies Breynaert
- Natural Products and Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Isabel Erreygers
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Peter A Bron
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Wannes Van Beeck
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Tom Eilers
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Abbas Alloul
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Naïm Blansaer
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Nina Hermans
- Natural Products and Food Research and Analysis (NatuRA), Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Research Group Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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