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Peerzade IJ, Mutturi S, Halami PM. Improved production of RNA-inhibiting antimicrobial peptide by Bacillus licheniformis MCC 2514 facilitated by a genetic algorithm optimized medium. Bioprocess Biosyst Eng 2024; 47:683-695. [PMID: 38521865 DOI: 10.1007/s00449-024-02998-2] [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: 08/18/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
One of the significant challenges during the purification and characterization of antimicrobial peptides (AMPs) from Bacillus sp. is the interference of unutilized peptides from complex medium components during analytical procedures. In this study, a semi-synthetic medium was devised to overcome this challenge. Using a genetic algorithm, the production medium of AMP is optimized. The parent organism, Bacillus licheniformis MCC2514, produces AMP in very small quantities. This AMP is known to inhibit RNA biosynthesis. The findings revealed that lactose, NH4Cl and NaNO3 were crucial medium constituents for enhanced AMP synthesis. The potency of the AMP produced was studied using bacterium, Kocuria rhizophila ATCC 9341. The AMP produced from the optimized medium was eightfold higher than that produced from the unoptimized medium. Furthermore, activity was increased by 1.5-fold when cultivation conditions were standardized using the optimized medium. Later, AMP was produced in a 5 L bioreactor under controlled conditions, which led to similar results as those of shake-flask production. The mode of action of optimally produced AMP was confirmed to be inhibition of RNA biosynthesis. Here, we demonstrate that improved production of AMP is possible with the developed semi-synthetic medium recipe and could help further AMP production in an industrial setup.
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Affiliation(s)
- Ishrat Jahan Peerzade
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Sarma Mutturi
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India
| | - Prakash M Halami
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka, India.
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Sharma A, Sharma N, Gupta D, Lee HJ, Park YS. Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways. Comput Struct Biotechnol J 2022; 20:4771-4785. [PMID: 36147676 PMCID: PMC9465122 DOI: 10.1016/j.csbj.2022.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/30/2022] [Accepted: 08/13/2022] [Indexed: 11/03/2022] Open
Abstract
Comparative genomic analysis of four Leuconostoc strains was performed. Leuconostoc spp. shared genomic similarity, but their genetic content differed. Leuconostoc spp. showed different genes encoding CAZymes. Oligosaccharide’s utilization and folate biosynthesis pathways were investigated.
Leuconostoc is mostly found in food, plants, and dairy products. Due to their innate genomic features, such as the presence of carbohydrate-active enzymes, bacteriocins, and plasmids, Leuconostoc spp. have great biotechnological potential. In this study, four strains were isolated and identified as Leuconostoc mesenteroides SG315 (LA), L. citreum SG255 (LB), L. lactis CCK940 (LC), and L. lactis SBC001 (LD). Comparative analysis was performed using their draft genome sequences. Differences among the four strains were analyzed using the average nucleotide identity, dot plot, and multiple alignments of conserved genomic sequences. Functional profiling revealed 2134, 1917, 1751, and 1816 open reading frames; 2023, 1823, 1655, and 1699 protein-coding genes; 60, 57, 83, and 82 RNA-coding genes; and GC content of 37.5 %, 38.8 %, 43.3 %, and 43.2 %, in LA, LB, LC, and LD, respectively. The total number of genes encoding carbohydrate-active enzymes was 76 (LA), 73 (LB), 57 (LC), and 67 (LD). These results indicate that the four strains shared a large number of genes, but their gene content is different. Furthermore, most genes with unknown functions were observed in the prophage regions of the genome. This study also elucidated the oligosaccharide utilization and folate biosynthesis pathways in Leuconostoc spp. Taken together, our findings provide useful information on the genomic diversity of CAZymes in the four Leuconostoc strains and suggest that these species could be used for potent exploitation.
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Viability, Storage Stabilityand In Vitro Gastrointestinal Tolerance of Lactiplantibacillus plantarum Grown in Model Sugar Systems with Inulin and Fructooligosaccharide Supplementation. FERMENTATION 2021. [DOI: 10.3390/fermentation7040259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This study aims to investigate the effects of inulin and fructooligosaccharides (FOS) supplementation on the viability, storage stability, and in vitro gastrointestinal tolerance of Lactiplantibacillus plantarum in different sugar systems using 24 h growth and 10 days survival studies at 37 °C, inulin, and FOS (0%, 0.5%, 1%, 2%, 3% and 4%) supplementation in 2%, 3%, and 4% glucose, fructose, lactose, and sucrose systems. Based on the highest percentage increase in growth index, sucrose and lactose were more suitable sugar substrates for inulin and FOS supplementation. In survival studies, based on cell viability, inulin supplementation showed a better protective effect than FOS in 3% and 4% sucrose and lactose systems. Four selected sucrose and lactose systems supplemented with inulin and FOS were used in a 12-week storage stability study at 4 °C. Inulin (3%, 4%) and FOS (2%, 4%) supplementation in sucrose and lactose systems greatly enhanced the refrigerated storage stability of L. plantarum. In the gastrointestinal tolerance study, an increase in the bacterial survival rate (%) showed that the supplementation of FOS in lactose and sucrose systems improved the storage viability of L. plantarum. Both inulin and FOS supplementation in sucrose and lactose systems improved the hydrophobicity, auto-aggregation, co-aggregation ability of L. plantarum with Escherichia coli and Enterococcus faecalis.
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Han YY, Yue HY, Zhang XY, Lyu YM, Liu L, Voglmeir J. Construction and Evaluation of Peptide-Linked Lactobacillus brevis β-Galactosidase Heterodimers. Protein Pept Lett 2021; 28:221-228. [PMID: 32798366 DOI: 10.2174/0929866527666200813201242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/27/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND β-galactosidases are enzymes that are utilized to hydrolyze lactose into galactose and glucose, and are is widely used in the food industry. OBJECTIVE We describe the recombinant expression of an unstudied, heterodimeric β-galactosidase originating from Lactobacillus brevis ATCC 367 in Escherichia coli. Furthermore, six different constructs, in which the two protein subunits were fused with different peptide linkers, were also investigated. METHODS The heterodimeric subunits of the β-galactosidase were cloned in expressed in various expression constructs, by using either two vectors for the independent expression of each subunit, or using a single Duet vector for the co-expression of the two subunits. RESULTS The co-expression in two independent expression vectors only resulted in low β-galactosidase activities, whereas the co-expression in a single Duet vector of the independent and fused subunits increased the β-galactosidase activity significantly. The recombinant β-galactosidase showed comparable hydrolyzing properties towards lactose, N-acetyllactosamine, and pNP-β-D-galactoside. CONCLUSION The usability of the recombinant L. brevis β-galactosidase was further demonstrated by the hydrolysis of human, bovine, and goat milk samples. The herein presented fused β-galactosidase constructs may be of interest for analytical research as well as in food- and biotechnological applications.
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Affiliation(s)
- Yuan-Yuan Han
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hai-Yun Yue
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Yang Zhang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yong-Mei Lyu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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Tarrah A, Pakroo S, Lemos Junior WJF, Guerra AF, Corich V, Giacomini A. Complete Genome Sequence and Carbohydrates-Active EnZymes (CAZymes) Analysis of Lactobacillus paracasei DTA72, a Potential Probiotic Strain with Strong Capability to Use Inulin. Curr Microbiol 2020; 77:2867-2875. [PMID: 32623485 DOI: 10.1007/s00284-020-02089-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023]
Abstract
The whole genome sequence of Lactobacillus paracasei DTA72, isolated from healthy infant feces, is reported, along with the Carbohydrates-Active enZymes (CAZymes) analysis and an in silico safety assessment. Strain DTA72 had previously demonstrated some interesting potential probiotic features, such as a good resistance to gastrointestinal conditions and an anti-Listeria activity. The 3.1 Mb sequenced genome consists of 3116 protein-coding sequences distributed on 340 SEED subsystems. In the present study, we analyzed the fermentation capability of strain DTA72 on six different carbohydrate sources, namely, glucose, fructose, lactose, galactose, xylose, and inulin by using phenotypical and genomic approaches. Interestingly, L. paracasei DTA72 evidenced the best growth performances on inulin with a much shorter lag phase and higher number of cells at the stationary phase in comparison with all the sugars tested. The CAZyme analysis using the predicted amino acid sequences detected 80 enzymes, distributed into the five CAZymes classes. Moreover, the in silico analysis revealed the absence of blood hemolytic genes, transmissible antibiotic resistances, and plasmids in DTA72. The results described in this study, together with those previously reported and particularly the strong capability to utilize inulin as energy source, make DTA72 a very interesting potential probiotic strain to be considered for the production of synbiotic foods. The complete genome data have been deposited in GenBank under the accession number WUJH00000000.
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Affiliation(s)
- Armin Tarrah
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - Shadi Pakroo
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy
| | | | - Andre Fioravante Guerra
- Department of Food Engineering, Federal Center of Technological Education Celso Suckow da Fonseca, Valença, RJ, 27.600-000, Brazil
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy.
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animal and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy
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Kalathinathan P, Kodiveri Muthukaliannan G. A statistical approach for enhanced production of β-galactosidase from Paracoccus sp. and synthesis of galacto-oligosaccharides. Folia Microbiol (Praha) 2020; 65:811-822. [DOI: 10.1007/s12223-020-00791-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
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Lough F, Perry JD, Stanforth SP, Dean JR. Detection of exogenous VOCs as a novel in vitro diagnostic technique for the detection of pathogenic bacteria. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2016.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Lasrado LD, Gudipati M. Antioxidant property of synbiotic combination of Lactobacillus sp. and wheat bran xylo-oligosaccharides. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2015; 52:4551-7. [PMID: 26139924 PMCID: PMC4486558 DOI: 10.1007/s13197-014-1481-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/10/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022]
Abstract
Wheat bran water unextractable portion (WB-WUP) was subjected to xylanase treatment to obtain a mixture of xylo-oligosaccharides (XOS). XOS mixture was purified on charcoal-celite column and the individual oligosaccharides were separated on a Bio-Gel P-2 column. The sugar composition of the purified oligosaccharides was determined by GLC and their structure was deduced by ESI-MS and (1)H and (13)C NMR. The major oligosaccharides identified were xylobiose and xylotriose (consisting of arabinose). Five strains of lactobacilli (probiotics), XOS (prebiotics) and a combination of both (synbiotics) in milk (as medium) were monitored for antioxidant activity. DPPH radical scavenging activity (~70 %) as well as ferric reducing power (~80 mg/100 ml FeSO4eq) were significantly higher (p < 0.05) in all the synbiotic preparations compared to that of control. The present study indicated that the synbiotic preparations consisting of XOS and lactobacilli can be effectively used as dietary supplement.
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Affiliation(s)
- Lyned D. Lasrado
- Department of Biochemistry and Nutrition, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, 570020, Karnataka India
| | - Muralikrishna Gudipati
- Department of Biochemistry and Nutrition, Council of Scientific and Industrial Research-Central Food Technological Research Institute, Mysore, 570020, Karnataka India
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