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Dinesen C, Vertot M, Jarmusch SA, Lozano-Andrade CN, Andersen AJC, Kovács ÁT. Subtilosin A production is influenced by surfactin levels in Bacillus subtilis. MICROLIFE 2025; 6:uqae029. [PMID: 39850962 PMCID: PMC11756287 DOI: 10.1093/femsml/uqae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 12/26/2024] [Accepted: 12/30/2024] [Indexed: 01/25/2025]
Abstract
Although not essential for their growth, the production of secondary metabolites increases the fitness of the producing microorganisms in their natural habitat by enhancing establishment, competition, and nutrient acquisition. The Gram-positive soil-dwelling bacterium, Bacillus subtilis, produces a variety of secondary metabolites. Here, we investigated the regulatory relationship between the non-ribosomal peptide surfactin and the sactipeptide bacteriocin subtilosin A. We discovered that B. subtilis mutants lacking surfactin production exhibited higher production of subtilosin A compared to their parental wild-type strain. Additionally, spatial visualization of B. subtilis production of metabolites demonstrated that surfactin secreted by a wild-type colony could suppress subtilosin A production in an adjacent mutant colony lacking surfactin production. Reporter assays were performed using mutants in specific transcriptional regulators, which confirmed the role of ResD as an activator of the subtilosin A encoding biosynthetic gene cluster (BGC), while the removal of Rok and AbrB repressors increased the expression of the BGC, which was further enhanced by additional deletion of surfactin, suggesting that a so-far-unidentified regulator might mediate the influence of surfactin on production of subtilosin A. Our study reveals a regulatory influence of one secondary metabolite on another, highlighting that the function of secondary metabolites could be more complex than its influence on other organisms and interactions among secondary metabolites could also contribute to their ecological significance.
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Affiliation(s)
- Caja Dinesen
- DTU Bioengineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Manca Vertot
- DTU Bioengineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Scott A Jarmusch
- DTU Bioengineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | | | - Aaron J C Andersen
- DTU Bioengineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Ákos T Kovács
- DTU Bioengineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
- Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
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2
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Jain PM, Nellikka A, Kammara R. Understanding bacteriocin heterologous expression: A review. Int J Biol Macromol 2024; 277:133916. [PMID: 39033897 DOI: 10.1016/j.ijbiomac.2024.133916] [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: 11/29/2023] [Revised: 07/12/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024]
Abstract
Bacteriocins are a diverse group of ribosomally synthesised antimicrobial peptides/proteins that play an important role in self-defence. They are widely used as bio-preservatives and effective substitutes for disease eradication. They can be used in conjunction with or as an alternative to antibiotics to minimize the risk of resistance development. There are remarkably few reports indicating resistance to bacteriocins. Although there are many research reports that emphasise heterologous expression of bacteriocin, there are no convincing reports on the significant role that intrinsic and extrinsic factors play in overexpression. A coordinated and cooperative expression system works in concert with multiple genetic elements encoding native proteins, immunoproteins, exporters, transporters and enzymes involved in the post-translational modification of bacteriocins. The simplest way could be to utilise the existing E. coli expression system, which is conventional, widely used for heterologous expression and has been further extended for bacteriocin expression. In this article, we will review the intrinsic and extrinsic factors, advantages, disadvantages and major problems associated with bacteriocin overexpression in E. coli. Finally, we recommend the most effective strategies as well as numerous bacteriocin expression systems from E. coli, Lactococcus, Kluveromyces lactis, Saccharomyces cerevisiae and Pichia pastoris for their suitability for successful overexpression.
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Affiliation(s)
- Priyanshi M Jain
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India
| | - Anagha Nellikka
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India
| | - Rajagopal Kammara
- Department of Microbiology and Fermentation Technology, CSIR-CFTRI, AcSIR, Mysore, India.
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3
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Lilge L, Kuipers OP. A two-step regulatory circuit involving Spo0A-AbrB activates mersacidin biosynthesis in Bacillus subtilis. Int J Antimicrob Agents 2024; 63:107155. [PMID: 38527561 DOI: 10.1016/j.ijantimicag.2024.107155] [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: 01/22/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 03/27/2024]
Abstract
Due to intramolecular ring structures, the ribosomally produced and post-translationally modified peptide mersacidin shows antimicrobial properties comparable to those of vancomycin without exhibiting cross-resistance. Although the principles of mersacidin biosynthesis are known, there is no information on the molecular control processes for the initial stimulation of mersacidin bioproduction. By using Bacillus subtilis for heterologous biosynthesis, a considerable amount of mersacidin could be produced without the mersacidin-specific immune system and the mersacidin-activating secretory protease. By using the established laboratory strain Bacillus subtilis 168 and strain 3NA, which is used for high cell density fermentation processes, in combination with the construction of reporter strains to determine the promoter strengths within the mersacidin core gene cluster, the molecular regulatory circuit of Spo0A, a master regulator of cell differentiation including sporulation initiation, and the global transcriptional regulator AbrB, which is involved in cell adaptation processes in the transient growth phase, was identified to control the initial stimulation of the mersacidin core gene cluster. In a second downstream regulatory step, the activator MrsR1, encoded in the core gene cluster, acts as a stimulatory element for mersacidin biosynthesis. These findings are important to understand the mechanisms linking environmental conditions and microbial responses with respect to the bioproduction of bioactive metabolites including antimicrobials such as mersacidin. This information will also support the construction of production strains for bioactive metabolites with antimicrobial properties.
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Affiliation(s)
- Lars Lilge
- Department of Molecular Genetics, University of Groningen, AG Groningen, The Netherlands; Department of Bioprocess Engineering, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany.
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, AG Groningen, The Netherlands
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4
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Precord T, Ramesh S, Dommaraju SR, Harris LA, Kille BL, Mitchell DA. Catalytic Site Proximity Profiling for Functional Unification of Sequence-Diverse Radical S-Adenosylmethionine Enzymes. ACS BIO & MED CHEM AU 2023; 3:240-251. [PMID: 37363077 PMCID: PMC10288494 DOI: 10.1021/acsbiomedchemau.2c00085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 06/28/2023]
Abstract
The radical S-adenosylmethionine (rSAM) superfamily has become a wellspring for discovering new enzyme chemistry, especially regarding ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, we report a compendium of nearly 15,000 rSAM proteins with high-confidence involvement in RiPP biosynthesis. While recent bioinformatics advances have unveiled the broad sequence space covered by rSAM proteins, the significant challenge of functional annotation remains unsolved. Through a combination of sequence analysis and protein structural predictions, we identified a set of catalytic site proximity residues with functional predictive power, especially among the diverse rSAM proteins that form sulfur-to-α carbon thioether (sactionine) linkages. As a case study, we report that an rSAM protein from Streptomyces sparsogenes (StsB) shares higher full-length similarity with MftC (mycofactocin biosynthesis) than any other characterized enzyme. However, a comparative analysis of StsB to known rSAM proteins using "catalytic site proximity" predicted that StsB would be distinct from MftC and instead form sactionine bonds. The prediction was confirmed by mass spectrometry, targeted mutagenesis, and chemical degradation. We further used "catalytic site proximity" analysis to identify six new sactipeptide groups undetectable by traditional genome-mining strategies. Additional catalytic site proximity profiling of cyclophane-forming rSAM proteins suggests that this approach will be more broadly applicable and enhance, if not outright correct, protein functional predictions based on traditional genomic enzymology principles.
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Affiliation(s)
- Timothy
W. Precord
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sangeetha Ramesh
- Department
of Microbiology, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shravan R. Dommaraju
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lonnie A. Harris
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Bryce L. Kille
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
- Department
of Microbiology, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Ishida K, Nakamura A, Kojima S. Crystal structure of the AlbEF complex involved in subtilosin A biosynthesis. Structure 2022; 30:1637-1646.e3. [DOI: 10.1016/j.str.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/12/2022] [Accepted: 09/30/2022] [Indexed: 12/05/2022]
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6
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
- Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
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7
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Helfrich M, Entian KD, Stein T. Antibiotic profiling of wild-type bacilli led to the discovery of new lanthipeptide subtilin-producing Bacillus spizizenii strains whose 16S rDNA sequences differ from the B. spizizenii typing strain. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:839-850. [PMID: 35902452 PMCID: PMC9526687 DOI: 10.1007/s10123-022-00266-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/12/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022]
Abstract
Two dozen field-collected Bacillus and a dozen Bacillus spizizenii wild-type strains from strain collections were selected on the basis of their antagonistic properties against the Gram-positive strain Micrococcus luteus. Based on their genetic and antibiotic profiles, they were characterized (subtilin encoding spaS gene sequences, mass spectrometric, and quantitative-reversed phase liquid chromatographic analyses, as well as the presence of the lanthionine cyclase protein SpaC by western blotting), seven novel producers of the lanthipeptide subtilin. Phylogenetic analyses of the subtilin-producing wild-type strains based on their 16S rRNA sequences showed that all seven strains could be classified as B. spizizenii: The field-collected strains HS and N5, as well as strains DSM 618, 1087, 6395, 6405, and 8439 from the German Collection of Microorganisms and Cell Cultures. To the best of our knowledge, all B. spizizenii strains described so far are characterized by the fact that they can produce a lanthipeptide of the subtilin family. Both the lanthipeptide structures and the organization and sequences of the 16S rRNA-encoding genes suggest a subdivision of B. spizizenii into subspecies: The subtilin-producing B. spizizenii strains are distinctly different from the entianin-producing B. spizizenii typing strain TU-B-10 T (DSM 15029 T).
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Affiliation(s)
- Markus Helfrich
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
- Jennewein Biotechnologie GmbH, Maarweg 32, 53619, Rheinbreitbach, Germany
| | - Karl-Dieter Entian
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
| | - Torsten Stein
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany.
- Chemistry & Molecular Biotechnology, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany.
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8
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Lu M, Chen Y, Li L, Ma Y, Tong Z, Guo D, Sun P, An D. Analysis and Evaluation of the Flagellin Activity of Bacillus amyloliquefaciens Ba168 Antimicrobial Proteins against Penicillium expansum. Molecules 2022; 27:4259. [PMID: 35807503 PMCID: PMC9268043 DOI: 10.3390/molecules27134259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/26/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
Blue mold caused by Penicillium expansum is one of the most common apple diseases, and it is becoming a serious threat in apple production. The strain Bacillus amyloliquefaciens Ba168 showed high levels of antimicrobial activity in our previous study. To analyze the antimicrobial protein of Ba168, a high-resolution LC-MS/MS proteomic analysis was performed. A total of 1155 proteins were identified from 5233 unique peptides. A total of 16 potential antimicrobial-activity-related proteins were identified; 10 of these proteins have direct antimicrobial effects, while 6 of these proteins are associated with the formation of antimicrobial substances. Then, an antifungal protein of Ba168 was isolated and purified by the sequential chromatography of DEAE Bio-sep FF anion exchange and Sephadex G-75. The single protein, named BP8-2, showed antifungal activity towards Penicillium expansum. The peptide mass fingerprinting of the protein band of BP8-2 had a high similarity with the amino acid sequences of flagellin protein. The results showed that BP8-2 significantly inhibited the growth of P. expansum and slowed the spread of apple blue mold. The results indicated that flagellin is one of the important antimicrobial substances from Ba168.
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Affiliation(s)
- Meihuan Lu
- Microbiology Institute of Shaanxi, Xi’an 710043, China; (M.L.); (L.L.); (Y.M.); (Z.T.)
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling 712100, China; (Y.C.); (D.G.)
| | - Yahan Chen
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling 712100, China; (Y.C.); (D.G.)
- College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China
| | - Lijun Li
- Microbiology Institute of Shaanxi, Xi’an 710043, China; (M.L.); (L.L.); (Y.M.); (Z.T.)
| | - Yinghui Ma
- Microbiology Institute of Shaanxi, Xi’an 710043, China; (M.L.); (L.L.); (Y.M.); (Z.T.)
| | - Zefang Tong
- Microbiology Institute of Shaanxi, Xi’an 710043, China; (M.L.); (L.L.); (Y.M.); (Z.T.)
| | - Dongsheng Guo
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling 712100, China; (Y.C.); (D.G.)
| | - Pingping Sun
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Derong An
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling 712100, China; (Y.C.); (D.G.)
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Alajlani MM. Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role. Sci Rep 2022; 12:10521. [PMID: 35732659 PMCID: PMC9217942 DOI: 10.1038/s41598-022-13804-y] [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: 12/29/2021] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
In a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.
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Affiliation(s)
- Muaaz Mutaz Alajlani
- Department of Pharmaceutical Biology/Pharmacognosy, Institute of Pharmacy, University of Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.
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10
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Alajlani MM. Characterization of subtilosin gene in wild type Bacillus spp. and possible physiological role. Sci Rep 2022; 12:10521. [DOI: https:/doi.org/10.1038/s41598-022-13804-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/27/2022] [Indexed: 08/08/2023] Open
Abstract
AbstractIn a designed study to screen for antimicrobial exhibiting bacteria using molecular aspects, Bacillus species were considered to investigate antibiotic biosynthesis genes. 28 bacterial strains and 3 induced mutants were screened for the presence of subtilosin gene (sbo) and subtilosin through PCR and Mass spectrometry respectively. Sbo gene was detected in 16 out of 28 Bacillus strains. The results from gene sequences deliberated by multiple sequence alignments revealed high-level homology to the sequences of the sbo-alb gene locus of B. subtilis 168 and the other limited reported strains. Hence, this report provided additional strains to support the idea of subtilosin gene predominance amongst Bacillus strains isolated from environment and to find different species containing homologous genes, furthermore the utilization of its conserved region as a means of identifying Bacillus spp. that produce subtilosin. This is the first report to confirm the detection of subtilosin production from B. amyloliquefaciens.
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Kaewnirat K, Chuaychob S, Chukamnerd A, Pomwised R, Surachat K, Phoo MTP, Phaothong C, Sakunrang C, Jeenkeawpiam K, Hortiwakul T, Charernmak B, Chusri S. In vitro Synergistic Activities of Fosfomycin in Combination with Other Antimicrobial Agents Against Carbapenem-Resistant Escherichia coli Harboring blaNDM-1 on the IncN2 Plasmid and a Study of the Genomic Characteristics of These Pathogens. Infect Drug Resist 2022; 15:1777-1791. [PMID: 35437346 PMCID: PMC9013254 DOI: 10.2147/idr.s357965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
Abstract
Purpose The spread of New Delhi metallo-β-lactamase (NDM) encoded by the blaNDM gene has been a global health crisis for many years. Most of blaNDM-harboring bacteria commonly carry various antimicrobial resistance (AMR) genes on their chromosomes or plasmids, leading to limited treatment options. Thus, we aimed to evaluate the synergistic effects of fosfomycin in combination with other antimicrobial agents against blaNDM-harboring carbapenem-resistant Escherichia coli (CREC) and to characterize the whole-genome and plasmid sequences of these pathogens. Methods Thirty-eight CREC isolates were collected from patients in the Medicine Ward, Songklanagarind Hospital, Thailand. The activity of fosfomycin in combination with other antimicrobial agents against CREC isolates harboring blaNDM on the plasmid was evaluated using the checkerboard method. In this method, the serial dilutions of two antibiotics were mixed with the cultured CREC, the mixtures were incubated, and FICI was calculated to interpret the synergistic activity of the combination. The whole-genome and particular plasmids of these pathogens were sequenced using next-generation sequencing. Sequence analysis, especially on antimicrobial resistance (AMR) genes, mobile-genetic elements (MGEs), and virulence genes was performed using many bioinformatics tools. Results Of the E. coli 38 isolates, only 3 isolates contained the blaNDM-1 gene, which is located on the IncN2 plasmid. The combinations of fosfomycin with aminoglycosides, colistin, tigecycline, sitafloxacin, and ciprofloxacin were synergies against blaNDM-1-harboring CREC isolates. Genomic analysis revealed that these isolates harbored many β-lactam resistance genes and other AMR genes that may confer resistance to aminoglycoside, fluoroquinolone, rifampicin, trimethoprim, sulfonamide, tetracycline, and macrolide. Also, various MGEs, especially the blaNDM-1-bearing IncN2 plasmid, were present in these isolates. Conclusion Our study demonstrated some synergistic effects of antimicrobial combination against CREC isolates harboring blaNDM-1 on the IncN2 plasmid. Also, our data on the whole-genome and plasmid sequences might be beneficial in the control of the spread of blaNDM-1-harboring CREC isolates. The linkages between blaNDM-1-carrying plasmid, patient information, and time of collection will be elucidated to track the horizontal gene transfer in the future.
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Affiliation(s)
- Kalyarat Kaewnirat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Surachat Chuaychob
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Komwit Surachat
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - May Thet Paing Phoo
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Chanitnart Phaothong
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Thanaporn Hortiwakul
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Boonsri Charernmak
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Sarunyou Chusri
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Correspondence: Sarunyou Chusri, Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand, Tel +66 8 973 40446, Email
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12
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Abstract
Bacillus subtilis is a soil bacterium that can form biofilms, which are communities of cells encased by an extracellular matrix. In these complex communities, cells perform numerous metabolic processes and undergo differentiation into functionally distinct phenotypes as a survival strategy. Because biofilms are often studied in bulk, it remains unclear how metabolite production spatially correlates with B. subtilis phenotypes within biofilm structures. In many cases, we still do not know where these biological processes are occurring in the biofilm. Here, we developed a method to analyze the localization of molecules within sagittal thin sections of B. subtilis biofilms using high-resolution mass spectrometry imaging. We correlated the organization of specific molecules to the localization of well-studied B. subtilis phenotypic reporters determined by confocal laser scanning fluorescence microscopy within analogous biofilm thin sections. The correlations between these two data sets suggest the role of surfactin as a signal for extracellular matrix gene expression in the biofilm periphery and the role of bacillibactin as an iron-scavenging molecule. Taken together, this method will help us generate hypotheses to discover relationships between metabolites and phenotypic cell states in B. subtilis and other biofilm-forming bacteria. IMPORTANCE Bacterial biofilms are complex and heterogeneous structures. Cells within biofilms carry out numerous metabolic processes in a nuanced and organized manner, details of which are still being discovered. Here, we used multimodal imaging to analyze B. subtilis biofilm processes at the metabolic and gene expression levels in biofilm sagittal thin sections. Often, imaging techniques analyze only the top of the surface of the biofilm and miss the multifaceted interactions that occur deep within the biofilm. Our analysis of the sagittal planes of B. subtilis biofilms revealed the distributions of metabolic processes throughout the depths of these structures and allowed us to draw correlations between metabolites and phenotypically important subpopulations of B. subtilis cells. This technique provides a platform to generate hypotheses about the role of specific molecules and their relationships to B. subtilis subpopulations of cells.
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Schoenborn AA, Yannarell SM, Wallace ED, Clapper H, Weinstein IC, Shank EA. Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation. J Bacteriol 2021; 203:e0033721. [PMID: 34460312 PMCID: PMC8544424 DOI: 10.1128/jb.00337-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria. IMPORTANCE Bacterially produced specialized metabolites are frequently studied for their potential use as antibiotics and antifungals. However, a growing body of work has suggested that the antagonistic potential of specialized metabolites is not their only function. Here, using Bacillus subtilis as our model bacterium, we demonstrated that developmental processes such as biofilm formation and sporulation are tightly linked to specialized metabolite gene expression and production. Additionally, under our differentiation-inducing conditions, six out of the nine specialized metabolites investigated behave as intraspecific signals that impact B. subtilis physiology and influence biofilm formation and sporulation. Our work supports the viewpoint that specialized metabolites have a clear role as cell-cell signaling molecules within differentiated populations of bacteria.
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Affiliation(s)
- Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E. Diane Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haley Clapper
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ilon C. Weinstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elizabeth A. Shank
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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14
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Cao L, Do T, Link AJ. Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs). J Ind Microbiol Biotechnol 2021; 48:6121428. [PMID: 33928382 PMCID: PMC8183687 DOI: 10.1093/jimb/kuab005] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/22/2021] [Indexed: 12/19/2022]
Abstract
Natural products remain a critical source of medicines and drug leads. One of the most rapidly growing superclasses of natural products is RiPPs: ribosomally synthesized and posttranslationally modified peptides. RiPPs have rich and diverse bioactivities. This review highlights examples of the molecular mechanisms of action that underly those bioactivities. Particular emphasis is placed on RiPP/target interactions for which there is structural information. This detailed mechanism of action work is critical toward the development of RiPPs as therapeutics and can also be used to prioritize hits in RiPP genome mining studies.
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Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Truc Do
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - A James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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15
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Bacteriocinogenic Bacillus spp. Isolated from Korean Fermented Cabbage (Kimchi)—Beneficial or Hazardous? FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7020056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacillus velezensis ST03 and ST32, Bacillus amyloliquefaciens ST06 and ST109, and Bacillus subtilis ST08 were isolated from artisanal-produced kimchi and were identified based on 16S rRNA partial sequencing. DNA obtained from the investigated bacilli generated positive results for lichenicidin, iturin, subtilosin, and surfactin on a strain-specific basis. The strains were found to produce antimicrobial metabolites with activity levels ranging between 800 and 1600 AU/mL on a strain-specific basis, as determined against Listeria monocytogenes ATCC15313. Moreover, all tested strains in this study were still active after treatment with proteolytic enzymes, even with reduced inhibition zones compared to the controls, pointing to additional antimicrobial activity possibly related to a non-proteinaceous molecular structure. Most probably these strains may express surfactin as an additional factor in their complex antimicrobial activity. B. amyloliquefaciens ST09 and B. velezensis ST03 and ST32 were characterized as positive for β-hemolysis. B. subtilis ST08 was shown to be positive for hblC and nheC and B. amyloliquefaciens ST109 for nheB. B. amyloliquefaciens ST109 generated positive results for gelatinase activity. The ability of the studied Bacillus strains to metabolize different carbohydrate sources was done based on the API50CHB test, while the enzyme production profile was recorded by the APIZym kit. All studied strains were positive producers for biogenic amines production. Studied Bacillus spp. strains were resistant to some of the evaluated antibiotics, tested according to recommendations of CLSI and EFSA.
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Prajapati B, Bernal-Cabas M, López-Álvarez M, Schaffer M, Bartel J, Rath H, Steil L, Becher D, Völker U, Mäder U, van Dijl JM. Double trouble: Bacillus depends on a functional Tat machinery to avoid severe oxidative stress and starvation upon entry into a NaCl-depleted environment. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118914. [PMID: 33245978 DOI: 10.1016/j.bbamcr.2020.118914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/08/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022]
Abstract
The widely conserved twin-arginine translocases (Tat) allow the transport of fully folded cofactor-containing proteins across biological membranes. In doing so, these translocases serve different biological functions ranging from energy conversion to cell division. In the Gram-positive soil bacterium Bacillus subtilis, the Tat machinery is essential for effective growth in media lacking iron or NaCl. It was previously shown that this phenomenon relates to the Tat-dependent export of the heme-containing peroxidase EfeB, which converts Fe2+ to Fe3+ at the expense of hydrogen peroxide. However, the reasons why the majority of tat mutant bacteria perish upon dilution in NaCl-deprived medium and how, after several hours, a sub-population adapts to this condition was unknown. Here we show that, upon growth in the absence of NaCl, the bacteria face two major problems, namely severe oxidative stress at the membrane and starvation leading to death. The tat mutant cells can overcome these challenges if they are fed with arginine, which implies that severe arginine depletion is a major cause of death and resumed arginine synthesis permits their survival. Altogether, our findings show that the Tat system of B. subtilis is needed to preclude severe oxidative stress and starvation upon sudden drops in the environmental Na+ concentration as caused by flooding or rain.
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Affiliation(s)
- Bimal Prajapati
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Margarita Bernal-Cabas
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Marina López-Álvarez
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Marc Schaffer
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Jürgen Bartel
- University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics, Greifswald, Germany
| | - Hermann Rath
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Leif Steil
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Dörte Becher
- University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics, Greifswald, Germany
| | - Uwe Völker
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Ulrike Mäder
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany.
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands.
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Jiao D, Liu Y, Liu Y, Zeng R, Hou X, Nie G, Sun L, Fang Z. Preparation of phosphatidylcholine nanovesicles containing bacteriocin CAMT2 and their anti-listerial activity. Food Chem 2020; 314:126244. [PMID: 31982854 DOI: 10.1016/j.foodchem.2020.126244] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/10/2019] [Accepted: 01/16/2020] [Indexed: 10/25/2022]
Abstract
A novel bacteriocin CAMT2, produced by Bacillus amyloliquefaciens ZJHD3-06, has potential as a natural biopreservative for the control of food-borne spoilage and pathogenic bacteria. To avoid interaction of CAMT2 with components of food that may adversely impact its antibacterial activity, CAMT2 was encapsulated into nanovesicles prepared from soybean phosphatidylcholine. The encapsulation of CAMT2 exhibited a limited impact on functional structure and crystallinity of bacteriocin CAMT2, but a high anti-listerial activity in agar, and increase its stability in food at refrigeration temperature (4 °C). The results also showed that both encapsulated and free CAMT2 had good anti-listerial effect in skim milk at refrigeration temperature. However, encapsulated CAMT2 performed better than free CAMT2 against Listeria in whole milk. These results showed that nano-encapsulation is an effective method of protecting bacteriocin from fat in milk and retaining its antimicrobial efficacy.
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Affiliation(s)
- Dongdong Jiao
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ying Liu
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ying Liu
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Ruchun Zeng
- School of Physics and Telecommunication Engineering, Yulin Normal University, Yulin 537000, China; Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin 537000, China
| | - Xiaoqin Hou
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang 524088, China
| | - Guochao Nie
- School of Physics and Telecommunication Engineering, Yulin Normal University, Yulin 537000, China; Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Yulin 537000, China.
| | - Lijun Sun
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhijia Fang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Marine Food, Key Laboratory of Advanced Processing of Aquatic Products of Guangdong Higher Education Institution, Guangdong Ocean University, Zhanjiang 524088, China.
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18
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Abstract
Bacterial biofilms are ubiquitous in natural environments and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis, very little is known about the role of metabolism in this complex developmental process. To address this important knowledge gap, we performed a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. Here, we report a widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. This report serves as a unique hypothesis-generating resource for future studies on bacterial biofilm physiology. Outside the biofilm research area, this work should also prove relevant to any investigators interested in microbial physiology and metabolism. Biofilms are structured communities of tightly associated cells that constitute the predominant state of bacterial growth in natural and human-made environments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilis has been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, we performed a time-resolved analysis of the metabolic changes associated with pellicle biofilm formation and development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. We report surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hitherto unrecognized as biofilm associated. For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was largely controlled at the transcriptional level. Our results also provide insights into the transcription factors and regulatory networks involved in this complex metabolic remodeling. Following upon these results, we demonstrated that acetoin production via acetolactate synthase is essential for robust biofilm growth and has the dual role of conserving redox balance and maintaining extracellular pH. This report represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilis biofilm development that will serve as a useful road map for future studies on biofilm physiology.
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19
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Stein T. Oxygen-Limiting Growth Conditions and Deletion of the Transition State Regulator Protein Abrb in Bacillus subtilis 6633 Result in an Increase in Subtilosin Production and a Decrease in Subtilin Production. Probiotics Antimicrob Proteins 2019; 12:725-731. [DOI: 10.1007/s12602-019-09547-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Morrison MD, Fajardo-Cavazos P, Nicholson WL. Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station. NPJ Microgravity 2019; 5:1. [PMID: 30623021 PMCID: PMC6323116 DOI: 10.1038/s41526-018-0061-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/06/2018] [Indexed: 11/12/2022] Open
Abstract
The human spaceflight environment is notable for the unique factor of microgravity, which exerts numerous physiologic effects on macroscopic organisms, but how this environment may affect single-celled microbes is less clear. In an effort to understand how the microbial transcriptome responds to the unique environment of spaceflight, the model Gram-positive bacterium Bacillus subtilis was flown on two separate missions to the International Space Station in experiments dubbed BRIC-21 and BRIC-23. Cells were grown to late-exponential/early stationary phase, frozen, then returned to Earth for RNA-seq analysis in parallel with matched ground control samples. A total of 91 genes were significantly differentially expressed in both experiments; 55 exhibiting higher transcript levels in flight samples and 36 showing higher transcript levels in ground control samples. Genes upregulated in flight samples notably included those involved in biofilm formation, biotin and arginine biosynthesis, siderophores, manganese transport, toxin production and resistance, and sporulation inhibition. Genes preferentially upregulated in ground control samples notably included those responding to oxygen limitation, e.g., fermentation, anaerobic respiration, subtilosin biosynthesis, and anaerobic regulatory genes. The results indicated differences in oxygen availability between flight and ground control samples, likely due to differences in cell sedimentation and the toroidal shape assumed by the liquid cultures in microgravity.
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Affiliation(s)
- Michael D. Morrison
- Department of Microbiology and Cell Science, University of Florida, Merritt Island, FL USA
| | | | - Wayne L. Nicholson
- Department of Microbiology and Cell Science, University of Florida, Merritt Island, FL USA
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21
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Yu WQ, Zheng GP, Qiu DW, Yan FC, Liu WZ, Liu WX. Draft genome sequence, disease-resistance genes, and phenotype of a Paenibacillus terrae strain (NK3-4) with the potential to control plant diseases. Genome 2018; 61:725-734. [PMID: 30184440 DOI: 10.1139/gen-2018-0113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Paenibacillus terrae NK3-4 is a plant growth-promoting rhizobacterium that may be useful for controlling plant diseases. We conducted a genomic analysis and identified the genes mediating antimicrobial functions. Additionally, an extracellular antifungal protein component was isolated and identified. The draft genome sequence was assembled into 54 contigs, with 5 458 568 bp and a G+C content of 47%. Moreover, 4 690 015 bp encoded 5090 proteins, 7 rRNAs, and 54 tRNAs. Forty-four genes involved in antimicrobial functions were detected. They mainly encode 19 non-ribosomal peptide synthetases (NRPSs); one polyketide synthase/NRPSs hybrid enzyme; four Zn-dependent metalloproteases; three antilisterial bacteriocin subtilosin biosynthesis proteins (AlbA); four serine proteases; five pectate lyases; three beta-glucanases; and four 1,4-beta-xylanases. These include four novel NRPSs that have not been found in any species of Paenibacillus. Furthermore, five proteins exhibiting antifungal activity were identified from the antifungal extracellular protein component based on MS/MS and the strain NK3-4 predicted protein library. On the basis of these features, we propose that strain NK3-4 represents a promising biocontrol agent for protecting plant from diseases. The draft genome sequence described herein may provide the genetic basis for the characterization of the molecular mechanisms underlying the biocontrol functions. It may also facilitate the development of rational strategies for improving the strain.
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Affiliation(s)
- Wen Qing Yu
- a College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China.,b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China.,c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
| | - Gui Ping Zheng
- a College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - De Wen Qiu
- c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
| | - Feng Chao Yan
- b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China
| | - Wen Zhi Liu
- b Heilongjiang Academy of Land Reclamation, Haerbin, Heilongjiang Province, 150038, China
| | - Wan Xue Liu
- c Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100094, China
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Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in Bacillus licheniformis. Appl Environ Microbiol 2018; 84:AEM.00262-18. [PMID: 29703732 DOI: 10.1128/aem.00262-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/11/2018] [Indexed: 01/27/2023] Open
Abstract
The cyclodipeptide pulcherriminic acid synthesized by Bacillus licheniformis is an iron chelator that antagonizes certain pathogens by removing iron from the environment. But since the insoluble iron-pulcherriminic acid complex cannot act as an iron carrier as siderophores do, excessive synthesized pulcherriminic acid causes iron starvation for the producer cells. At present, the regulation of pulcherriminic acid synthesis and the mechanism by which B. licheniformis strikes a balance between biocontrol and self-protection from excessive iron removal remain unclear. This study provides insights into the regulatory network and explains the mechanism of pulcherriminic acid biosynthesis. The yvmC-cypX synthetic gene cluster was directly negatively regulated by three regulators: AbrB, YvnA, and YvmB. Within the regulatory network, YvnA expression was repressed not only by AbrB but also by iron-limiting environments, while YvmB expression was repressed by YvnA. The transporter gene yvmA is repressed by YvmB and is required for pulcherriminic acid secretion. The biosynthesis window is determined by the combined concentration of the three regulators in an iron-rich environment. Under iron-limiting conditions, cells close the pulcherriminic acid synthesis pathway by downregulating YvnA expression.IMPORTANCE The cyclodipeptides are widespread in nature and exhibit a broad variety of biological and pharmacological activities. The cyclodipeptide scaffold is synthesized by nonribosomal peptide synthetases (NRPSs) and cyclodipeptide synthases (CDPSs). At present, it is clear that CDPSs use aminoacyl tRNAs as substrates to synthesize the two peptide bonds, and the pulcherriminic acid synthase YvmC is a member of the eight identified CDPSs. However, little is known about the regulation of cyclodipeptide synthesis and secretion. In this study, we show that AbrB, which is considered to be the main regulator of NRPS-dependent pathways, is also involved in the regulation of CDPS genes. However, AbrB is not the decisive factor for pulcherriminic acid synthesis, as the expression of YvnA determines the fate of pulcherriminic acid synthesis. With this information on how CDPS gene transcription is regulated, a clearer understanding of cyclodipeptide synthesis can be developed for B. licheniformis Similar approaches may be used to augment our knowledge on CDPSs in other bacteria.
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Zhang RY, Thapa P, Espiritu MJ, Menon V, Bingham JP. From nature to creation: Going around in circles, the art of peptide cyclization. Bioorg Med Chem 2018; 26:1135-1150. [DOI: 10.1016/j.bmc.2017.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 02/02/2023]
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24
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Duarte AFDS, Ceotto-Vigoder H, Barrias ES, Souto-Padrón TCBS, Nes IF, Bastos MDCDF. Hyicin 4244, the first sactibiotic described in staphylococci, exhibits an anti-staphylococcal biofilm activity. Int J Antimicrob Agents 2017; 51:349-356. [PMID: 28705677 DOI: 10.1016/j.ijantimicag.2017.06.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/13/2017] [Accepted: 06/24/2017] [Indexed: 11/19/2022]
Abstract
Hyicin 4244 is a small antimicrobial peptide with a broad spectrum of activity that was found in the culture supernatant of Staphylococcus hyicus 4244, the genome of which was then sequenced. The bacteriocin gene cluster (hyiSABCDEFG) was mined from its single chromosome and exhibited a genetic organization similar to that of subtilosin A. All genes involved in hyicin 4244 biosynthesis proved to be transcribed and encode proteins that share at least 42% similarity to proteins encoded by the subtilosin A gene cluster. Due to its resemblance to subtilosin A and the presence of three thioether bonds in its structure, hyicin 4244 is assumed to be a 35-amino acid circular sactibiotic, the first to be described in staphylococci. Hyicin 4244 inhibited 14 staphylococcal isolates from either human infections or bovine mastitis, all biofilm formers. Hyicin 4244 significantly reduced the number of colony-forming units (CFU) and the biofilm formation by two strong biofilm-forming strains randomly chosen as representatives of the strains involved in human infections and bovine mastitis. It also reduced the proliferation and viability of sessile cells in established biofilms. Therefore, hyicin 4244 proved not only to prevent biofilm formation by planktonic cells, but also to penetrate the biofilm matrix in vitro, exerting bactericidal activity against staphylococcal sessile cells. This bacteriocin has the potential to become an alternative antimicrobial for either prevention or treatment of biofilm-related infections caused by different staphylococcal species.
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Affiliation(s)
- Andreza Freitas de Souza Duarte
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Hilana Ceotto-Vigoder
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Emile Santos Barrias
- Instituto Nacional de Metrologia, Qualidade e Tecnologia, Duque de Caxias, Brazil
| | | | - Ingolf Figved Nes
- Laboratory of Microbial Gene Technology, Norwegian University of Life Science, Ås, Norway
| | - Maria do Carmo de Freire Bastos
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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25
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Parveen Rani R, Anandharaj M, Hema S, Deepika R, David Ravindran A. Purification of Antilisterial Peptide (Subtilosin A) from Novel Bacillus tequilensis FR9 and Demonstrate Their Pathogen Invasion Protection Ability Using Human Carcinoma Cell Line. Front Microbiol 2016; 7:1910. [PMID: 27990138 PMCID: PMC5133052 DOI: 10.3389/fmicb.2016.01910] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/15/2016] [Indexed: 11/13/2022] Open
Abstract
This study focuses on isolation, screening, and characterization of novel probiotics from gastrointestinal tract of free-range chicken (Gallus gallus domesticus). Fifty seven colonies were isolated and three isolates (FR4, FR9, and FR12) were selected and identified as Lactobacillus gasseri FR4, Bacillus tequilensis FR9, and L. animalis FR12 by 16S rRNA sequencing. Three strains were able to survive in stimulated acidic and bile conditions and inhibit the growth of pathogens. Especially, FR9 exhibited maximum inhibition against Listeria monocytogenes and none of them exhibited hemolytic activity. Native-PAGE revealed the presence of low molecular weight (3.4-5.0 KDa) antimicrobial peptide. The peptide was further purified by Sephadex G-50 column and RP-HPLC using C18 column. N-terminal amino acid sequencing of antimicrobial peptide showed 100% consensus to antilisterial peptide Subtilosin A and SboA gene was amplified from FR9 genome. FR9 showed maximum aggregation activity, exopolysaccharide production (85.46 mg/L) and cholesterol assimilation (63.12 ± 0.05 μg/mL). Strong adhesion property (12.6%) and pathogen invasion protection ability was revealed by B. tequilensis FR9 towards HCT-116 human colon carcinoma cell line. This is the first study to demonstrate antilisterial Subtilosin A production of B. tequilensis. Our results indicate that B. tequilensis FR9 strain furnish the essential characteristics of a potential probiotics and might be incorporated into human and animal food supplements.
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Affiliation(s)
- Rizwana Parveen Rani
- Department of Biology, The Gandhigram Rural Institute – Deemed UniversityGandhigram, India
| | | | - Subramani Hema
- Department of Biology, The Gandhigram Rural Institute – Deemed UniversityGandhigram, India
| | - Ramasamy Deepika
- Department of Biology, The Gandhigram Rural Institute – Deemed UniversityGandhigram, India
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Liu H, Qu X, Gao L, Zhao S, Lu Z, Zhang C, Bie X. Characterization of a Bacillus subtilis surfactin synthetase knockout and antimicrobial activity analysis. J Biotechnol 2016; 237:1-12. [PMID: 27576183 DOI: 10.1016/j.jbiotec.2016.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 11/15/2022]
Abstract
Gene knockout is an important approach to improve the production of antimicrobial compounds. B. subtilis PB2-LS10, derived from B. subtilis PB2-L by a surfactin synthetase (srf) genes knockout, exhibits stronger inhibitory action than its parental strain against all tested pathogenic bacteria and fungi. The antimicrobial extracts produced by B. subtilis PB2-L and B. subtilis PB2-LS10 respectively were characterized by the high-resolution LC-ESI-MS. To provide further insight into the distinct antimicrobial activities, we investigated the impact of the srf genes deletion on the growth and gene transcriptional profile of the strains. The mutant strain grew quickly and reached stationary phase 2h earlier than the wild-type. Prominent expression changes in the modified strain involved genes that were essential to metabolic pathways and processes. Genes related to amino acid transport, ATP-binding cassette (ABC) transporters and protein export were up-regulated in strain PB2-LS10. However, amino acid metabolism, carbohydrate metabolism and fatty acid metabolism were repressed. Because of its excellent antimicrobial activity, strain PB2-LS10 has potential for use in food preservation.
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Affiliation(s)
- Hongxia Liu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Xiaoxu Qu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Ling Gao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Shengming Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Chong Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Key Laboratory of Food Processing and Quality Control, Ministry of Agriculture of China, 1 Weigang, Nanjing 210095, PR China, PR China.
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Zhao X, Kuipers OP. Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species. BMC Genomics 2016; 17:882. [PMID: 27821051 PMCID: PMC5100339 DOI: 10.1186/s12864-016-3224-y] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/27/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. RESULTS We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. CONCLUSIONS Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified.
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Affiliation(s)
- Xin Zhao
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.
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28
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Islam MM, Yang CJ. Efficacy of mealworm and super mealworm larvae probiotics as an alternative to antibiotics challenged orally with Salmonella and E. coli infection in broiler chicks. Poult Sci 2016; 96:27-34. [PMID: 27520069 DOI: 10.3382/ps/pew220] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/10/2016] [Accepted: 05/10/2016] [Indexed: 12/11/2022] Open
Abstract
This study was conducted to evaluate dry mealworm (Tenebrio molitor) (DMLP) and super mealworm (Zophobas morio) (DSMLP) larvae probiotics as alternatives to antibiotics in broiler chicks. A total of 240 one-day old Ross 308 male broiler chicks were randomly assigned to three dietary treatments consisting of ten replications with eight birds each in a completely randomized design. The dietary treatments were, (i) control (basal diet), (ii) 0.4% DMLP (basal diet + 0.4% DMLP, DM basis), and (iii) 0.4% DSMLP (basal diet + 0.4% DSMLP, DM basis). On day one, 1 mL of mixed broth agar consisting of 2.4 × 107 cfu Salmonella enteritidis KCTC 2021 and 3.7 × 107 cfu Escherichia coli KCTC 2571 was injected orally into each chick. After one week, growth performance, immunity, mortality, internal organ weight, and cecal and fecal microbiota were investigated. Average daily gain ( ADG: ) and average daily feed intake (ADFI) increased, while feed conversion ratio (FCR) (g intake/g gain per bird) decreased in response to DMLP and DSMLP supplementation (P < 0.05). Additionally, mortality decreased (P < 0.05), while IgG and IgA levels increased following DMLP and DSMLP supplementation (P < 0.05). Internal organs remained unaffected, except for a reduced bursa of Fabricius weight in DSMLP supplementation (P < 0.05). Cecal E. coli and Salmonella contents were reduced in DMLP and DSMLP supplementation (P < 0.05), while fecal microbiota contents and pH of cecal and fecal digesta remained unaffected. In conclusion, dietary supplementation with DMLP and DSMLP increased ADG and IgG and IgA levels, while reducing FCR, mortality and cecal E. coli and Salmonella spp. CONTENTS Thus, DMLP and DSMLP can be utilized as an alternative to antibiotics in broiler diets.
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Affiliation(s)
- Md Manirul Islam
- Department of Animal Science and Technology, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Chul-Ju Yang
- Department of Animal Science and Technology, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea
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Mhatre E, Troszok A, Gallegos-Monterrosa R, Lindstädt S, Hölscher T, Kuipers OP, Kovács ÁT. The impact of manganese on biofilm development of Bacillus subtilis. MICROBIOLOGY-SGM 2016; 162:1468-1478. [PMID: 27267987 DOI: 10.1099/mic.0.000320] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial biofilms are dynamic and structurally complex communities, involving cell-to-cell interactions. In recent years, various environmental signals that induce the complex biofilm development of the Gram-positive bacterium Bacillus subtilis have been identified. These signalling molecules are often media components or molecules produced by the cells themselves, as well as those of other interacting species. The responses can also be due to depletion of certain molecules in the vicinity of the cells. Extracellular manganese (Mn2+) is essential for proper biofilm development of B. subtilis. Mn2+ is also a component of practically all laboratory biofilm-promoting media used for B. subtilis. Comparison of complex colony biofilms in the presence or absence of supplemented Mn2+ using microarray analyses revealed that genes involved in biofilm formation are indeed downregulated in the absence of Mn2+. In addition, Mn2+ also affects the transcription of several other genes involved in distinct differentiation pathways of various cellular processes. The effects of Mn2+ on other biofilm-related traits like motility, antimicrobial production, stress and sporulation were followed using fluorescent reporter strains. The global transcriptome and morphology studies highlight the importance of Mn2+ during biofilm development and provide an overview on the expressional changes in colony biofilms in B. subtilis.
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Affiliation(s)
- Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Agnieszka Troszok
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ramses Gallegos-Monterrosa
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Stefanie Lindstädt
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Theresa Hölscher
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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30
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Abstract
The dense aggregation of cells on a surface, as seen in biofilms, inevitably results in both environmental and cellular heterogeneity. For example, nutrient gradients can trigger cells to differentiate into various phenotypic states. Not only do cells adapt physiologically to the local environmental conditions, but they also differentiate into cell types that interact with each other. This allows for task differentiation and, hence, the division of labor. In this article, we focus on cell differentiation and the division of labor in three bacterial species: Myxococcus xanthus, Bacillus subtilis, and Pseudomonas aeruginosa. During biofilm formation each of these species differentiates into distinct cell types, in some cases leading to cooperative interactions. The division of labor and the cooperative interactions between cell types are assumed to yield an emergent ecological benefit. Yet in most cases the ecological benefits have yet to be elucidated. A notable exception is M. xanthus, in which cell differentiation within fruiting bodies facilitates the dispersal of spores. We argue that the ecological benefits of the division of labor might best be understood when we consider the dynamic nature of both biofilm formation and degradation.
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31
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Isolation and characterization of a Bacillus atrophaeus strain and its potential use in food preservation. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.08.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Application of bacterial cytological profiling to crude natural product extracts reveals the antibacterial arsenal of Bacillus subtilis. J Antibiot (Tokyo) 2015; 69:353-61. [PMID: 26648120 DOI: 10.1038/ja.2015.116] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/01/2015] [Indexed: 11/09/2022]
Abstract
Although most clinically used antibiotics are derived from natural products, identifying new antibacterial molecules from natural product extracts is difficult due to the complexity of these extracts and the limited tools to correlate biological activity with specific molecules. Here, we show that bacterial cytological profiling (BCP) provides a rapid method for mechanism of action determination on plates and in complex natural product extracts and for activity-guided purification. We prepared an extract from Bacillus subtilis 3610 that killed the Escherichia coli lptD mutant and used BCP to observe two types of bioactivities in the unfractionated extract: inhibition of translation and permeablization of the cytoplasmic membrane. We used BCP to guide purification of the molecules responsible for each activity, identifying the translation inhibitors bacillaene and bacillaene B (glycosylated bacillaene) and demonstrating that two molecules contribute to cell permeabilitization, the bacteriocin subtilosin and the cyclic peptide sporulation killing factor. Our results suggest that bacillaene mediates translational arrest, and show that bacillaene B has a minimum inhibitory concentration 10 × higher than unmodified bacillaene. Finally, we show that BCP can be used to screen strains on an agar plate without the need for extract preparation, greatly saving time and improving throughput. Thus, BCP simplifies the isolation of novel natural products, by identifying strains, crude extracts and fractions with interesting bioactivities even when multiple activities are present, allowing investigators to focus labor-intensive steps on those with desired activities.
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34
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35
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Antibacterial activity and genotypic–phenotypic characteristics of bacteriocin-producing Bacillus subtilis KKU213: Potential as a probiotic strain. Microbiol Res 2015; 170:36-50. [DOI: 10.1016/j.micres.2014.09.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 07/07/2014] [Accepted: 09/12/2014] [Indexed: 11/20/2022]
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36
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Daszczuk A, Dessalegne Y, Drenth I, Hendriks E, Jo E, van Lente T, Oldebesten A, Parrish J, Poljakova W, Purwanto AA, van Raaphorst R, Boonstra M, van Heel A, Herber M, van der Meulen S, Siebring J, Sorg RA, Heinemann M, Kuipers OP, Veening JW. Bacillus subtilis biosensor engineered to assess meat spoilage. ACS Synth Biol 2014; 3:999-1002. [PMID: 25524109 DOI: 10.1021/sb5000252] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we developed a cell-based biosensor that can assess meat freshness using the Gram-positive model bacterium Bacillus subtilis as a chassis. Using transcriptome analysis, we identified promoters that are specifically activated by volatiles released from spoiled meat. The most strongly activated promoter was PsboA, which drives expression of the genes required for the bacteriocin subtilosin. Next, we created a novel BioBrick compatible integration plasmid for B. subtilis and cloned PsboA as a BioBrick in front of the gene encoding the chromoprotein amilGFP inside this vector. We show that the newly identified promoter could efficiently drive fluorescent protein production in B. subtilis in response to spoiled meat and thus can be used as a biosensor to detect meat spoilage.
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Affiliation(s)
- Alicja Daszczuk
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Yonathan Dessalegne
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Ismaêl Drenth
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Elbrich Hendriks
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Emeraldo Jo
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Tom van Lente
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Arjan Oldebesten
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jonathon Parrish
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Wlada Poljakova
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Annisa A. Purwanto
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Renske van Raaphorst
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Mirjam Boonstra
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Auke van Heel
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Martijn Herber
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Sjoerd van der Meulen
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jeroen Siebring
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Robin A. Sorg
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Matthias Heinemann
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Oscar P. Kuipers
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jan-Willem Veening
- iGEM Teaching Program, Team 2012, ‡Molecular Genetics
Group, and §Molecular Systems Biology, Groningen
Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic
Biology, University of Groningen, 9747 AG Groningen, The Netherlands
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Ahmed ST, Mun HS, Islam MM, Kim SS, Hwang JA, Kim YJ, Yang CJ. Effects of Citrus junos by-products fermented with multistrain probiotics on growth performance, immunity, caecal microbiology and meat oxidative stability in broilers. Br Poult Sci 2014; 55:540-7. [PMID: 25005143 DOI: 10.1080/00071668.2014.938021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
1. The present study was conducted to develop Citrus junos probiotics (CJP), using by-products of Citrus junos fermented with multispecies probiotic bacteria including Saccharomyces cerevisiae, Enterococcus faecium, Lactobacillus acidophilus and Bacillus subtilis. The effects of dietary CJP on the growth performance, immune status, caecal microbiology and meat oxidative stability of broiler were investigated. 2. A total of 240 one-day-old Ross broiler chicks were used in a 35-d experiment in which the chicks were randomly allotted to one of the 4 dietary treatments (0, 5, 10 and 20 g CJP/kg diet) in a completely randomised design. 3. Dietary supplementation of 5 g/kg CJP significantly increased body weight, average daily gain and average daily feed intake of broiler during the overall experimental period. 4. Serum immunoglobulin (Ig)M concentration was significantly increased by 10 and 20 g/kg CJP, whereas the IgG and IgA concentration remained unaffected. In addition, 20 g/kg CJP significantly inhibited proliferation of Escherichia coli without affecting the concentration of Lactobacillus or Bacillus spp. 5. A significant reduction in the thiobarbituric acid reactive substances values of breast and thigh meat was observed in response to increasing concentration of dietary CJP. 6. Thus, the results suggest that CJP up to a concentration of 20 g/kg can be used in the diet of broilers to improve immunity and to reduce caecal E. coli and TBARS values of breast and thigh meat without any adverse effects on growth performance.
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Affiliation(s)
- S T Ahmed
- a Department of Animal Science and Technology , Sunchon National University , Suncheon , Republic of Korea
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38
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Ahmed ST, Islam M, Mun HS, Sim HJ, Kim YJ, Yang CJ. Effects of Bacillus amyloliquefaciens as a probiotic strain on growth performance, cecal microflora, and fecal noxious gas emissions of broiler chickens. Poult Sci 2014; 93:1963-71. [PMID: 24902704 DOI: 10.3382/ps.2013-03718] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This experiment was conducted to investigate the effects of Bacillus amyloliquefaciens probiotic (BAP) as a direct-fed microbial on growth performance, cecal microflora, serum immunoglobulin levels, and fecal noxious gas emissions of broiler chickens. A total of 400 one-day-old broiler chicks (Ross 308) were randomly assigned to 1 of 5 treatment diets formulated to supply 0, 1, 5, 10, and 20 g/kg of BAP and were fed for 35 d. Each treatment had 8 replicate pens with 10 birds per replicate. On completion of the growth trial, fecal samples were collected, and ammonia (NH3) and hydrogen sulfide (H2S) emissions were measured. Increasing concentration of BAP had positive linear effect on the ADG of broilers (P < 0.05) throughout the experimental period, with the highest values being observed in broilers offered 20 g/kg of BAP. The ADFI increased linearly (P < 0.02) with the inclusion of BAP during the overall experimental period (d 0 to 35). Providing BAP had a negative linear effect on FCR from d 0 to 21 and d 0 to 35 (P < 0.01). Supplementation with BAP did not affect cecal Lactobacillus and Bacillus content, but exerted negative linear effect on cecal Escherichia coli (P < 0.05) with increasing the level of BAP in broiler diets. Additionally, BAP modified immune response of broilers by linearly increasing serum IgG and IgA (P < 0.01). Dietary BAP resulted in decreased fecal NH3 emissions at 0 (linear, P < 0.001), 3, 6, 12, 24, and 48 h of incubation (linear, P < 0.05; quadratic, P < 0.01). Supplementation of BAP exerted negative linear and quadratic effects on fecal emissions of H2S (P < 0.001) throughout the incubation period except at 48 h, and the optimum effect was found when BAP was provided at 5 g/kg of diet. Based on these results, Bacillus amyloliquefaciens could be suggested as a potential feed additive of broiler diets.
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Affiliation(s)
- Sonia Tabasum Ahmed
- Department of Animal Science and Technology, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Manirul Islam
- Department of Animal Science and Technology, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Hong-Seok Mun
- Department of Animal Science and Technology, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Hyeon-Ju Sim
- Department of Animal Science and Technology, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Ye-Jin Kim
- Department of Animal Science and Technology, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea
| | - Chul-Ju Yang
- Department of Animal Science and Technology, Sunchon National University, 255 Jungangno, Suncheon, Jeonnam 540-950, Republic of Korea
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39
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Potter A, Ceotto H, Coelho MLV, Guimarães AJ, Bastos MDCDF. The gene cluster of aureocyclicin 4185: the first cyclic bacteriocin of Staphylococcus aureus. Microbiology (Reading) 2014; 160:917-928. [DOI: 10.1099/mic.0.075689-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus 4185 was previously shown to produce at least two bacteriocins. One of them is encoded by pRJ101. To detect the bacteriocin-encoding gene cluster, an ~9160 kb region of pRJ101 was sequenced. In silico analyses identified 10 genes (aclX, aclB, aclI, aclT, aclC, aclD, aclA, aclF, aclG and aclH) that might be involved in the production of a novel cyclic bacteriocin named aureocyclicin 4185. The organization of these genes was quite similar to that of the gene cluster responsible for carnocyclin A production and immunity. Four putative proteins encoded by these genes (AclT, AclC, AclD and AclA) also exhibited similarity to proteins encoded by cyclic bacteriocin gene clusters. Mutants derived from insertion of Tn917-lac into aclC, aclF, aclH and aclX were affected in bacteriocin production and growth. AclX is a 205 aa putative protein not encoded by the gene clusters of other cyclic bacteriocins. AclX exhibits 50 % similarity to a permease and has five putative membrane-spanning domains. Transcription analyses suggested that aclX is part of the aureocyclicin 4185 gene cluster, encoding a protein required for bacteriocin production. The aclA gene is the structural gene of aureocyclicin 4185, which shows 65 % similarity to garvicin ML. AclA is proposed to be cleaved off, generating a mature peptide with a predicted M
r of 5607 Da (60 aa). By homology modelling, AclA presents four α-helices, like carnocyclin A. AclA could not be found at detectable levels in the culture supernatant of a strain carrying only pRJ101. To our knowledge, this is the first report of a cyclic bacteriocin gene cluster in the genus Staphylococcus.
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Affiliation(s)
- Amina Potter
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, UFRJ, Rio de Janeiro, Brazil
| | - Hilana Ceotto
- Instituto Federal de Educação Tecnológica do Estado do Rio de Janeiro, IFRJ, Rio de Janeiro, Brazil
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, UFRJ, Rio de Janeiro, Brazil
| | - Marcus Lívio Varella Coelho
- Instituto Nacional da Propriedade Industrial, INPI, Rio de Janeiro, Brazil
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, UFRJ, Rio de Janeiro, Brazil
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40
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 594] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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41
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Identification of 4″-isovaleryl-spiramycin III produced by Bacillus sp. fmbJ. Arch Microbiol 2013; 196:87-95. [PMID: 24356910 DOI: 10.1007/s00203-013-0939-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 10/11/2013] [Accepted: 11/01/2013] [Indexed: 10/25/2022]
Abstract
The production of secondary metabolites with antibiotic properties is a common characteristic to Bacillus spp. These metabolites not only have diverse chemical structures but also have a wide range of bioactivities with medicinal and agricultural interests such as antibiotic. Bacillus sp. fmbJ has been found to produce lipopeptides fengycin and surfactin in accordance with our previous report. In this study, another antimicrobial substance was separated and purified from the culture supernatant of strain fmbJ using the silica gel column chromatography and preparative reversed-phase high-performance liquid chromatography. By means of electrospray ionization mass spectroscopy, infrared spectroscopy, and nuclear magnetic resonance, the antagonistic compound was determined to be 4″-isovaleryl-spiramycin III with the molecular weight of 982 Da. This report is the first to introduce the finding of spiramycin produced from Bacillus sp. The study provides a novel source for the production of spiramycin in pharmaceutical industries.
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Abstract
The study of bacteriophages infecting the model organism Bacillus subtilis has provided an abundance of general knowledge and a platform for advances in biotechnology. Here, we announce the annotated genome of CampHawk, a B. subtilis phage. CampHawk was found to be an SPO1-like phage with similar gene content and arrangement.
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Berić T, Stanković S, Draganić V, Kojić M, Lozo J, Fira D. Novel antilisterial bacteriocin licheniocin 50.2 from Bacillus licheniformis VPS50.2 isolated from soil sample. J Appl Microbiol 2013; 116:502-10. [PMID: 24238327 DOI: 10.1111/jam.12393] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/08/2013] [Accepted: 11/08/2013] [Indexed: 11/28/2022]
Abstract
AIM To isolate and characterize bacteriocin, licheniocin 50.2, from soil bacteria identified as Bacillus licheniformis. METHODS AND RESULTS The strain B. licheniformis VPS50.2 was identified as bacteriocin producer, effective against Gram-positive bacteria, including Listeria monocytogenes, methicillin-resistant Staphylococcus aureus (MRSA) and β-haemolytic streptococci. The start of bacteriocin production coincides with the beginning of sporulation. Ammonium sulfate precipitation, chloroform extraction and ultrafiltration were used for bacteriocin purification. MALDI TOF/TOF mass spectrometry of purified sample detected the protein with molecular mass of 3253·209 Da. N-terminal sequencing recognized first 15 amino acids with the sequence: W E E Y N I I X Q L G N K G Q. We named the newly characterized bacteriocin as subclass II.3 bacteriocin, licheniocin 50·2. The bacteriocin activity was insensitive to lysozyme and proteinase K, heat stable after incubation at 100°C for 30 min and over wide range of pH (2-12). MICs of crude bacteriocin extract were determined for L. monocytogenes and MRSA. Time-kill study showed that licheniocin had bactericidal effect to L. monocytogenes. CONCLUSION A novel, thermostable, pH-tolerant bacteriocin active against Gram-positive bacteria was isolated. SIGNIFICANCE AND IMPACT OF THE STUDY Attributes of new, stable licheniocin 50.2 make it a promising agent for application as biopreservative in food industry.
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Affiliation(s)
- T Berić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
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44
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Stationary phase and nutrient levels trigger transcription of a genomic locus containing a novel peptide (TM1316) in the hyperthermophilic bacterium Thermotoga maritima. Appl Environ Microbiol 2013; 79:6637-46. [PMID: 23974142 DOI: 10.1128/aem.01627-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The genome of the hyperthermophilic bacterium Thermotoga maritima encodes numerous putative peptides/proteins of 100 amino acids or less. While most of these open reading frames (ORFs) are transcribed during growth, their corresponding physiological roles are largely unknown. The onset of stationary phase in T. maritima was accompanied by significant morphological changes and upregulation of several ORFs located in the TM1298-TM1336 genome locus. This region contains putative HicAB toxin-antitoxin pairs, hypothetical proteins, radical S-adenosylmethionine (SAM) enzymes, and ABC transporters. Of particular note was the TM1315-TM1319 operon, which includes a putative 31-amino-acid peptide (TM1316) that was the most highly transcribed gene in the transcriptome during stationary phase. Antibodies directed against a synthetic version of TM1316 were used to track its production, which correlated closely with transcriptomic data. Immunofluorescence microscopy revealed that TM1316 was localized to the cell envelope and prominent in cell aggregates formed during stationary phase. The only functionally characterized locus with an organization similar to that of TM1315-TM1319 is in Bacillus subtilis, which contains subtilosin A, a cyclic peptide with Cys-to-α-carbon linkages that functions as an antilisterial bacteriocin. While the organization of TM1316 resembled that of the Bacillus peptide (e.g., in its number of amino acids and spacing of Cys residues), preparations containing high levels of TM1316 affected the growth of neither Thermotoga species nor Pyrococcus furiosus, a hyperthermophilic archaeon isolated from the same locale as T. maritima. Several other putative Cys-rich peptides could be identified in the TM1298-TM1336 locus, and while their roles are also unclear, they merit examination as potential antimicrobial agents in hyperthermophilic biotopes.
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Radical S-adenosylmethionine enzyme catalyzed thioether bond formation in sactipeptide biosynthesis. Curr Opin Chem Biol 2013; 17:605-12. [DOI: 10.1016/j.cbpa.2013.06.031] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/03/2013] [Accepted: 06/25/2013] [Indexed: 11/19/2022]
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46
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Mu F, Masuda Y, Zendo T, Ono H, Kitagawa H, Ito H, Nakayama J, Sonomoto K. Biological function of a DUF95 superfamily protein involved in the biosynthesis of a circular bacteriocin, leucocyclicin Q. J Biosci Bioeng 2013; 117:158-164. [PMID: 23906710 DOI: 10.1016/j.jbiosc.2013.06.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
Abstract
Biological functions of a DUF95 superfamily protein in the biosynthesis gene cluster of a novel circular bacteriocin, leucocyclicin Q (LcyQ), were characterized in this paper. Sequence analysis and database search of the regions flanking the LcyQ structural gene lcyQ revealed four open reading frames (lcyR, lcyB, lcyC, and lcyD) related to bacteriocin biosynthesis. LcyD shares some similarity to the DUF95 superfamily proteins, often found in the biosynthetic gene clusters of circular bacteriocins. Mass spectrometry analysis showed accumulation of active mature LcyQ inside lcyD knockout cells. Heterologous expression of lcyD demonstrated that it confers robust immunity against LcyQ. Peptide release/binding assay revealed that the immunity could be attributed to the secretion of LcyQ to the cell exterior. Thus, the DUF95 superfamily protein has a dual function in the biosynthesis of LcyQ, as an immunity-associated transporter and as a secretion-aiding agent. Accumulation of mature LcyQ inside the cell in lcyD knockout strains, further implied that cyclization occurs within the cell. To the best of our knowledge, this is the first report on LcyQ cyclization inside the cell and the dual role of a DUF95 superfamily protein in circular bacteriocin biosynthesis.
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Affiliation(s)
- Fuqin Mu
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yoshimitsu Masuda
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Takeshi Zendo
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hiroshi Ono
- R&D Laboratories, Tokai Pickling Co. Ltd., 78-1 Mukaigo, Mukokusamacho, Toyohashi 441-8142, Japan
| | - Hiroshi Kitagawa
- R&D Laboratories, Tokai Pickling Co. Ltd., 78-1 Mukaigo, Mukokusamacho, Toyohashi 441-8142, Japan
| | - Haruo Ito
- R&D Laboratories, Tokai Pickling Co. Ltd., 78-1 Mukaigo, Mukokusamacho, Toyohashi 441-8142, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Kenji Sonomoto
- Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan; Laboratory of Functional Food Design, Department of Functional Metabolic Design, Bio-Architecture Center, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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Gassericin A: a circular bacteriocin produced by Lactic acid bacteria Lactobacillus gasseri. World J Microbiol Biotechnol 2013; 29:1977-87. [DOI: 10.1007/s11274-013-1368-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/03/2013] [Indexed: 10/26/2022]
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Production of the cannibalism toxin SDP is a multistep process that requires SdpA and SdpB. J Bacteriol 2013; 195:3244-51. [PMID: 23687264 DOI: 10.1128/jb.00407-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
During the early stages of sporulation, a subpopulation of Bacillus subtilis cells secrete toxins that kill their genetically identical siblings in a process termed cannibalism. One of these toxins is encoded by the sdpC gene of the sdpABC operon. The active form of the SDP toxin is a 42-amino-acid peptide with a disulfide bond which is processed from an internal fragment of pro-SdpC. The factors required for the processing of pro-SdpC into mature SDP are not known. We provide evidence that pro-SdpC is secreted via the general secretory pathway and that signal peptide cleavage is a required step in the production of SDP. We also demonstrate that SdpAB are essential to produce mature SDP, which has toxin activity. Our data indicate that SdpAB are not required for secretion, translation, or stability of SdpC. Thus, SdpAB may participate in a posttranslation step in the production of SDP. The mature form of the SDP toxin contains a disulfide bond. Our data indicate that while the disulfide bond does increase activity of SDP, it is not essential for SDP activity. We demonstrate that the disulfide bond is formed independently of SdpAB. Taken together, our data suggest that SDP production is a multistep process and that SdpAB are required for SDP production likely by controlling, directly or indirectly, cleavage of SDP from the pro-SdpC precursor.
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49
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Yang X, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: new insights into the role of leader and core peptides during biosynthesis. Chemistry 2013; 19:7662-77. [PMID: 23666908 DOI: 10.1002/chem.201300401] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Indexed: 11/08/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural products with a high degree of structural diversity and a wide variety of bioactivities. Understanding the biosynthetic machinery of these RiPPs will benefit the discovery and development of new molecules with potential pharmaceutical applications. In this Concept article, we discuss the features of the biosynthetic pathways to different RiPP classes, and propose mechanisms regarding recognition of the precursor peptide by the post-translational modification enzymes. We propose that the leader peptides function as allosteric regulators that bind the active form of the biosynthetic enzymes in a conformational selection process. We also speculate how enzymes that generate polycyclic products of defined topologies may have been selected for during evolution.
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Affiliation(s)
- Xiao Yang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, USA
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50
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Dunbar KL, Mitchell DA. Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol 2013; 8:473-87. [PMID: 23286465 DOI: 10.1021/cb3005325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.
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Affiliation(s)
- Kyle L. Dunbar
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
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