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Introduction: Levilactobacillus brevis CRL 2013, a plant-derived lactic acid bacterium (LAB) with immunomodulatory properties, has emerged as an efficient producer of γ-aminobutyric acid (GABA). Notably, not all LAB possess the ability to produce GABA, highlighting the importance of specific genetic and environmental conditions for GABA synthesis. This study aimed to elucidate the intriguing GABA-producing machinery of L. brevis CRL 2013 and support its potential for safe application through comprehensive genome analysis. Methods: A comprehensive genome analysis of L. brevis CRL 2013 was performed to identify the presence of antibiotic resistance genes, virulence markers, and genes associated with the glutamate decarboxylase system, which is essential for GABA biosynthesis. Then, an optimized chemically defined culture medium (CDM) was supplemented with monosodium glutamate (MSG) and yeast extract (YE) to analyze their influence on GABA production. Proteomic and transcriptional analyses were conducted to assess changes in protein and gene expression related to GABA production. Results: The absence of antibiotic resistance genes and virulence markers in the genome of L. brevis CRL 2013 supports its safety for potential probiotic applications. Genes encoding the glutamate decarboxylase system, including two gad genes (gadA and gadB) and the glutamate antiporter gene (gadC), were identified. The gadB gene is located adjacent to gadC, while gadA resides separately on the chromosome. The transcriptional regulator gadR was found upstream of gadC, with transcriptional analyses demonstrating cotranscription of gadR with gadC. Although MSG supplementation alone did not activate GABA synthesis, the addition of YE significantly enhanced GABA production in the optimized CDM containing glutamate. Proteomic analysis revealed minimal differences between MSG-supplemented and non-supplemented CDM cultures, whereas YE supplementation resulted in significant proteomic changes, including upregulation of GadB. Transcriptional analysis confirmed increased expression of gadB and gadR upon YE supplementation, supporting its role in activating GABA production. Conclusion: These findings provide valuable insights into the influence of nutrient composition on GABA production. Furthermore, they unveil the potential of L. brevis CRL 2013 as a safe, nonpathogenic strain with valuable biotechnological traits which can be further leveraged for its probiotic potential in the food industry.
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BACKGROUND Planctomycetes is a phylum of biofilm-forming bacteria with numerous biosynthetic gene clusters, offering a promising source of new bioactive secondary metabolites. However, the current generation of chemically defined media achieves only low biomass yields, hindering research on these species. We therefore developed a chemically defined medium for the model organism Planctopirus limnophila to increase biomass production. RESULTS We found that P. limnophila grows best with a 10 mM sodium phosphate buffer. The replacement of complex nitrogen sources with defined amino acid solutions did not inhibit growth. Screening for vitamin requirements revealed that only cyanocobalamin (B12) is needed for growth. We used response surface methodology to optimize the medium, resulting in concentrations of 10 g/L glucose, 34 mL/L Hutner's basal salts, 23.18 mM KNO3, 2.318 mM NH4Cl and 0.02 mg/L cyanocobalamin. The analysis of amino acid consumption allowed us to develop a customized amino acid solution lacking six of the amino acids present in Aminoplasmal 10%. Fed-batch cultivation in a bioreactor using the optimized medium achieved a final DOD600 of 46.8 ± 0.5 after 108 h, corresponding to a cell dry weight of 13.6 ± 0.7 g/L. CONCLUSIONS The optimized chemically defined medium allowed us to produce larger amounts of biomass more quickly than reported in earlier studies. Further research should focus on triggering P. limnophila biofilm formation to activate the gene clusters responsible for secondary metabolism
Assuntos
Planctomycetales/metabolismo , Planctomycetales/química , Aminoácidos/química , Biomassa , Planctomycetales/crescimento & desenvolvimento , Aminoácidos/metabolismoRESUMO
Extensive use of antibiotics has been the primary treatment for the Salmonid Rickettsial Septicemia, a salmonid disease caused by the bacterium Piscirickettsia salmonis. Occurrence of antibiotic resistance has been explored in various P. salmonis isolates using different assays; however, P. salmonis is a nutritionally demanding intracellular facultative pathogen; thus, assessing its antibiotic susceptibility with standardized and validated protocols is essential. In this work, we studied the pathogen response to antibiotics using a genomic, a transcriptomic, and a phenotypic approach. A new defined medium (CMMAB) was developed based on a metabolic model of P. salmonis. CMMAB was formulated to increase bacterial growth in nutrient-limited conditions and to be suitable for performing antibiotic susceptibility tests. Antibiotic resistance was evaluated based on a comprehensive search of antibiotic resistance genes (ARGs) from P. salmonis genomes. Minimum inhibitory concentration assays were conducted to test the pathogen susceptibility to antibiotics from drug categories with predicted ARGs. In all tested P. salmonis strains, resistance to erythromycin, ampicillin, penicillin G, streptomycin, spectinomycin, polymyxin B, ceftazidime, and trimethoprim was medium-dependent, showing resistance to higher antibiotic concentrations in the CMMAB medium. The mechanism for antibiotic resistance to ampicillin in the defined medium was further explored and was proven to be associated to a decrease in the bacterial central metabolism, including the TCA cycle, the pentose-phosphate pathway, energy production, and nucleotide metabolism, and it was not associated with decreased growth rate of the bacterium or with the expression of any predicted ARG. Our results suggest that nutrient scarcity plays a role in the bacterial antibiotic resistance, protecting against the detrimental effects of antibiotics, and thus, we propose that P. salmonis exhibits a metabolic resistance to ampicillin when growing in a nutrient-limited medium.
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Piscirickettsia salmonis is a facultative Gram-negative intracellular bacterium that produces piscirickettsiosis, disease that causes a high negative impact in salmonid cultures. The so-far-unidentified nutritional requirements have hindered its axenic culture at laboratory and industrial scales for the formulation of vaccines. The present study describes the development of a defined culture medium for P. salmonis. The culture medium was formulated through rational design involving auxotrophy test and statistical designs of experiments, considering the genome-scale metabolic reconstruction of P. salmonis reported by our group. The whole optimization process allowed for a twofold increase in biomass and a reduction of about 50% of the amino acids added to the culture medium. The final culture medium contains twelve amino acids, where glutamic acid, threonine and arginine were the main carbon and energy sources, supporting 1.65 g/L of biomass using 6.5 g/L of amino acids in the formulation. These results will contribute significantly to the development of new operational strategies to culture this bacterium for the production of vaccines.
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Piscirickettsia/crescimento & desenvolvimento , Vacinas/imunologia , Meios de Cultura , Vacinas/metabolismoRESUMO
Haemophilus influenzae b (Hib), an encapsulated Gram-negative coccobacillus, is one of the most common agents of meningitis worldwide. The Hib vaccine is included in the routine immunization schedule of several countries. The capsular polysaccharide, Poliribosyl-Ribitol-Phosphate (PRP), conjugated to a carrier protein is the antigen of the vaccine against Hib. Currently in industrial processes, Hib is cultivated in a soy peptone and yeast-extract based complex medium (MMP). This work aimed to evaluate whether a chemically defined medium could replace the MMP medium in the PRP production. The use of a defined media could offer several advantages in the whole process and would be of great interest to the industrial PRP production in vaccination programs. The PRP production ranged from 100 to 290 mg L-1 in the studied semi-defined and defined media. The formulation of several chemically defined media based on literature led to a promising composition as is the case of medium G which presented a production of 295 mg PRPL-1 with a lower biomass value of 4.8 UA (O.D.540 nm) when compared to MMP medium with 395 mg PRPL-1 and 6.45 UA respectively.
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The CRISPR-Cas9 system is a new tool that has been extensively used for genome editing. The system is composed of a Cas9 endonuclease, which has the function of cleaving DNA at a specific site, and a guide RNA (gRNA), which contains the sequence of the cleavage site that is the target of editing. Despite the great interest that has been generated because of the utility of Cas 9 as a molecular tool and a potential therapeutic protein, the production of the 158â¯kDa recombinant Cas9 protein derived from Streptococcus pyogenes remains a challenge. Here, we systematically evaluated the expression of recombinant Cas9 protein in two different E. coli strains in complex and defined media. The recombinant protein showed improved expression in E. coli BL21(DE3), while only traces of Cas9 protein could be detected in the Rosetta (DE3) strain as a result of much lower mRNA levels. The greatest Cas9 protein expression in defined media containing glucose was observed at an induction temperature of 30⯰C and with 8â¯h of post induction time using IPTG in shake flasks. The protein concentration obtained during a batch bioreactor culture was approximately 420.1â¯mg/L with 6â¯h of post induction time. The results demonstrated the possibility of efficient Cas9 protein expression in batch mode using E. coli BL21(DE3) and a simple defined medium and also showed the potential for further improvements that could facilitate large-scale production.
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Proteína 9 Associada à CRISPR/genética , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Técnicas de Cultura Celular por Lotes , Reatores Biológicos , Proteína 9 Associada à CRISPR/metabolismo , Meios de Cultura/química , Escherichia coli/crescimento & desenvolvimento , Escherichia coli/isolamento & purificação , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Expressão Gênica , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Especificidade da Espécie , Temperatura , Fatores de TempoRESUMO
Mycoplasmas belong to the Mollicutes class and possess low GC content and lack a cell wall, and also simplified metabolic pathways. Due to its reduced metabolic ability mycoplasmas are fastidious organisms growing with difficult under laboratory conditions. Its complex nutritional requirements render mycoplasmas to depend on external supplies of biosynthetic precursors. Aiming to develop and test defined media that could be used as a tool for Mycoplasma research, Mycoplasma hyopneumoniae and Mycoplasma hyorhinis were cultivated in a complex medium supplemented with serum (Friis broth) and in four different defined media (YUS, YUSm, CMRL and CMRL+, that was developed in the present study). The cell concentration of both Mycoplasma species was assessed, by flow cytometry. Cellular viability was also analyzed in all defined media, indicating the presence of viable mycoplasma cells. All the defined media tested were able to maintain cell concentrations and viability and, amongst them, CMRL+ was the most suitable. For both Mycoplasma species, only the CMRL+ media showed similar cell density when compared to the complex medium. The transcriptional response of M. hyopneumoniae in CMRL+ broth was assessed by RT-qPCR, and the transcriptional profile of 18 genes in three cultures conditions (standard, heat shock and oxidative stress) was analyzed demonstrating gene expression regulation in response to the medium composition and to the culture conditions tested. The medium developed enables the definition of mycoplasmal nutritional requirements and metabolic pathways as well as genetic analysis.
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Mycoplasma hyopneumoniae/genética , Mycoplasma hyorhinis/genética , Meios de Cultura/química , Expressão Gênica/genética , Regulação Bacteriana da Expressão Gênica/genética , Redes e Vias Metabólicas , Mycoplasma hyopneumoniae/crescimento & desenvolvimento , Mycoplasma hyorhinis/crescimento & desenvolvimento , Especificidade da EspécieRESUMO
Piscirickettsia salmonis is a fish bacterium that causes the disease piscirickettsiosis in salmonids. This pathology is partially controlled by vaccines. The lack of knowledge has hindered its culture on laboratory and industrial scale. The study describes the metabolic phenotype of P. salmonis in culture. This study presents the first genome-scale model (iPF215) of the LF-89 strain of P. salmonis, describing the central metabolic pathway, biosynthesis and molecule degradation and transport mechanisms. The model was adjusted with experiment data, allowing the identification of the capacities that were not predicted by the automatic annotation of the genome sequences. The iPF215 model is comprised of 417 metabolites, 445 reactions and 215 genes, was used to reproduce the growth of P. salmonis (µmax 0.052±0.005h-1). The metabolic reconstruction of the P. salmonis LF-89 strain obtained in this research provides a baseline that describes the metabolic capacities of the bacterium and is the basis for developing improvements to its cultivation for vaccine formulation.
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Aquicultura , Doenças dos Peixes/genética , Modelos Biológicos , Piscirickettsiaceae/genética , Salmonidae/microbiologia , Animais , Sequência de Bases , Infecções por PiscirickettsiaceaeRESUMO
Riboflavin (vitamin B2 ) is one of the B-group water-soluble vitamins and is essential for energy metabolism of the cell. The aim of this study was to determine factors that affect riboflavin production by Lactobacillus (L.) plantarum CRL 725 grown in a semi defined medium and evaluate the expression of its rib genes. The factors found to enhance riboflavin production in this medium were incubation at 30 °C, and the addition of specific medium constituents, such as casamino acids (10 g L-1 ), guanosine (0.04 g L-1 ), and sucrose as carbon source (20 g L-1 ). In these conditions, higher riboflavin concentrations were directly associated with significant increases in the expression of ribA, ribB, and ribC genes. The culture conditions defined in this work and its application to a roseoflavin resistant mutant of L. plantarum allowed for a sixfold increase in riboflavin concentrations in our semi-defined medium which were also significantly higher than those obtained previously using the same strain to ferment soymilk. These conditions should thus be evaluated to increase vitamin production in fermented foods.
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Genes Bacterianos , Lactobacillus plantarum/genética , Lactobacillus plantarum/metabolismo , Riboflavina/biossíntese , Aminoácidos/metabolismo , Proteínas de Bactérias/genética , Meios de Cultura/química , Fermentação , Guanosina/metabolismo , Lactobacillus plantarum/efeitos dos fármacos , Mutação , Nucleotidiltransferases/genética , Fosfotransferases (Aceptor do Grupo Álcool)/genética , Leite de Soja/metabolismo , Sacarose/metabolismoRESUMO
Neste trabalho avaliou-se a influência de fontes de carbono (FC) e composições de meio definido no crescimento celular e na produção do polissacarídeo PS14. Em batelada, testou-se como FC glicose, sacarose e frutose em diferentes concentrações. Testou-se também meios com ausência dos aminoácidos asparagina, ácido aspártico, fenilalanina, serina, alanina, treonina, triptofano, lisina e tirosina, das vitaminas/cofatores ácido fólico, piridoxamina, ácido p-aminobenzóico, b-NAD e riboflavina, além bem como da adição de maiores concentrações de aminoácidos identificados como importantes. Em cultivo contínuo foram avaliadas vazões específicas de alimentação (D) de 0,1h-1a 0,5h-1 e a influência das bases nitrogenadas. O meio com sacarose como FC, retirada dos aminoácidos e vitaminas citados e adição do dobro de glicina isoleucina, leucina, valina e o triplo de glutamina levou à maior produção de PS14 (441mg/L). Obteve-se a maior produtividade com D=0,4h-1e a maior quantidade de PS14 com adenina na concentração original no meio de cultura.
In this work we assessed the influence of different carbon sources (CS) and defined medium compositions on cell growth and polysaccharide PS14 production. In bath, glucose, sucrose and fructose were tested at different concentrations. Also, media were tested with absence of the amino acids: asparagine, aspartic acid, phenylalanine, serine, alanine, threonine, tryptophan, lysine, and tyrosine, and vitamins/cofactors: folic acid, pyridoxamine, p-aminobenzoic acid, riboflavin and b-NAD, besides the addition of higher concentration of amino acids identified as important. In continuous cultivation, dilution rates (D) from 0.1 h-1 to 0.5 h-1 were evaluated as well as the influence of nitrogenous bases. The medium containing sucrose as CS, absence of amino acids and vitamins and addition of twice glycine isoleucine, leucine, valine, and triple glutamine led to higher production of PS14 (441mg/L). D of 0.4 h-1 showed higher productivity and adenine in standard concentration produced greater amounts of PS14.