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Nazir A, Shad M, Rashid N, Azim N, Sajjad M. Recombinant production and characterization of a metal ion-independent Lysophospholipase from a hyperthermophilic archaeon Pyrococcus abyssi DSM25543. Int J Biol Macromol 2024; 259:129345. [PMID: 38219941 DOI: 10.1016/j.ijbiomac.2024.129345] [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: 10/22/2023] [Revised: 12/13/2023] [Accepted: 01/07/2024] [Indexed: 01/16/2024]
Abstract
Genome sequence of Pyrococcus abyssi DSM25543 contains a coding sequence (PAB_RS01410) for α/β hydrolase (WP_010867387.1). Structural analysis revealed the presence of a consensus motif GXSXG and a highly conserved catalytic triad in the amino acid sequence of α/β hydrolase that were characteristic features of lysophospholipases. A putative lysophospholipase from P. abyssi with its potential applications in oil degumming and starch processing was heterologously produced in E. coli Rosetta (DE3) pLysS in soluble form followed by its purification and characterization. The recombinant enzyme was found to be active at temperature of 40-90 °C and pH 5.5-7.0. However, the enzyme exhibited its optimum activity at 65 °C and pH 6.5. None of the metal ions (Mn2+, Mg2+, Ni2+, Cu2+, Fe2+, Co2+, Zn2+ and Ca2+) being tested had stimulatory effect on lysophospholipase activity. Km and Vmax for hydrolysis of 4-nitrophenyl butyrate were calculated to be 1 ± 0.089 mM and 1637 ± 24.434 U/mg, respectively. It is the first report on the soluble production and characterization of recombinant lysophospholipase from P. abyssi which exhibits its lipolytic activity in the absence of divalent metal ions. Broad substrate specificity, activity and stability at elevated temperatures make recombinant lysophospholipase an ideal candidate for potential industrial applications.
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Affiliation(s)
- Arshia Nazir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mohsin Shad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naseema Azim
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Sajjad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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Altavas PJD, Amoranto MBC, Kim SH, Kang DK, Balolong MP, Dalmacio LMM. Safety assessment of five candidate probiotic lactobacilli using comparative genome analysis. Access Microbiol 2024; 6:000715.v4. [PMID: 38361650 PMCID: PMC10866033 DOI: 10.1099/acmi.0.000715.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Micro-organisms belonging to the Lactobacillus genus complex are often used for oral consumption and are generally considered safe but can exhibit pathogenicity in rare and specific cases. Therefore, screening and understanding genetic factors that may contribute to pathogenicity can yield valuable insights regarding probiotic safety. Limosilactobacillus mucosae LM1, Lactiplantibacillus plantarum SK151, Lactiplantibacillus plantarum BS25, Limosilactobacillus fermentum SK152 and Lactobacillus johnsonii PF01 are current probiotics of interest; however, their safety profiles have not been explored. The genome sequences of LM1, SK151, SK152 and PF01 were downloaded from the NCBI GenBank, while that of L. plantarum BS25 was newly sequenced. These genomes were then annotated using the Rapid Annotation using Subsystem Technology tool kit pipeline. Subsequently, a command line blast was performed against the Virulence Factor Database (VFDB) and the Comprehensive Antibiotic Resistance Database (CARD) to identify potential virulence factors and antibiotic resistance (AR) genes. Furthermore, ResFinder was used to detect acquired AR genes. The query against the VFDB identified genes that have a role in bacterial survivability, platelet aggregation, surface adhesion, biofilm formation and immunoregulation; and no acquired AR genes were detected using CARD and ResFinder. The study shows that the query strains exhibit genes identical to those present in pathogenic bacteria with the genes matched primarily having roles related to survival and surface adherence. Our results contribute to the overall strategies that can be employed in pre-clinical safety assessments of potential probiotics. Gene mining using whole-genome data, coupled with experimental validation, can be implemented in future probiotic safety assessment strategies.
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Affiliation(s)
- Patrick Josemaria d.R Altavas
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Mia Beatriz C. Amoranto
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Sang Hoon Kim
- Department of Animal Resources Science, College of Biotechnology and Bioengineering, Dankook University, Gyeonggi-do, Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, College of Biotechnology and Bioengineering, Dankook University, Gyeonggi-do, Republic of Korea
| | - Marilen P. Balolong
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Leslie Michelle M. Dalmacio
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines
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Wang A, Guan C, Wang T, Mu G, Tuo Y. Changes in Intracellular and Extracellular Metabolites of Mixed Lactobacillus Strains Enhance Inhibition of Pathogenic Bacterial Growth and Lipopolysaccharide-Induced Alleviation of RAW264.7 Cellular Inflammation. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10132-z. [PMID: 37632677 DOI: 10.1007/s12602-023-10132-z] [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] [Accepted: 07/27/2023] [Indexed: 08/28/2023]
Abstract
It is important to explore whether there are antagonistic and synergistic effects between different strains of Lactobacillus when developing mixed Lactobacillus strain products. In this study, we investigated the antagonistic and symbiotic effects of co-cultured Lactobacillus strains, as well as their amelioratory effects on lipopolysaccharide (LPS)-induced inflammation and oxidative stress in RAW264.7 cells. The Lactobacillus strains tested in this paper showed no antagonism. Co-culture of Lactiplantibacillus plantarum Y44 and L. plantarum AKS-WS9 was found to show inhibiting effects on the growth of Escherichia coli and Staphylococcus aureus. Additionally, the co-cultured Lactiplantibacillus plantarum Y44 and L. plantarum AKS-WS9 relieved inflammation in RAW264.7 cells induced by LPS by inhibiting the activation of NF-κB and P38 signaling pathways and down-regulating the expression of pro-inflammatory cytokines NO, ROS, iNOs and TNF-α. And the co-cultured Lactobacillus strains activated the Nrf2 signaling pathway in the LPS-induced RAW264.7 cells to promote the expression of antioxidant enzymes in response to oxidative stress. There was a difference in intracellular and extracellular metabolites between single or co-cultured Lactobacillus strains, and the co-cultured Lactobacillus strains significantly increased extracellular metabolites 4-chlorobenzaldehyde, psoromic acid, and 2-dodecylbenzenesulfonic acid and intracellular metabolites 9(S)-HODE, pyocyanin, and LysoPA. We inferred that the better antibacterial and anti-inflammatory ability of the co-cultured Lactobacillus strains were related to the changes in the metabolites of the co-cultured Lactobacillus strains. The co-cultured L. plantarum Y44 and L. plantarum AKS-WS9 strains exhibited better anti-inflammatory abilities and had the potential to alleviate the symptoms of inflammatory diseases as mixed probiotics.
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Affiliation(s)
- Arong Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
- Dalian Probiotics, Function Research Key Laboratory, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Chen Guan
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
- Dalian Probiotics, Function Research Key Laboratory, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Tieqi Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
- Dalian Probiotics, Function Research Key Laboratory, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Guangqing Mu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
- Dalian Probiotics, Function Research Key Laboratory, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Yanfeng Tuo
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, People's Republic of China.
- Dalian Probiotics, Function Research Key Laboratory, Dalian Polytechnic University, Dalian, 116034, People's Republic of China.
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Salvador PBU, Dalmacio LMM, Kim SH, Kang DK, Balolong MP. Immunomodulatory potential of four candidate probiotic Lactobacillus strains from plant and animal origin using comparative genomic analysis. Access Microbiol 2022; 3:000299. [PMID: 35024559 PMCID: PMC8749136 DOI: 10.1099/acmi.0.000299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
Probiotic strains from different origins have shown promise in recent decades for their health benefits, for example in promoting and regulating the immune system. The immunomodulatory potential of four Lactobacillus strains from animal and plant origins was evaluated in this paper based on their genomic information. Comparative genomic analysis was performed through genome alignment, average nucleotide identity (ANI) analysis and gene mining for putative immunomodulatory genes. The genomes of the four Lactobacillus strains show relative similarities in multiple regions, as observed in the genome alignment. However, ANI analysis showed that L. mucosae LM1 and L. fermentum SK152 are the most similar when considering their nucleotide sequences alone. Gene mining of putative immunomodulatory genes studied from L. plantarum WCFS1 yielded multiple results in the four potential probiotic strains, with L. plantarum SK151 showing the largest number of genes at around 74 hits, followed by L. johnsonii PF01 at 41 genes when adjusted for matches with at least 30 % identity. Looking at the immunomodulatory genes in each strain, L. plantarum SK151 and L. johnsonii PF01 may have wider activity, covering both immune activation and immune suppression, as compared to L. mucosae LM1 and L. fermentum SK152, which could be more effective in activating immune cells and the pro-inflammatory cascade rather than suppressing it. The similarities and differences between the four Lactobacillus species showed that there is no definitive trend based on the origin of isolation alone. Moreover, higher percentage identities between genomes do not directly correlate with higher similarities in potential activity, such as in immunomodulation. The immunomodulatory function of each of the four Lactobacillus strains should be observed and verified experimentally in the future, since some the activity of some genes may be strain-specific, which would not be identified through comparative genomics alone.
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Affiliation(s)
- Paul Benedic U Salvador
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Leslie Michelle M Dalmacio
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Ermita, Manila 1000, Philippines
| | - Sang Hoon Kim
- Department of Animal Resources Science, College of Biotechnology and Bioengineering, Dankook University, Republic of Korea
| | - Dae-Kyung Kang
- Department of Animal Resources Science, College of Biotechnology and Bioengineering, Dankook University, Republic of Korea
| | - Marilen P Balolong
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Ermita, Manila 1000, Philippines
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