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Fernando CM, Breaker RR. Bioinformatic prediction of proteins relevant to functions of the bacterial OLE ribonucleoprotein complex. mSphere 2024; 9:e0015924. [PMID: 38771028 DOI: 10.1128/msphere.00159-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
OLE (ornate, large, extremophilic) RNAs are members of a noncoding RNA class present in many Gram-positive, extremophilic bacteria. The large size, complex structure, and extensive sequence conservation of OLE RNAs are characteristics consistent with the hypothesis that they likely function as ribozymes. The OLE RNA representative from Halalkalibacterium halodurans is known to localize to the phospholipid membrane and requires at least three essential protein partners: OapA, OapB, and OapC. However, the precise biochemical functions of this unusual ribonucleoprotein (RNP) complex remain unknown. Genetic disruption of OLE RNA or its partners revealed that the complex is beneficial under diverse stress conditions. To search for additional links between OLE RNA and other cellular components, we used phylogenetic profiling to identify proteins that are either correlated or anticorrelated with the presence of OLE RNA in various bacterial species. This analysis revealed strong correlations between the essential protein-binding partners of OLE RNA and organisms that carry the ole gene. Similarly, proteins involved in sporulation are correlated, suggesting a potential role for the OLE RNP complex in spore formation. Intriguingly, the Mg2+ transporter MpfA is strongly anticorrelated with OLE RNA. Evidence indicates that MpfA is structurally related to OapA and therefore MpfA may serve as a functional replacement for some contributions otherwise performed by the OLE RNP complex in species that lack this device. Indeed, OLE RNAs might represent an ancient RNA class that enabled primitive organisms to sense and respond to major cellular stresses.IMPORTANCEOLE (ornate, large, extremophilic) RNAs were first reported nearly 20 years ago, and they represent one of the largest and most intricately folded noncoding RNA classes whose biochemical function remains to be established. Other RNAs with similar size, structural complexity, and extent of sequence conservation have proven to catalyze chemical transformations. Therefore, we speculate that OLE RNAs likewise operate as ribozymes and that they might catalyze a fundamental reaction that has persisted since the RNA World era-a time before the emergence of proteins in evolution. To seek additional clues regarding the function of OLE RNA, we undertook a computational effort to identify potential protein components of the OLE ribonucleoprotein (RNP) complex or other proteins that have functional links to this device. This analysis revealed known protein partners and several additional proteins that might be physically or functionally linked to the OLE RNP complex. Finally, we identified a Mg2+ transporter protein, MpfA, that strongly anticorrelates with the OLE RNP complex. This latter result suggests that MpfA might perform at least some functions that are like those carried out by the OLE RNP complex.
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Affiliation(s)
- Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
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2
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Rosazza T, Earl C, Eigentler L, Davidson FA, Stanley-Wall NR. Reciprocal sharing of extracellular proteases and extracellular matrix molecules facilitates Bacillus subtilis biofilm formation. Mol Microbiol 2024. [PMID: 38922753 DOI: 10.1111/mmi.15288] [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: 09/22/2023] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Extracellular proteases are a class of public good that support growth of Bacillus subtilis when nutrients are in a polymeric form. Bacillus subtilis biofilm matrix molecules are another class of public good that are needed for biofilm formation and are prone to exploitation. In this study, we investigated the role of extracellular proteases in B. subtilis biofilm formation and explored interactions between different public good producer strains across various conditions. We confirmed that extracellular proteases support biofilm formation even when glutamic acid provides a freely available nitrogen source. Removal of AprE from the NCIB 3610 secretome adversely affects colony biofilm architecture, while sole induction of WprA activity into an otherwise extracellular protease-free strain is sufficient to promote wrinkle development within the colony biofilm. We found that changing the nutrient source used to support growth affected B. subtilis biofilm structure, hydrophobicity and architecture. We propose that the different phenotypes observed may be due to increased protease dependency for growth when a polymorphic protein presents the sole nitrogen source. We however cannot exclude that the phenotypic changes are due to alternative matrix molecules being made. Co-culture of biofilm matrix and extracellular protease mutants can rescue biofilm structure, yet reliance on extracellular proteases for growth influences population coexistence dynamics. Our findings highlight the intricate interplay between these two classes of public goods, providing insights into microbial social dynamics during biofilm formation across different ecological niches.
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Affiliation(s)
- Thibault Rosazza
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chris Earl
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Fordyce A Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
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3
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Guan P, Fan S, Dong W, Wang X, Li Z, Song M, Suo B. Comparative genomic analysis and multilocus sequence typing of Staphylococcus aureus reveals candidate genes for low-temperature tolerance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171331. [PMID: 38428609 DOI: 10.1016/j.scitotenv.2024.171331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Staphylococcus aureus is one of the most frequently detected foodborne pathogens in cold chain foods. Worryingly, small colony variants (SCVs) can survive in cold environments for a long time and can revert to rapidly growing cells in suitable environments, causing serious food safety issues. This study investigated the underlying mechanism of SCV formation at low temperature (4 °C) via comparative genomics. Multilocus sequence typing (MLST) of 105 strains of S. aureus was divided into 9 sequence types. The ST352 strains exhibited the greatest tolerance to low temperature, with a mean reduction in survival rate of 10.34 % (p < 0.05). Comparative genomics revealed a total of 1941 core genes in the three S. aureus strains, and BB-1 had 468 specific genes, which were enriched mainly in translation, DNA recombination, DNA repair, metabolic pathways, two-component systems, and quorum sensing. Molecular docking analysis revealed that the binding of the RsbW protein to the SigB protein of BB-1 decreased due to base mutations in rsbW, while the binding to the RsbV protein was enhanced. In addition, the results of real-time quantitative PCR showed that the RsbV-RsbW/SigB system of BB-1 may play a role in the low-temperature survival of S. aureus and the formation of SCVs. These results suggest that genes specific to BB-1 may contribute to the mechanism of adaptation to low temperature and the formation of SCVs. This study helps elucidate the causes of SCV formation by S. aureus at low temperature at the molecular level and provides a basis for exploring the safety control of cold chain food environments.
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Affiliation(s)
- Peng Guan
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Shijia Fan
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Wenjing Dong
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xiaojie Wang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Zhen Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Miao Song
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China
| | - Biao Suo
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Staple Grain Processing, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; National R&D Center for Frozen Rice & Wheat Products Processing Technology, Henan Engineering Laboratory of Quick-Frozen Flour-Rice Food and Prepared Food, Henan Agricultural University, Zhengzhou, China.
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4
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Öktem A, Pranoto DA, van Dijl JM. Post-translational secretion stress regulation in Bacillus subtilis is controlled by intra- and extracellular proteases. N Biotechnol 2024; 79:71-81. [PMID: 38158017 DOI: 10.1016/j.nbt.2023.12.009] [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: 10/26/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The Gram-positive bacterium Bacillus subtilis is a prolific producer of industrial enzymes that are effectively harvested from the fermentation broth. However, the high capacity of B. subtilis for protein secretion has so far not been exploited to the full due to particular bottlenecks, including product degradation by extracellular proteases and counterproductive secretion stress responses. To unlock the Bacillus secretion pathway for difficult-to-produce proteins, various cellular interventions have been explored, including genome engineering. Our previous research has shown a superior performance of genome-reduced B. subtilis strains in the production of staphylococcal antigens compared to the parental strain 168. This was attributed, at least in part, to redirected secretion stress responses, including the presentation of elevated levels of the quality control proteases HtrA and HtrB that also catalyse protein folding. Here we show that this relates to the elimination of two homologous serine proteases, namely the cytosolic protease AprX and the extracellular protease AprE. This unprecedented posttranslational regulation of secretion stress effectors, like HtrA and HtrB, by the concerted action of cytosolic and extracellular proteases has important implications for the biotechnological application of microbial cell factories. In B. subtilis, this conclusion is underscored by extracellular degradation of the staphylococcal antigen IsaA by both AprX and AprE. Extracellular activity of the cytosolic protease AprX is remarkable since it shows that not only extracellular, but also intracellular proteases impact extracellular product levels. We therefore conclude that intracellular proteases represent new targets for improved recombinant protein production in microbial cell factories like B. subtilis.
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Affiliation(s)
- Ayşegül Öktem
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Dicky A Pranoto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands.
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5
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Zbylicki BR, Murphy CE, Petsche JA, Müh U, Dobrila HA, Ho TD, Daum MN, Pannullo AG, Weiss DS, Ellermeier CD. Identification of Clostridioides difficile mutants with increased daptomycin resistance. J Bacteriol 2024; 206:e0036823. [PMID: 38376203 PMCID: PMC10955854 DOI: 10.1128/jb.00368-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/20/2024] [Indexed: 02/21/2024] Open
Abstract
Daptomycin is a cyclic lipopeptide antibiotic used to treat infections caused by some Gram-positive bacteria. Daptomycin disrupts synthesis of the peptidoglycan (PG) cell wall by inserting into the cytoplasmic membrane and binding multiple forms of the undecaprenyl carrier lipid required for PG synthesis. Membrane insertion requires phosphatidylglycerol, so studies of daptomycin can provide insight into assembly and maintenance of the cytoplasmic membrane. Here, we studied the effects of daptomycin on Clostridioides difficile, the leading cause of healthcare-associated diarrhea. We observed that growth of C. difficile strain R20291 in the presence of sub-MIC levels of daptomycin resulted in a chaining phenotype, minicell formation, and lysis-phenotypes broadly consistent with perturbation of membranes and PG synthesis. We also selected for and characterized eight mutants with elevated daptomycin resistance. The mutations in these mutants were mapped to four genes: cdsA (cdr20291_2041), ftsH2 (cdr20291_3396), esrR (cdr20291_1187), and draS (cdr20291_2456). Of these four genes, only draS has been characterized previously. Follow-up studies indicate these mutations confer daptomycin resistance by two general mechanisms: reducing the amount of phosphatidylglycerol in the cytoplasmic membrane (cdsA) or altering the regulation of membrane processes (ftsH2, esrR, and draS). Thus, the mutants described here provide insights into phospholipid synthesis and identify signal transduction systems involved in cell envelope biogenesis and stress response in C. difficile. IMPORTANCE C. difficile is the leading cause of healthcare-associated diarrhea and is a threat to public health due to the risk of recurrent infections. Understanding biosynthesis of the atypical cell envelope of C. difficile may provide insight into novel drug targets to selectively inhibit C. difficile. Here, we identified mutations that increased daptomycin resistance and allowed us to better understand phospholipid synthesis, cell envelope biogenesis, and stress response in C. difficile.
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Affiliation(s)
- Brianne R. Zbylicki
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
| | - Claire E. Murphy
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
| | - Jennifer A. Petsche
- Interdisciplinary Graduate Program in Molecular Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ute Müh
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
| | - Horia A. Dobrila
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
| | - Theresa D. Ho
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
| | - Mikaela N. Daum
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
| | - Anthony G. Pannullo
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
| | - David S. Weiss
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
| | - Craig D. Ellermeier
- Department of Microbiology and Immunology, The University of Iowa, Iowa City, Iowa, USA
- Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
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6
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Khadka DB, Pahadi T, Aryal S, Karki DB. Partial purification and characterization of protease extracted from kinema. Heliyon 2024; 10:e27173. [PMID: 38463843 PMCID: PMC10923713 DOI: 10.1016/j.heliyon.2024.e27173] [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: 08/05/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024] Open
Abstract
Proteases are large group of highly demanded enzymes having huge application in food and pharmaceutical industries. Numerous sources, including plants, microorganisms, and animals, can be used to obtain protease. Due to its affordability and safety consideration, fermented foods have recently attracted more attention as a source of microbial protease. The present study aimed to extract protease from kinema, partially purify the extracted protease following dialysis after precipitation with ammonium sulfate, and determine general characteristics of protease. The kinema having highest proteolysis activity after three days of control fermentation (Temperature 30±2 °C, RH 66 ± 2%) was taken for the study. About 2.45 fold of purification with overall recovery of 63.21% was achieved after precipitation with ammonium sulfate at 30-70% saturation level followed by dialysis of crude extracted protease. The dialysed kinema protease had specific activity of 7.90 U/mg. The enzyme remained actively functional across a wider pH (5-9) and temperature (40-60 °C) range. SDS-PAGE and Zymogram confirmed the presence of three major active bands respectively of 29.04 kDa, 36.09 kDa and 46.35 kDa in the kinema protease extract. The enzyme kinetics data on casein, fitted to Mechaelis Mentens' plots showed the protease had Vmax of 1.001 U/ml with corresponding Km value of 0.825 mg/ml. Metal ions such as iron, mercury and aluminium showed the inhibition effect whereas presence of sodium, zinc, and calcium shows the activation effect on protease performance. The enzyme was active over various natural substrates; showing maximal activity on casein, and subsequent to bovine serum albumin, gelatin, hemoglobin and whey protein respectively. Furthermore, molecular weight distribution of the protease extract and activity inhibition with ethylenediaminetetraacetic acid and phenylmethylsulfonyl fluoride, suggesting the protease from kinema could be a metal dependent serine protease or mixture of them.
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Affiliation(s)
- Dambar Bahadur Khadka
- Central Department of Food Technology, Tribhuvan University, Dharan, Nepal
- Central Campus of Technology, Tribhuvan University, Dharan, Nepal
| | - Tikaram Pahadi
- Central Campus of Technology, Tribhuvan University, Dharan, Nepal
| | - Sunil Aryal
- Central Department of Food Technology, Tribhuvan University, Dharan, Nepal
| | - Dhan Bahadur Karki
- Central Department of Food Technology, Tribhuvan University, Dharan, Nepal
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7
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Lyon SE, Wencker FDR, Fernando CM, Harris KA, Breaker RR. Disruption of the bacterial OLE RNP complex impairs growth on alternative carbon sources. PNAS NEXUS 2024; 3:pgae075. [PMID: 38415217 PMCID: PMC10898510 DOI: 10.1093/pnasnexus/pgae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
Ornate, large, extremophilic (OLE) RNAs comprise a class of large noncoding RNAs in bacteria whose members form a membrane-associated ribonucleoprotein (RNP) complex. This complex facilitates cellular adaptation to diverse stresses such as exposure to cold, short-chain alcohols, and elevated Mg2+ concentrations. Here, we report additional phenotypes exhibited by Halalkalibacterium halodurans (formerly called Bacillus halodurans) strains lacking functional OLE RNP complexes. Genetic disruption of the complex causes restricted growth compared to wild-type cells when cultured in minimal media (MM) wherein glucose is replaced with alternative carbon/energy sources. Genetic suppressor selections conducted in glutamate MM yielded isolates that carry mutations in or near genes relevant to Mn2+ homeostasis (ykoY and mntB), phosphate homeostasis (phoR), and putative multidrug resistance (bmrCD). These functional links between OLE RNA, carbon/energy management, and other fundamental processes including protein secretion are consistent with the hypothesis that the OLE RNP complex is a major contributor to cellular adaptation to unfavorable growth conditions.
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Affiliation(s)
- Seth E Lyon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Freya D R Wencker
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
| | - Chrishan M Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Kimberly A Harris
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ronald R Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
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8
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Gu X, Zhao R, Li H, Dong X, Meng M, Li T, Zhao Q, Li Y. Patterns of the Nutrients and Metabolites in Apostichopus japonicus Fermented by Bacillus natto and Their Ability to Alleviate Acute Alcohol Intoxication. Foods 2024; 13:262. [PMID: 38254563 PMCID: PMC10814447 DOI: 10.3390/foods13020262] [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: 10/30/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
The aim of this study was to understand the changes in nutrient composition and differences in metabolites in Apostichopus japonicus fermented by Bacillus natto and their function in alleviating acute alcohol intoxication (AAI) through in vivo studies. The results showed no significant difference between the basic components of sea cucumber (SC) and fermented sea cucumber (FSC). The SC proteins were degraded after fermentation, and the amino acid content in FSC was significantly increased. The differentially abundant metabolites of SC and FSC were identified by LC-MS/MS. The contents of amino acid metabolites increased after fermentation, and arachidonic acid metabolism was promoted. The results demonstrated that FSC alleviated AAI by improving the activities of alcohol-metabolizing enzymes and antioxidant enzymes in the liver but did not alleviate the accumulation of triglycerides. Our results will provide beneficial information for the development and application of new products from FSC.
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Affiliation(s)
- Xingyu Gu
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China; (X.G.); (R.Z.); (H.L.); (X.D.); (M.M.)
| | - Ran Zhao
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China; (X.G.); (R.Z.); (H.L.); (X.D.); (M.M.)
- Liaoning Provincial Marine Healthy Food Engineering Research Centre, Dalian 116023, China
| | - Haiman Li
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China; (X.G.); (R.Z.); (H.L.); (X.D.); (M.M.)
- Dalian Key Laboratory of Marine Bioactive Substances Development and High Value Utilization, Dalian 116023, China
| | - Xinyu Dong
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China; (X.G.); (R.Z.); (H.L.); (X.D.); (M.M.)
- Liaoning Provincial Marine Healthy Food Engineering Research Centre, Dalian 116023, China
| | - Meishan Meng
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China; (X.G.); (R.Z.); (H.L.); (X.D.); (M.M.)
| | - Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Dalian 116650, China;
| | - Qiancheng Zhao
- Liaoning Provincial Marine Healthy Food Engineering Research Centre, Dalian 116023, China
- Dalian Key Laboratory of Marine Bioactive Substances Development and High Value Utilization, Dalian 116023, China
| | - Ying Li
- College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China; (X.G.); (R.Z.); (H.L.); (X.D.); (M.M.)
- Key Laboratory of Biotechnology and Bioresources Utilization, Dalian Minzu University, Dalian 116650, China;
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
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9
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Schilling T, Ferrero-Bordera B, Neef J, Maaβ S, Becher D, van Dijl JM. Let There Be Light: Genome Reduction Enables Bacillus subtilis to Produce Disulfide-Bonded Gaussia Luciferase. ACS Synth Biol 2023; 12:3656-3668. [PMID: 38011677 PMCID: PMC10729301 DOI: 10.1021/acssynbio.3c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Bacillus subtilis is a major workhorse for enzyme production in industrially relevant quantities. Compared to mammalian-based expression systems, B. subtilis presents intrinsic advantages, such as high growth rates, high space-time yield, unique protein secretion capabilities, and low maintenance costs. However, B. subtilis shows clear limitations in the production of biopharmaceuticals, especially proteins from eukaryotic origin that contain multiple disulfide bonds. In the present study, we deployed genome minimization, signal peptide screening, and coexpression of recombinant thiol oxidases as strategies to improve the ability of B. subtilis to secrete proteins with multiple disulfide bonds. Different genome-reduced strains served as the chassis for expressing the model protein Gaussia Luciferase (GLuc), which contains five disulfide bonds. These chassis lack extracellular proteases, prophages, and key sporulation genes. Importantly, compared to the reference strain with a full-size genome, the best-performing genome-minimized strain achieved over 3000-fold increased secretion of active GLuc while growing to lower cell densities. Our results show that high-level GLuc secretion relates, at least in part, to the absence of major extracellular proteases. In addition, we show that the thiol-disulfide oxidoreductase requirements for disulfide bonding have changed upon genome reduction. Altogether, our results highlight genome-engineered Bacillus strains as promising expression platforms for proteins with multiple disulfide bonds.
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Affiliation(s)
- Tobias Schilling
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB Groningen, The Netherlands
| | - Borja Ferrero-Bordera
- Institute
of Microbiology Department of Microbial Proteomics, University of Greifswald, D-17489 Greifswald, Germany
| | - Jolanda Neef
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB Groningen, The Netherlands
| | - Sandra Maaβ
- Institute
of Microbiology Department of Microbial Proteomics, University of Greifswald, D-17489 Greifswald, Germany
| | - Dörte Becher
- Institute
of Microbiology Department of Microbial Proteomics, University of Greifswald, D-17489 Greifswald, Germany
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University of Groningen,
University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700RB Groningen, The Netherlands
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10
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Kobayashi J, Wen R, Nishikawa T, Nunomura Y, Suzuki T, Sejima Y, Gokan T, Furukawa M, Yokota T, Osawa N, Sato Y, Nibu Y, Mizutani T, Oba M. Natto extract inhibits infection caused by the Aujeszky's disease virus in mice. Microbiol Immunol 2023; 67:514-519. [PMID: 37815203 DOI: 10.1111/1348-0421.13099] [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: 04/12/2023] [Revised: 08/24/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
Aujeszky's disease virus (ADV), also known as Suid alphaherpesvirus 1, which mainly infects swine, causes life-threatening neurological disorders. This disease is a serious global risk factor for economic losses in the swine industry. The development of new anti-ADV drugs is highly anticipated and required. Natto, a traditional Japanese fermented food made from soybeans, is a well-known health food. In our previous study, we confirmed that natto has the potential to inhibit viral infections by severe acute respiratory syndrome coronavirus 2 and bovine alphaherpesvirus 1 through their putative serine protease(s). In this study, we found that an agent(s) in natto functionally impaired ADV infection in cell culture assays. In addition, ADV treated with natto extract lost viral infectivity in the mice. We conducted an HPLC gel-filtration analysis of natto extract and molecular weight markers and confirmed that Fraction No. 10 had ADV-inactivating ability. Furthermore, the antiviral activity of Fraction No. 10 was inhibited by the serine protease inhibitor 4-(2-Aminoethyl) benzene sulfonyl fluoride hydrochloride (AEBSF). These results also suggest that Fraction No. 10, adjacent to the 12.5 kDa peak of the marker in natto extract, may inactivate ADV by proteolysis. Our findings provide new avenues of research for the prevention of Aujeszky's disease.
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Affiliation(s)
- Junya Kobayashi
- Center for Infectious Diseases of Epidemiology and Prevention Research (CEPiR), Tokyo University of Agriculture and Technology, Saiwai-cho, Tokyo, Japan
- Graduate School of Agriculture, Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Research Institute for Animal Science in Biochemistry and Toxicology (RIAS), Sagamihara, Kanagawa, Japan
| | - Rongduo Wen
- Center for Infectious Diseases of Epidemiology and Prevention Research (CEPiR), Tokyo University of Agriculture and Technology, Saiwai-cho, Tokyo, Japan
- Graduate School of Agriculture, Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Yuka Nunomura
- Center for Infectious Diseases of Epidemiology and Prevention Research (CEPiR), Tokyo University of Agriculture and Technology, Saiwai-cho, Tokyo, Japan
| | | | | | | | | | - Tomoko Yokota
- Center for Infectious Diseases of Epidemiology and Prevention Research (CEPiR), Tokyo University of Agriculture and Technology, Saiwai-cho, Tokyo, Japan
| | - Nanako Osawa
- Center for Infectious Diseases of Epidemiology and Prevention Research (CEPiR), Tokyo University of Agriculture and Technology, Saiwai-cho, Tokyo, Japan
- Graduate School of Agriculture, Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yoko Sato
- Center for Infectious Diseases of Epidemiology and Prevention Research (CEPiR), Tokyo University of Agriculture and Technology, Saiwai-cho, Tokyo, Japan
| | - Yutaka Nibu
- The University Research Administration Center (URAC), Tokyo University of Agriculture and Technology, Tokyo, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Tokai National Higher Education and Research System, Nagoya, Japan
| | - Tetsuya Mizutani
- Center for Infectious Diseases of Epidemiology and Prevention Research (CEPiR), Tokyo University of Agriculture and Technology, Saiwai-cho, Tokyo, Japan
- Graduate School of Agriculture, Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Mami Oba
- Center for Infectious Diseases of Epidemiology and Prevention Research (CEPiR), Tokyo University of Agriculture and Technology, Saiwai-cho, Tokyo, Japan
- Graduate School of Agriculture, Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
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11
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He B, Sachla AJ, Helmann JD. TerC proteins function during protein secretion to metalate exoenzymes. Nat Commun 2023; 14:6186. [PMID: 37794032 PMCID: PMC10550928 DOI: 10.1038/s41467-023-41896-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023] Open
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA
| | - Ankita J Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA.
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12
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Belcher LJ, Dewar AE, Hao C, Ghoul M, West SA. Signatures of kin selection in a natural population of the bacteria Bacillus subtilis. Evol Lett 2023; 7:315-330. [PMID: 37829498 PMCID: PMC10565896 DOI: 10.1093/evlett/qrad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 10/14/2023] Open
Abstract
Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.
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Affiliation(s)
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
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13
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Bareia T, Pollak S, Guler P, Puyesky S, Eldar A. Major distinctions between the two oligopeptide permease systems of Bacillus subtilis with respect to signaling, development and evolutionary divergence. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001382. [PMID: 37755230 PMCID: PMC10569065 DOI: 10.1099/mic.0.001382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/02/2023] [Indexed: 09/28/2023]
Abstract
Oligopeptide-permeases (Opps) are used by bacteria to import short peptides. In addition to their metabolic benefit, imported short peptides are used in many Gram-positive bacteria as signalling molecules of the RRNPP super-family of quorum-sensing systems, making Opps an integral part of cell–cell communication. In some Gram-positive bacteria there exist multiple Opps and the relative importance of those to RRNPP quorum sensing are not fully clear. Specifically, in Bacillus subtilis , the Gram-positive model species, there exist two homologous oligopeptide permeases named Opp and App. Previous work showed that the App system is mutated in lab strain 168 and its recovery partially complements an Opp mutation for several developmental processes. Yet, the nature of the impact of App on signalling and development in wild-type strains, where both permeases are active was not studied. Here we re-examine the impact of the two permease systems. We find that App has a minor contribution to biofilm formation, surfactin production and phage infection compared to the effect of Opp. This reduced effect is also reflected in its lower ability to import the signals of four different Rap-Phr RRNPP systems. Further analysis of the App system revealed that, unlike Opp, some App genes have undergone horizontal transfer, resulting in two distinct divergent alleles of this system in B. subtilis strains. We found that both alleles were substantially better adapted than the Opp system to import an exogenous RRNPP signal of the Bacillus cereus group PlcR-PapR system. In summary, we find that the App system has only a minor role in signalling but may still be crucial for the import of other peptides.
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Affiliation(s)
- Tasneem Bareia
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
- Present address: Department of Plant & Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Shaul Pollak
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
- Present address: Division of Microbial Ecology, Centre for Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Polina Guler
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Shani Puyesky
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
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14
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Xie CY, Li WJ, Feng H. Tuning transcription factor DegU for developing extracellular protease overproducer in Bacillus pumilus. Microb Cell Fact 2023; 22:163. [PMID: 37635205 PMCID: PMC10464342 DOI: 10.1186/s12934-023-02177-0] [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: 05/24/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND Global transcription machinery engineering (gTME) is an effective approach employed in strain engineering to rewire gene expression and reshape cellular metabolic fluxes at the transcriptional level. RESULTS In this study, we utilized gTME to engineer the positive transcription factor, DegU, in the regulation network of major alkaline protease, AprE, in Bacillus pumilus. To validate its functionality when incorporated into the chromosome, we performed several experiments. First, three negative transcription factors, SinR, Hpr, and AbrB, were deleted to promote AprE synthesis. Second, several hyper-active DegU mutants, designated as DegU(hy), were selected using the fluorescence colorimetric method with the host of the Bacillus subtilis ΔdegSU mutant. Third, we integrated a screened degU(L113F) sequence into the chromosome of the Δhpr mutant of B. pumilus SCU11 to replace the original degU gene using a CRISPR/Cas9 system. Finally, based on transcriptomic and molecular dynamic analysis, we interpreted the possible mechanism of high-yielding and found that the strain produced alkaline proteases 2.7 times higher than that of the control strain (B. pumilus SCU11) in LB medium. CONCLUSION Our findings serve as a proof-of-concept that tuning the global regulator is feasible and crucial for improving the production performance of B. pumilus. Additionally, our study established a paradigm for gene function research in strains that are difficult to handle.
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Affiliation(s)
- Chao-Ying Xie
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Wen-Jin Li
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Hong Feng
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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15
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Rosazza T, Eigentler L, Earl C, Davidson FA, Stanley‐Wall NR. Bacillus subtilis extracellular protease production incurs a context-dependent cost. Mol Microbiol 2023; 120:105-121. [PMID: 37380434 PMCID: PMC10952608 DOI: 10.1111/mmi.15110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/30/2023]
Abstract
Microbes encounter a wide range of polymeric nutrient sources in various environmental settings, which require processing to facilitate growth. Bacillus subtilis, a bacterium found in the rhizosphere and broader soil environment, is highly adaptable and resilient due to its ability to utilise diverse sources of carbon and nitrogen. Here, we explore the role of extracellular proteases in supporting growth and assess the cost associated with their production. We provide evidence of the essentiality of extracellular proteases when B. subtilis is provided with an abundant, but polymeric nutrient source and demonstrate the extracellular proteases as a shared public good that can operate over a distance. We show that B. subtilis is subjected to a public good dilemma, specifically in the context of growth sustained by the digestion of a polymeric food source. Furthermore, using mathematical simulations, we uncover that this selectively enforced dilemma is driven by the relative cost of producing the public good. Collectively, our findings reveal how bacteria can survive in environments that vary in terms of immediate nutrient accessibility and the consequent impact on the population composition. These findings enhance our fundamental understanding of how bacteria respond to diverse environments, which has importance to contexts ranging from survival in the soil to infection and pathogenesis scenarios.
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Affiliation(s)
- Thibault Rosazza
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
| | - Lukas Eigentler
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
- Mathematics, School of Science and EngineeringUniversity of DundeeDundeeUK
- Present address:
Evolutionary Biology DepartmentUniversität BielefeldKonsequenz 45Bielefeld33615Germany
| | - Chris Earl
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
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16
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Ngamnok T, Nimlamool W, Amador-Noguez D, Palaga T, Meerak J. Efficiency of Lactiplantibacillus plantarum JT-PN39 and Paenibacillus motobuensis JT-A29 for Fermented Coffee Applications and Fermented Coffee Characteristics. Foods 2023; 12:2894. [PMID: 37569163 PMCID: PMC10418488 DOI: 10.3390/foods12152894] [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: 06/07/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 08/13/2023] Open
Abstract
To develop a process for low-cost and ecologically friendly coffee fermentation, civet gut bacteria were isolated and screened to be used for fermentation. Among 223 isolates from civet feces, two bacteria exhibited strong protease, amylase, lipase, pectinase, and cellulase activities. By analyzing 16S rDNA phylogeny, those bacteria were identified to be Lactiplantibacillus plantarum JT-PN39 (LP) and Paenibacillus motobuensis JT-A29 (PM), where their potency (pure or mixed bacterial culture) for fermenting 5 L of arabica parchment coffee in 48-72 h was further determined. To characterize the role of bacteria in coffee fermentation, growth and pH were also determined. For mixed starter culture conditions, the growth of PM was not detected after 36 h of fermentation due to the low acid conditions generated by LP. Coffee quality was evaluated using a cupping test, and LP-fermented coffee expressed a higher cupping score, with a main fruity and sour flavor, and a dominant caramel-honey-like aroma. Antioxidant and anti-foodborne pathogenic bacteria activity, including total phenolic compounds of PM and LP fermented coffee extracts, was significantly higher than those of ordinary coffee. In addition, LP-fermented coffee expressed the highest antibacterial and antioxidant activities among the fermented coffee. The toxicity test was examined in the murine macrophage RAW 264.7 cell, and all fermented coffee revealed 80-90% cell variability, which means that the fermentation process does not generate any toxicity. In addition, qualifications of non-volatile and volatile compounds in fermented coffee were examined by LC-MS and GC-MS to discriminate the bacterial role during the process by PCA plot. The flavors of fermented coffee, including volatile and non-volatile compounds, were totally different between the non-fermented and fermented conditions. Moreover, the PCA plot showed slightly different flavors among fermentations with different starter cultures. For both the cupping test and biological activities, this study suggests that LP has potential for health benefits in coffee fermentation.
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Affiliation(s)
- Teerawat Ngamnok
- Master’s Degree Program in Applied Microbiology, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- The Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wutigri Nimlamool
- Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin—Madison, Madison, WI 53706, USA;
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Jomkhwan Meerak
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Excellence in Materials Science and Technology, Chiang Mai University, Chiang Mai 50200, Thailand
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17
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Keshapaga UR, Jathoth K, Singh SS, Gogada R, Burgula S. Characterization of high-yield Bacillus subtilis cysteine protease for diverse industrial applications. Braz J Microbiol 2023; 54:739-752. [PMID: 37157054 PMCID: PMC10235272 DOI: 10.1007/s42770-023-00992-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
Bacterial proteases have extensive applications in various fields of industrial microbiology. In this study, protease-producing organisms were screened on skimmed milk agar media using serial dilution. Through microbial biomass production, biochemical tests, protease-specific activity, and 16 s RNA gene sequencing, the isolates were identified as Bacillus subtilis and submitted to NCBI. The strain accession numbers were designated as A1 (MT903972), A2 (MT903996), A4 (MT904091), and A5 (MT904796). The strain A4 Bacillus subtilis showed highest protease-specific activity as 76,153.84 U/mg. A4 Bacillus subtilis was unaffected by Ca2+, Cu2+, Fe2+, Hg2+, Mg2+, Na, Fe2+, and Zn2+ but was inhibited by 80% by Mn2+ (5 mM). The protease activity was inhibited by up to 30% by iodoacetamide (5 mM). These findings confirm the enzyme to be a cysteine protease which was further confirmed by MALDI-TOF. The identified protease showed 71% sequence similarity with Bacillus subtilis cysteine protease. The crude cysteine protease significantly aided in fabric stain removal when added to a generic detergent. It also aided in the recovery of silver from used X-ray films and de-hairing of goat skin hides and showed decent application in meat tenderization. Thus, the isolated cysteine protease has high potential for industrial applications.
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Affiliation(s)
- Usha Rani Keshapaga
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Kalyani Jathoth
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Surya Satyanarayana Singh
- Department of Biochemistry , University College of Science, Osmania University , Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Raghu Gogada
- Department of Biochemistry , University College of Science, Osmania University , Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Sandeepta Burgula
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India.
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18
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He B, Sachla AJ, Helmann JD. TerC Proteins Function During Protein Secretion to Metalate Exoenzymes. RESEARCH SQUARE 2023:rs.3.rs-2860473. [PMID: 37292672 PMCID: PMC10246235 DOI: 10.21203/rs.3.rs-2860473/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - Ankita J. Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
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19
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He B, Sachla AJ, Helmann JD. TerC Proteins Function During Protein Secretion to Metalate Exoenzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536223. [PMID: 37090602 PMCID: PMC10120614 DOI: 10.1101/2023.04.10.536223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn 2+ -dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn 2+ -dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - Ankita J. Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, New York 14853-8101, USA
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20
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Bremer E, Calteau A, Danchin A, Harwood C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D, Zuniga A, Zuniga C. A model industrial workhorse:
Bacillus subtilis
strain 168 and its genome after a quarter of a century. Microb Biotechnol 2023; 16:1203-1231. [PMID: 37002859 DOI: 10.1111/1751-7915.14257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).
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Affiliation(s)
- Erhard Bremer
- Department of Biology, Laboratory for Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Philipps‐University Marburg Marburg Germany
| | - Alexandra Calteau
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine Hong Kong University Pokfulam SAR Hong Kong China
| | - Colin Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute Newcastle University Baddiley Clark Building Newcastle upon Tyne UK
| | - John D. Helmann
- Department of Microbiology Cornell University Ithaca New York USA
| | - Claudine Médigue
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Bernhard O. Palsson
- Department of Bioengineering University of California San Diego La Jolla USA
| | | | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut de Biologie François Jacob Université d'Évry, Université Paris‐Saclay, CNRS Évry France
| | - Abril Zuniga
- Department of Biology San Diego State University San Diego California USA
| | - Cristal Zuniga
- Bioinformatics and Medical Informatics Graduate Program San Diego State University San Diego California USA
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21
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Das M, Ghosh M. Screening, characterization, and kinetic studies of a serine alkaline protease from kitchen wastewater bacteria P2S1An and evaluation of its application in nutraceutical production. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2023; 95:e10848. [PMID: 36813755 DOI: 10.1002/wer.10848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 01/11/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
This present investigation aimed at characterizing the biochemical potential and kinetic study of the protease isolated from kitchen wastewater bacteria, P2S1An. The enzymatic activity was optimum when incubated for 96 h, at 30°C and pH 9.0. The enzymatic activity of the purified protease (PrA) was 10.47-folds that of crude protease (S1). PrA was about 35 kDa in molecular weight. The broad pH and thermal stability, chelators, surfactants and solvent tolerance, and favorable thermodynamics suggested the potentiality of the extracted protease PrA. Thermal activity and stability were enhanced in presence of 1-mM Ca2+ ion at high temperatures. The protease was a serine one as its activity was completely diminished in presence of 1-mM PMSF. The Vmax , Km , and Kcat /Km suggested stability and catalytic efficiency of the protease. PrA hydrolyzes fish protein with 26.61 ± 0.16% of peptide bond cleavage after 240 min, comparable to Alcalase 2.4L (27.13 ± 0.31%). PRACTITIONER POINTS: A serine alkaline protease PrA was extracted from kitchen wastewater bacteria Bacillus tropicus Y14. Protease PrA showed significant activity and stability in a wide temperature and pH range. Protease showed great stability towards additives like metal ions, solvents, surfactants, polyols, and inhibitors. Kinetic study showed that the protease PrA had a prominent affinity and catalytic efficiency for the substrates. PrA hydrolysed fish proteins into short bioactive peptides which signify its potential in the formation of functional food ingredients.
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Affiliation(s)
- Madhushrita Das
- Department of Chemical Technology, University of Calcutta, Kolkata, West Bengal, India
| | - Mahua Ghosh
- Department of Chemical Technology, University of Calcutta, Kolkata, West Bengal, India
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22
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Lee S, Seo S, Sul S, Jeong DW, Lee JH. Genomic insight into the salt tolerance and proteolytic activity of Bacillus subtilis. FEMS Microbiol Lett 2023; 370:fnad105. [PMID: 37816668 DOI: 10.1093/femsle/fnad105] [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: 08/03/2023] [Revised: 10/03/2023] [Accepted: 10/09/2023] [Indexed: 10/12/2023] Open
Abstract
We assessed the salt tolerance and proteolytic activity of 40 genome-published Bacillus subtilis strains isolated from fermented Korean foods to illuminate the genomic background behind the functionality of B. subtilis in high-salt fermentation. On the basis of the salt tolerance and phenotypic proteolytic activity of the 40 strains, we selected five strains exhibiting different phenotypic characteristics. Comparative genomic analyses of these five strains provided genomic insight into the salt tolerance and proteolytic activity of B. subtilis. Two-component system (TCS) genes annotated as ybdGJK and laterally acquired authentic ATP-binding cassette (ABC) transporter system genes of tandem repeat structure might contribute to increase salt tolerance. The additional possession of gene homologs for CAAX protease family proteins and components of Clp (caseinolytic protease) complex, ATP-dependent Clp proteolytic subunit ClpP and AAA+ (ATPases associated with diverse cellular Activities) family ATPases, might determine the proteolytic activity of B. subtilis. This study established the scientific foundation for the viability and functionality of B. subtilis in high-salt fermentation.
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Affiliation(s)
- Sugyeong Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
| | - Sumin Seo
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
| | - Sooyoung Sul
- Division of Sports Science, Kyonggi University, Suwon 16227, Republic of Korea
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women's University, Seoul 02748, Republic of Korea
| | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
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23
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Danchin A, Huang JD. SynBio 2.0, a new era for synthetic life: Neglected essential functions for resilience. Environ Microbiol 2023; 25:64-78. [PMID: 36045561 DOI: 10.1111/1462-2920.16140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Jian Dong Huang
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
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24
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Zhang R, Song X, Liu W, Xiang Q. Mixed fermentation of Chlorella pyrenoidosa and Bacillus velezensis SW-37 by optimization. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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25
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Secretome Analysis of the Plant Biostimulant Bacteria Strains Bacillus subtilis (EB2004S) and Lactobacillus helveticus (EL2006H) in Response to pH Changes. Int J Mol Sci 2022; 23:ijms232315144. [PMID: 36499471 PMCID: PMC9739546 DOI: 10.3390/ijms232315144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
It is well-known that there is a high frequency of plant-growth-promoting strains in Bacillus subtilis and that these can be effective under both stressful and stress-free conditions. There are very few studies of this activity in the case of Lactobacillus helveticus. In this study, the effects of pH on the secretome (proteins) in the cell-free supernatants of two bacterial strains were evaluated. The bacteria were cultured at pH 5, 7 and 8, and their secretome profiles were analyzed, with pH 7 (optimal growth pH) considered as the "control". The results showed that acidity (lower pH 5) diminishes the detectable production of most of the secretome proteins, whereas alkalinity (higher pH 8) increases the detectable protein production. At pH 5, five (5) new proteins were produced by L. helveticus, including class A sortase, fucose-binding lectin II, MucBP-domain-containing protein, SLAP-domain-containing protein and hypothetical protein LHEJCM1006_11110, whereas for B. subtilis, four (4) types of proteins were uniquely produced (p ≤ 0.05), including helicase-exonuclease AddAB subunit AddB, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase, a cluster of ABC-F family ATP-binding-cassette-domain-containing proteins and a cluster of excinuclease ABC (subunit B). At pH 8, Bacillus subtilis produced 56 unique proteins. Many of the detected proteins were involved in metabolic processes, whereas the others had unknown functions. The unique and new proteins with known and unknown functions suggest potential the acclimatization of the microbes to pH stress.
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