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Güngör E, Savary J, Adema K, Dijkhuizen LW, Keilwagen J, Himmelbach A, Mascher M, Koppers N, Bräutigam A, Van Hove C, Riant O, Nierzwicki-Bauer S, Schluepmann H. The crane fly glycosylated triketide δ-lactone cornicinine elicits akinete differentiation of the cyanobiont in aquatic Azolla fern symbioses. PLANT, CELL & ENVIRONMENT 2024; 47:2675-2692. [PMID: 38600764 DOI: 10.1111/pce.14907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024]
Abstract
The restriction of plant-symbiont dinitrogen fixation by an insect semiochemical had not been previously described. Here we report on a glycosylated triketide δ-lactone from Nephrotoma cornicina crane flies, cornicinine, that causes chlorosis in the floating-fern symbioses from the genus Azolla. Only the glycosylated trans-A form of chemically synthesized cornicinine was active: 500 nM cornicinine in the growth medium turned all cyanobacterial filaments from Nostoc azollae inside the host leaf-cavities into akinetes typically secreting CTB-bacteriocins. Cornicinine further inhibited akinete germination in Azolla sporelings, precluding re-establishment of the symbiosis during sexual reproduction. It did not impact development of the plant Arabidopsis thaliana or several free-living cyanobacteria from the genera Anabaena or Nostoc but affected the fern host without cyanobiont. Fern-host mRNA sequencing from isolated leaf cavities confirmed high NH4-assimilation and proanthocyanidin biosynthesis in this trichome-rich tissue. After cornicinine treatment, it revealed activation of Cullin-RING ubiquitin-ligase-pathways, known to mediate metabolite signaling and plant elicitation consistent with the chlorosis phenotype, and increased JA-oxidase, sulfate transport and exosome formation. The work begins to uncover molecular mechanisms of cyanobiont differentiation in a seed-free plant symbiosis important for wetland ecology or circular crop-production today, that once caused massive CO2 draw-down during the Eocene geological past.
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Affiliation(s)
- Erbil Güngör
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Jérôme Savary
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Kelvin Adema
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | | | | | - Axel Himmelbach
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Nils Koppers
- Computational Biology, Center for Biotechnology and Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Andrea Bräutigam
- Computational Biology, Center for Biotechnology and Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Charles Van Hove
- Emeritus Professor from the Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Olivier Riant
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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Arbulu S, Kjos M. Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins. MICROBIAL ECOLOGY 2024; 87:41. [PMID: 38351266 PMCID: PMC10864542 DOI: 10.1007/s00248-024-02357-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.
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Affiliation(s)
- Sara Arbulu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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3
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Arias-Orozco P, Zhou L, Yi Y, Cebrián R, Kuipers OP. Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains. Microbiol Spectr 2024; 12:e0361123. [PMID: 38088546 PMCID: PMC10783134 DOI: 10.1128/spectrum.03611-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Genome mining studies have revealed the remarkable combinatorial diversity of ribosomally synthesized and post-translationally modified peptides (RiPPs) in marine bacteria, including prochlorosins. However, mining strategies also prove valuable in investigating the genomic landscape of associated genes within biosynthetic gene cluster (BGC) specific to targeted RiPPs of interest. Our study contributes to the enrichment of knowledge regarding prochlorosin diversity. It offers insights into potential mechanisms involved in their biosynthesis and modification, such as hyper-modification, which may give rise to active lantibiotics. Additionally, our study uncovers putative novel promiscuous post-translational enzymes, thereby expanding the chemical space explored within the Synechococcus genus. Moreover, this research extends the applications of mining techniques beyond the discovery of new RiPP-like clusters, allowing for a deeper understanding of genomics and diversity. Furthermore, it holds the potential to reveal previously unknown functions within the intriguing RiPP families, particularly in the case of prochlorosins.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs.GRANADA, San Cecilio University Hospital, Granada, Spain
- CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
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4
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Budhwani Z, Buragina JT, Lang J, Acedo JZ. Characterization of the Novel Leaderless Bacteriocin, Bawcin, from Bacillus wiedmannii. Int J Mol Sci 2023; 24:16965. [PMID: 38069290 PMCID: PMC10707071 DOI: 10.3390/ijms242316965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The rise of drug-resistant bacteria is a major threat to public health, highlighting the urgent need for new antimicrobial compounds and treatments. Bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, hold promise as alternatives to conventional antibiotics. In this study, we identified and characterized a novel leaderless bacteriocin, bawcin, the first bacteriocin to be characterized from a Bacillus wiedmannii species. Chemically synthesized and purified bawcin was shown to be active against a broad range of Gram-positive bacteria, including foodborne pathogens Staphylococcus aureus, Bacillus cereus, and Listeria monocytogenes. Stability screening revealed that bawcin is stable over a wide range of pH (2.0-10.0), temperature conditions (25-100 °C), and against the proteases, papain and pepsin. Lastly, three-dimensional structure homology modeling suggests that bawcin contains a saposin-fold with amphipathic helices and a highly cationic surface that may be critical for membrane interaction and the subsequent cell death of its targets. This study provides the foundational understanding of the activity and properties of bawcin, offering valuable insights into its applications across different antimicrobial uses, including as a natural preservative in food and livestock industries.
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Affiliation(s)
- Zafina Budhwani
- Department of Chemistry and Physics, Mount Royal University, Calgary, AB T3E 6K6, Canada;
| | - Jenna T. Buragina
- Department of Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada; (J.T.B.)
| | - Jen Lang
- Department of Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada; (J.T.B.)
| | - Jeella Z. Acedo
- Department of Chemistry and Physics, Mount Royal University, Calgary, AB T3E 6K6, Canada;
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5
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Dinata R, Baindara P. Laterosporulin25: A probiotically produced, novel defensin-like bacteriocin and its immunogenic properties. Int Immunopharmacol 2023; 121:110500. [PMID: 37352569 DOI: 10.1016/j.intimp.2023.110500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/01/2023] [Accepted: 06/11/2023] [Indexed: 06/25/2023]
Abstract
Although multiple vaccines have been developed against infectious diseases, the rapid emergence of new pathogens develops an urgent need for novel strategies to combat infectious diseases. Antimicrobial peptides (AMPs) are excellent agents to fight against infectious diseases having unique multiple mechanisms of action against various pathogens. Apart from the direct applications, AMPs can also be developed as subunit vaccines or could be used as a highly immunogenic carrier protein with highly antigenic but non-immunogenic antigens. Here in the present study, we have identified a novel defensin-like bacteriocin, laterosporulin25 (LS25) upon genome mining of Brevibacillus laterosporus DSM25, a probiotic bacterial strain. By using immunoinformatic tools, we have studied the immunogenic and physiochemical properties of LS25. LS25 is characterized as defensin-like bacteriocin, having 51 amino acids and a molecular weight of 5862.7 Da. The modeled tertiary structure of LS25 is docked with TLR3 and TLR4-MD2 complex to confirm the facilitation of induced immune response that is further validated using molecular dynamics simulations and In-silico immune stimulations. Overall, detailed immunoinformatics analysis suggested LS25 as a potential candidate to be used as an adjuvant or carrier protein for subunit vaccine development, however, further in-vitro and in-vivo experiments are essential to validate its potential.
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Affiliation(s)
- Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram 796004, India
| | - Piyush Baindara
- Department of Radiation Oncology, School of Medicine, University of Missouri, Columbia, MO 65211, USA.
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Peptide Designs for Use in Caries Management: A Systematic Review. Int J Mol Sci 2023; 24:ijms24044247. [PMID: 36835657 PMCID: PMC9961499 DOI: 10.3390/ijms24044247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
The objective of this study was to review the design methods that have been used to create peptides for use in caries management. Two independent researchers systematically reviewed many in vitro studies in which peptides were designed for use in caries management. They assessed the risk of bias in the included studies. This review identified 3592 publications, of which 62 were selected. Forty-seven studies reported 57 antimicrobial peptides. Among them, 31 studies (66%, 31/47) used the template-based design method; 9 studies (19%, 9/47) used the conjugation method; and 7 studies (15%, 7/47) used other methods, such as the synthetic combinatorial technology method, the de novo design method and cyclisation. Ten studies reported mineralising peptides. Seven of these (70%, 7/10) used the template-based design method, two (20%, 2/10) used the de novo design method, and one study (10%, 1/10) used the conjugation method. In addition, five studies developed their own peptides with antimicrobial and mineralising properties. These studies used the conjugation method. Our assessment for the risk of bias in the 62 reviewed studies showed that 44 publications (71%, 44/62) had a medium risk and that 3 publications had a low risk (5%, 3/62). The two most common methods for developing peptides for use in caries management that were used in these studies were the template-based design method and the conjugation method.
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Exploring the Relationship between Biosynthetic Gene Clusters and Constitutive Production of Mycosporine-like Amino Acids in Brazilian Cyanobacteria. Molecules 2023; 28:molecules28031420. [PMID: 36771087 PMCID: PMC9918943 DOI: 10.3390/molecules28031420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Cyanobacteria are oxygenic phototrophic prokaryotes that have evolved to produce ultraviolet-screening mycosporine-like amino acids (MAAs) to lessen harmful effects from obligatory exposure to solar UV radiation. The cyanobacterial MAA biosynthetic cluster is formed by a gene encoding 2-epi-5-epi-valiolone synthase (EVS) located immediately upstream from an O-methyltransferase (OMT) encoding gene, which together biosynthesize the expected MAA precursor 4-deoxygadusol. Accordingly, these genes are typically absent in non-producers. In this study, the relationship between gene cluster architecture and constitutive production of MAAs was evaluated in cyanobacteria isolated from various Brazilian biomes. Constitutive production of MAAs was only detected in strains where genes formed a co-linear cluster. Expectedly, this production was enhanced upon exposure of the strains to UV irradiance and by using distinct culture media. Constitutive production of MAAs was not detected in all other strains and, unexpectedly, production could not be induced by exposure to UV irradiation or changing growth media. Other photoprotection strategies which might be employed by these MAA non-producing strains are discussed. The evolutionary and ecological significance of gene order conservation warrants closer experimentation, which may provide a first insight into regulatory interactions of genes encoding enzymes for MAA biosynthesis.
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Dijamentiuk A, Mangavel C, Elfassy A, Michaux F, Burgain J, Rondags E, Delaunay S, Ferrigno S, Revol-Junelles AM, Borges F. Invert emulsions alleviate biotic interactions in bacterial mixed culture. Microb Cell Fact 2023; 22:16. [PMID: 36670385 PMCID: PMC9854087 DOI: 10.1186/s12934-022-02014-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023] Open
Abstract
The large application potential of microbiomes has led to a great need for mixed culture methods. However, microbial interactions can compromise the maintenance of biodiversity during cultivation in a reactor. In particular, competition among species can lead to a strong disequilibrium in favor of the fittest microorganism. In this study, an invert emulsion system was designed by dispersing culture medium in a mixture of sunflower oil and the surfactant PGPR. Confocal laser scanning microscopy revealed that this system allowed to segregate microorganisms in independent droplets. Granulomorphometric analysis showed that the invert emulsion remains stable during at least 24 h, and that the introduction of bacteria did not have a significant impact on the structure of the invert emulsion. A two-strain antagonistic model demonstrated that this invert emulsion system allows the propagation of two strains without the exclusion of the less-fit bacterium. The monitoring of single-strain cultures of bacteria representative of a cheese microbiota revealed that all but Brevibacterium linens were able to grow. A consortium consisting of Lactococcus lactis subsp. lactis biovar diacetylactis, Streptococcus thermophilus, Leuconostoc mesenteroides, Staphylococcus xylosus, Lactiplantibacillus plantarum and Carnobacterium maltaromaticum was successfully cultivated without detectable biotic interactions. Metabarcoding analysis revealed that the system allowed a better maintenance of alpha diversity and produced a propagated bacterial consortium characterized by a structure closer to the initial state compared to non-emulsified medium. This culture system could be an important tool in the field of microbial community engineering.
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Affiliation(s)
- Alexis Dijamentiuk
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Cécile Mangavel
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Annelore Elfassy
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Florentin Michaux
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Jennifer Burgain
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Emmanuel Rondags
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Stéphane Delaunay
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Sandie Ferrigno
- grid.29172.3f0000 0001 2194 6418IECL, Equipe BIGS, INRIA Nancy, Université de Lorraine, Nancy, France
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Parker JK, Davies BW. Microcins reveal natural mechanisms of bacterial manipulation to inform therapeutic development. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001175. [PMID: 35438625 PMCID: PMC10233263 DOI: 10.1099/mic.0.001175] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/17/2022] [Indexed: 12/20/2022]
Abstract
Microcins are an understudied and poorly characterized class of antimicrobial peptides. Despite the existence of only 15 examples, all identified from the Enterobacteriaceae, microcins display diversity in sequence, structure, target cell uptake, cytotoxic mechanism of action and target specificity. Collectively, these features describe some of the unique means nature has contrived for molecules to cross the 'impermeable' barrier of the Gram-negative bacterial outer membrane and inflict cytotoxic effects. Microcins appear to be widely dispersed among different species and in different environments, where they function in regulating microbial communities in diverse ways, including through competition. Growing evidence suggests that microcins may be adapted for therapeutic uses such as antimicrobial drugs, microbiome modulators or facilitators of peptide uptake into cells. Advancing our biological, ecological and biochemical understanding of the roles of microcins in bacterial interactions, and learning how to regulate and modify microcin activity, is essential to enable such therapeutic applications.
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Affiliation(s)
| | - Bryan William Davies
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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10
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Cao H, Xu D, Zhang T, Ren Q, Xiang L, Ning C, Zhang Y, Gao R. Comprehensive and functional analyses reveal the genomic diversity and potential toxicity of Microcystis. HARMFUL ALGAE 2022; 113:102186. [PMID: 35287927 DOI: 10.1016/j.hal.2022.102186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Microcystis is a cyanobacteria that is widely distributed across the world. It has attracted great attention because it produces the hepatotoxin microcystin (MC) that can inhibit eukaryotic protein phosphatases and pose a great risk to animal and human health. Due to the high diversity of morphospecies and genomes, it is still difficult to classify Microcystis species. In this study, we investigated the pangenome of 23 Microcystis strains to detect the genetic diversity and evolutionary dynamics. Microcystis revealed an open pangenome containing 22,009 gene families and exhibited different functional constraints. The core-genome phylogenetic analysis accurately differentiated the toxic and nontoxic strains and could be used as a taxonomic standard at the genetic level. We also investigated the functions of HGT events, of which were mostly conferred from cyanobacteria and closely related species. In order to detect the potential toxicity of Microcystis, we searched and characterized MC biosynthetic gene clusters and other secondary metabolite gene clusters. Our work provides insights into the genetic diversity, evolutionary dynamics, and potential toxicity of Microcystis, which could benefit the species classification and development of new methods for drinking water quality control and management of bloom formation in the future.
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Affiliation(s)
- Hengchun Cao
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Da Xu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Tiantian Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Qiufang Ren
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Li Xiang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Chunhui Ning
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, Shandong, China.
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan 250061, Shandong, China.
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Popin RV, Alvarenga DO, Castelo-Branco R, Fewer DP, Sivonen K. Mining of Cyanobacterial Genomes Indicates Natural Product Biosynthetic Gene Clusters Located in Conjugative Plasmids. Front Microbiol 2021; 12:684565. [PMID: 34803938 PMCID: PMC8600333 DOI: 10.3389/fmicb.2021.684565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
Microbial natural products are compounds with unique chemical structures and diverse biological activities. Cyanobacteria commonly possess a wide range of biosynthetic gene clusters (BGCs) to produce natural products. Although natural product BGCs have been found in almost all cyanobacterial genomes, little attention has been given in cyanobacterial research to the partitioning of these biosynthetic pathways in chromosomes and plasmids. Cyanobacterial plasmids are believed to disperse several natural product BGCs, such as toxins, by plasmids through horizontal gene transfer. Therefore, plasmids may confer the ability to produce toxins and may play a role in the evolution of diverse natural product BGCs from cyanobacteria. Here, we performed an analysis of the distribution of natural product BGCs in 185 genomes and mapped the presence of genes involved in the conjugation in plasmids. The 185 analyzed genomes revealed 1817 natural products BGCs. Individual genomes contained 1–42 biosynthetic pathways (mean 8), 95% of which were present in chromosomes and the remaining 5% in plasmids. Of the 424 analyzed cyanobacterial plasmids, 12% contained homologs of genes involved in conjugation and natural product biosynthetic pathways. Among the biosynthetic pathways in plasmids, manual curation identified those to produce aeruginosin, anabaenopeptin, ambiguine, cryptophycin, hassallidin, geosmin, and microcystin. These compounds are known toxins, protease inhibitors, odorous compounds, antimicrobials, and antitumorals. The present study provides in silico evidence using genome mining that plasmids may be involved in the distribution of natural product BGCs in cyanobacteria. Consequently, cyanobacterial plasmids have importance in the context of biotechnology, water management, and public health risk assessment. Future research should explore in vivo conjugation and the end products of natural product BGCs in plasmids via chemical analyses.
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Affiliation(s)
| | - Danillo Oliveira Alvarenga
- Department of Microbiology, University of Helsinki, Helsinki, Finland.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Raquel Castelo-Branco
- Department of Microbiology, University of Helsinki, Helsinki, Finland.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - David Peter Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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Oftedal TF, Ovchinnikov KV, Hestad KA, Goldbeck O, Porcellato D, Narvhus J, Riedel CU, Kjos M, Diep DB. Ubericin K, a New Pore-Forming Bacteriocin Targeting mannose-PTS. Microbiol Spectr 2021; 9:e0029921. [PMID: 34643411 PMCID: PMC8515946 DOI: 10.1128/spectrum.00299-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Bovine mastitis infection in dairy cattle is a significant economic burden for the dairy industry globally. To reduce the use of antibiotics in treatment of clinical mastitis, new alternative treatment options are needed. Antimicrobial peptides from bacteria, also known as bacteriocins, are potential alternatives for combating mastitis pathogens. In search of novel bacteriocins against mastitis pathogens, we screened samples of Norwegian bovine raw milk and found a Streptococcus uberis strain with potent antimicrobial activity toward Enterococcus, Streptococcus, Listeria, and Lactococcus. Whole-genome sequencing of the strain revealed a multibacteriocin gene cluster encoding one class IIb bacteriocin, two class IId bacteriocins, in addition to a three-component regulatory system and a dedicated ABC transporter. Isolation and purification of the antimicrobial activity from culture supernatants resulted in the detection of a 6.3-kDa mass peak by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, a mass corresponding to the predicted size of one of the class IId bacteriocins. The identification of this bacteriocin, called ubericin K, was further confirmed by in vitro protein synthesis, which showed the same inhibitory spectrum as the purified antimicrobial compound. Ubericin K shows highest sequence similarity to the class IId bacteriocins bovicin 255, lactococcin A, and garvieacin Q. We found that ubericin K uses the sugar transporter mannose phosphotransferase (PTS) as a target receptor. Further, by using the pHlourin sensor system to detect intracellular pH changes due to leakage across the membrane, ubericin K was shown to be a pore former, killing target cells by membrane disruption. IMPORTANCE Bacterial infections in dairy cows are a major burden to farmers worldwide because infected cows require expensive treatments and produce less milk. Today, infected cows are treated with antibiotics, a practice that is becoming less effective due to antibiotic resistance. Compounds other than antibiotics also exist that kill bacteria causing infections in cows; these compounds, known as bacteriocins, are natural products produced by other bacteria in the environment. In this work, we discover a new bacteriocin that we call ubericin K, which kills several species of bacteria known to cause infections in dairy cows. We also use in vitro synthesis as a novel method for rapidly characterizing bacteriocins directly from genomic data, which could be useful for other researchers. We believe that ubericin K and the methods described in this work will aid in the transition away from antibiotics in the dairy industry.
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Affiliation(s)
- Thomas F. Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kirill V. Ovchinnikov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kai A. Hestad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Goldbeck
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Judith Narvhus
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Tee HS, Wood SA, Bouma-Gregson K, Lear G, Handley KM. Genome Streamlining, Plasticity, and Metabolic Versatility Distinguish Co-occurring Toxic and Nontoxic Cyanobacterial Strains of Microcoleus. mBio 2021; 12:e0223521. [PMID: 34700377 PMCID: PMC8546630 DOI: 10.1128/mbio.02235-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/20/2021] [Indexed: 01/21/2023] Open
Abstract
Harmful cyanobacterial bloom occurrences have increased worldwide due to climate change and eutrophication, causing nuisance and animal deaths. Species from the benthic cyanobacterial genus Microcoleus are ubiquitous and form thick mats in freshwater systems, such as rivers, that are sometimes toxic due to the production of potent neurotoxins (anatoxins). Anatoxin-producing (toxic) strains typically coexist with non-anatoxin-producing (nontoxic) strains in mats, although the reason for this is unclear. To determine the genetic mechanisms differentiating toxic and nontoxic Microcoleus, we sequenced and assembled genomes from 11 cultures and compared these to another 31 Microcoleus genomes. Average nucleotide identities (ANI) indicate that toxic and nontoxic strains are distinct species (ANI, <95%), and only 6% of genes are shared across all 42 genomes, suggesting a high level of genetic divergence among Microcoleus strains. Comparative genomics showed substantial genome streamlining in toxic strains and a potential dependency on external sources for thiamine and sucrose. Toxic and nontoxic strains are further differentiated by an additional set of putative nitrate transporter (nitrogen uptake) and cyanophycin (carbon and nitrogen storage) genes, respectively. These genes likely confer distinct competitive advantages based on nutrient availability and suggest nontoxic strains are more robust to nutrient fluctuations. Nontoxic strains also possess twice as many transposable elements, potentially facilitating greater genetic adaptation to environmental changes. Our results offer insights into the divergent evolution of Microcoleus strains and the potential for cooperative and competitive interactions that contribute to the co-occurrence of toxic and nontoxic species within mats. IMPORTANCE Microcoleus autumnalis, and closely related Microcoleus species, compose a geographically widespread group of freshwater benthic cyanobacteria. Canine deaths due to anatoxin-a poisoning, following exposure to toxic proliferations, have been reported globally. While Microcoleus proliferations are on the rise, the mechanisms underpinning competition between, or coexistence of, toxic and nontoxic strains are unknown. This study identifies substantial genetic differences between anatoxin-producing and non-anatoxin-producing strains, pointing to reduced metabolic flexibility in toxic strains, and potential dependence on cohabiting nontoxic strains. Results provide insights into the metabolic and evolutionary differences between toxic and nontoxic Microcoleus, which may assist in predicting and managing aquatic proliferations.
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Affiliation(s)
- Hwee Sze Tee
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Keith Bouma-Gregson
- U.S. Geological Survey, California Water Science Center, Sacramento, California, USA
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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14
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Dextro RB, Delbaje E, Cotta SR, Zehr JP, Fiore MF. Trends in Free-access Genomic Data Accelerate Advances in Cyanobacteria Taxonomy. JOURNAL OF PHYCOLOGY 2021; 57:1392-1402. [PMID: 34291461 DOI: 10.1111/jpy.13200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Free access databases of DNA sequences containing microbial genetic information have changed the way scientists look at the microbial world. Currently, the NCBI database includes about 516 distinct search results for Cyanobacterial genomes distributed in a taxonomy based on a polyphasic approach. While their classification and taxonomic relationships are widely used as is, recent proposals to alter their grouping include further exploring the relationship between Cyanobacteria and Melainabacteria. Nowadays, most cyanobacteria still are named under the Botanical Code; however, there is a proposal made by the Genome Taxonomy Database (GTDB) to harmonize cyanobacteria nomenclature with the other bacteria, an initiative to standardize microbial taxonomy based on genome phylogeny, in order to contribute to an overall better phylogenetic resolution of microbiota. Furthermore, the assembly level of the genomes and their geographical origin demonstrates some trends of cyanobacteria genomics on the scientific community, such as low availability of complete genomes and underexplored sampling locations. By describing how available cyanobacterial genomes from free-access databases fit within different taxonomic classifications, this mini-review provides a holistic view of the current knowledge of cyanobacteria and indicates some steps towards improving our efforts to create a more cohesive and inclusive classifying system, which can be greatly improved by using large-scale sequencing and metagenomic techniques.
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Affiliation(s)
- Rafael B Dextro
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, 13416-000, Piracicaba, SP, Brazil
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, 13416-000, Piracicaba, SP, Brazil
| | - Simone R Cotta
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, 13416-000, Piracicaba, SP, Brazil
| | - Jonathan P Zehr
- Ocean Sciences Department, University of California, 1156 High Street, Santa Cruz, California, 95064, USA
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, 13416-000, Piracicaba, SP, Brazil
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15
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Anabaenopeptins: What We Know So Far. Toxins (Basel) 2021; 13:toxins13080522. [PMID: 34437393 PMCID: PMC8402340 DOI: 10.3390/toxins13080522] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Cyanobacteria are microorganisms with photosynthetic mechanisms capable of colonizing several distinct environments worldwide. They can produce a vast spectrum of bioactive compounds with different properties, resulting in an improved adaptative capacity. Their richness in secondary metabolites is related to their unique and diverse metabolic apparatus, such as Non-Ribosomal Peptide Synthetases (NRPSs). One important class of peptides produced by the non-ribosomal pathway is anabaenopeptins. These cyclic hexapeptides demonstrated inhibitory activity towards phosphatases and proteases, which could be related to their toxicity and adaptiveness against zooplankters and crustaceans. Thus, this review aims to identify key features related to anabaenopeptins, including the diversity of their structure, occurrence, the biosynthetic steps for their production, ecological roles, and biotechnological applications.
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16
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Teso-Pérez C, Martínez-Bueno M, Peralta-Sánchez JM, Valdivia E, Maqueda M, Fárez-Vidal ME, Martín-Platero AM. Enterocin Cross-Resistance Mediated by ABC Transport Systems. Microorganisms 2021; 9:microorganisms9071411. [PMID: 34208875 PMCID: PMC8306556 DOI: 10.3390/microorganisms9071411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022] Open
Abstract
In their struggle for life, bacteria frequently produce antagonistic substances against competitors. Antimicrobial peptides produced by bacteria (known as bacteriocins) are active against other bacteria, but harmless to their producer due to an associated immunity gene that prevents self-inhibition. However, knowledge of cross-resistance between different types of bacteriocin producer remains very limited. The immune function of certain bacteriocins produced by the Enterococcus genus (known as enterocins) is mediated by an ABC transporter. This is the case for enterocin AS-48, a gene cluster that includes two ABC transporter-like systems (Transporter-1 and 2) and an immunity protein. Transporter-2 in this cluster shows a high similarity to the ABC transporter-like system in MR10A and MR10B enterocin gene clusters. The aim of our study was to determine the possible role of this ABC transporter in cross-resistance between these two different types of enterocin. To this end, we designed different mutants (Tn5 derivative and deletion mutants) of the as-48 gene cluster in Enterococcus faecalis and cloned them into the pAM401 shuttle vector. Antimicrobial activity assays showed that enterocin AS-48 Transporter-2 is responsible for cross-resistance between AS-48 and MR10A/B enterocin producers and allowed identification of the MR10A/B immunity gene system. These findings open the way to the investigation of resistance beyond homologous bacteriocins.
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Affiliation(s)
- Claudia Teso-Pérez
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain; (M.M.-B.); (J.M.P.-S.); (E.V.); (M.M.)
- Correspondence: (C.T.-P.); (M.E.F.-V.); (A.M.M.-P.)
| | - Manuel Martínez-Bueno
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain; (M.M.-B.); (J.M.P.-S.); (E.V.); (M.M.)
| | - Juan Manuel Peralta-Sánchez
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain; (M.M.-B.); (J.M.P.-S.); (E.V.); (M.M.)
| | - Eva Valdivia
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain; (M.M.-B.); (J.M.P.-S.); (E.V.); (M.M.)
| | - Mercedes Maqueda
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain; (M.M.-B.); (J.M.P.-S.); (E.V.); (M.M.)
| | - M. Esther Fárez-Vidal
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain
- Instituto de Investigación Biomédica IBS, Granada, Complejo Hospitalario Universitario de Granada, Universidad de Granada, 18071 Granada, Spain
- Correspondence: (C.T.-P.); (M.E.F.-V.); (A.M.M.-P.)
| | - Antonio M. Martín-Platero
- Departamento de Microbiología, Universidad de Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain; (M.M.-B.); (J.M.P.-S.); (E.V.); (M.M.)
- Correspondence: (C.T.-P.); (M.E.F.-V.); (A.M.M.-P.)
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17
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Ghosh S, Sarangi AN, Mukherjee M, Singh D, Madhavi M, Tripathy S. Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India. Bioinform Biol Insights 2021; 15:11779322211025332. [PMID: 34220198 PMCID: PMC8221699 DOI: 10.1177/11779322211025332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022] Open
Abstract
Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.
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Affiliation(s)
- Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Mayuri Mukherjee
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Madduluri Madhavi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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18
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Recipe for Success: Suggestions and Recommendations for the Isolation and Characterisation of Bacteriocins. Int J Microbiol 2021; 2021:9990635. [PMID: 34257667 PMCID: PMC8249226 DOI: 10.1155/2021/9990635] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 12/29/2022] Open
Abstract
Bacteriocins are bacterially produced antimicrobial peptides. Although only two peptides have been approved for use as natural preservatives foods, current research is focusing on expanding their application as potential therapeutics against clinical pathogens. Our laboratory group has been working on bacteriocins for over 25 years, and during that time, we have isolated bacteriocin-producing microorganisms from a variety of sources including human skin, human faeces, and various foods. These bacteriocins were purified and characterised, and their potential applications were examined. We have also identified bioengineered derivatives of the prototype lantibiotic nisin which possess more desirable properties than the wild-type, such as enhanced antimicrobial activity. In the current communication, we discuss the main methods that were employed to identify such peptides. Furthermore, we provide a step-by-step guide to carrying out these methods that include accompanying diagrams. We hope that our recommendations and advice will be of use to others in their search for, and subsequent analysis of, novel bacteriocins, and derivatives thereof.
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19
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Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe. Mar Drugs 2021; 19:md19060298. [PMID: 34073758 PMCID: PMC8225149 DOI: 10.3390/md19060298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.
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20
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Malit JJL, Wu C, Liu LL, Qian PY. Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters. Front Microbiol 2021; 12:635389. [PMID: 33995295 PMCID: PMC8120280 DOI: 10.3389/fmicb.2021.635389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Thioamidated ribosomally synthesized and post-translationally modified peptides (RiPPs) are recently characterized natural products with wide range of potent bioactivities, such as antibiotic, antiproliferative, and cytotoxic activities. These peptides are distinguished by the presence of thioamide bonds in the peptide backbone catalyzed by the YcaO-TfuA protein pair with its genes adjacent to each other. Genome mining has facilitated an in silico approach to identify biosynthesis gene clusters (BGCs) responsible for thioamidated RiPP production. In this work, publicly available genomic data was used to detect and illustrate the diversity of putative BGCs encoding for thioamidated RiPPs. AntiSMASH and RiPPER analysis identified 613 unique TfuA-related gene cluster families (GCFs) and 797 precursor peptide families, even on phyla where the presence of these clusters have not been previously described. Several additional biosynthesis genes are colocalized with the detected BGCs, suggesting an array of possible chemical modifications. This study shows that thioamidated RiPPs occupy a widely unexplored chemical landscape.
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Affiliation(s)
- Jessie James Limlingan Malit
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chuanhai Wu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ling-Li Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.,Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
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21
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Khalifa SAM, Shedid ES, Saied EM, Jassbi AR, Jamebozorgi FH, Rateb ME, Du M, Abdel-Daim MM, Kai GY, Al-Hammady MAM, Xiao J, Guo Z, El-Seedi HR. Cyanobacteria-From the Oceans to the Potential Biotechnological and Biomedical Applications. Mar Drugs 2021; 19:241. [PMID: 33923369 PMCID: PMC8146687 DOI: 10.3390/md19050241] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/25/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
Cyanobacteria are photosynthetic prokaryotic organisms which represent a significant source of novel, bioactive, secondary metabolites, and they are also considered an abundant source of bioactive compounds/drugs, such as dolastatin, cryptophycin 1, curacin toyocamycin, phytoalexin, cyanovirin-N and phycocyanin. Some of these compounds have displayed promising results in successful Phase I, II, III and IV clinical trials. Additionally, the cyanobacterial compounds applied to medical research have demonstrated an exciting future with great potential to be developed into new medicines. Most of these compounds have exhibited strong pharmacological activities, including neurotoxicity, cytotoxicity and antiviral activity against HCMV, HSV-1, HHV-6 and HIV-1, so these metabolites could be promising candidates for COVID-19 treatment. Therefore, the effective large-scale production of natural marine products through synthesis is important for resolving the existing issues associated with chemical isolation, including small yields, and may be necessary to better investigate their biological activities. Herein, we highlight the total synthesized and stereochemical determinations of the cyanobacterial bioactive compounds. Furthermore, this review primarily focuses on the biotechnological applications of cyanobacteria, including applications as cosmetics, food supplements, and the nanobiotechnological applications of cyanobacterial bioactive compounds in potential medicinal applications for various human diseases are discussed.
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Affiliation(s)
- Shaden A. M. Khalifa
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Eslam S. Shedid
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt;
| | - Essa M. Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt;
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489 Berlin, Germany
| | - Amir Reza Jassbi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz 71348-53734, Iran; (A.R.J.); (F.H.J.)
| | - Fatemeh H. Jamebozorgi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz 71348-53734, Iran; (A.R.J.); (F.H.J.)
| | - Mostafa E. Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, High Street, Paisley PA1 2BE, UK;
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian 116034, China;
| | - Mohamed M. Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Guo-Yin Kai
- Laboratory of Medicinal Plant Biotechnology, College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 311402, China;
| | | | - Jianbo Xiao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China;
| | - Zhiming Guo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
| | - Hesham R. El-Seedi
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt;
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Pharmacognosy Group, Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, P.O. Box 574, SE-751 23 Uppsala, Sweden
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22
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Dreher TW, Davis EW, Mueller RS, Otten TG. Comparative genomics of the ADA clade within the Nostocales. HARMFUL ALGAE 2021; 104:102037. [PMID: 34023075 DOI: 10.1016/j.hal.2021.102037] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
The ADA clade of Nostocales cyanobacteria, a group that is prominent in current harmful algal bloom events, now includes over 40 genome sequences with the recent addition of sixteen novel sequenced genomes (Dreher et al., Harmful Algae, 2021). Fourteen genomes are complete (closed), enabling highly detailed assessments of gene content and genome architecture. ADA genomes contain 5 rRNA operons, genes expected to support a photoautotrophic and diazotrophic lifestyle, and a varied array of genes for the synthesis of bioactive secondary metabolites. Genes for the production of the taste-and-odor compound geosmin and the four major classes of cyanotoxins - anatoxin-a, cylindrospermopsin, microcystin and saxitoxin - are represented in members of the ADA clade. Notably, the gene array for the synthesis of cylindrospermopsin by Dolichospermum sp. DET69 was located on a plasmid, raising the possibility of facile horizontal transmission. However, genes supporting independent conjugative transfer of this plasmid are lacking. Further, analysis of genomic loci containing this and other cyanotoxin gene arrays shows evidence that these arrays have long-term stability and do not appear to be genomic islands easily capable of horizontal transmission to other cells. There is considerable diversity in the gene complements of individual ADA genomes, including the variable presence of physiologically important genes: genomes in three species-level subclades lack the gas vesicle genes that facilitate a planktonic lifestyle, and, surprisingly, the genome of Cuspidothrix issatschenkoi CHARLIE-1, a reported diazotroph, lacks the genes for nitrogen fixation. Notably, phylogenetically related genomes possess limited synteny, indicating a prominent role for chromosome rearrangements during ADA strain evolution. The genomes contain abundant insertion sequences and repetitive transposase genes, which could be the main drivers of genome rearrangement through active transposition and homologous recombination. No prophages were found, and no evidence of viral infection was observed in the bloom population samples from which the genomes discussed here were derived. Phages thus seem to have a limited influence on ADA evolution.
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Affiliation(s)
- Theo W Dreher
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 USA.
| | - Edward W Davis
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 USA
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Timothy G Otten
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 USA.
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23
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Current Knowledge on Microviridin from Cyanobacteria. Mar Drugs 2021; 19:md19010017. [PMID: 33406599 PMCID: PMC7823629 DOI: 10.3390/md19010017] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Cyanobacteria are a rich source of secondary metabolites with a vast biotechnological potential. These compounds have intrigued the scientific community due their uniqueness and diversity, which is guaranteed by a rich enzymatic apparatus. The ribosomally synthesized and post-translationally modified peptides (RiPPs) are among the most promising metabolite groups derived from cyanobacteria. They are interested in numerous biological and ecological processes, many of which are entirely unknown. Microviridins are among the most recognized class of ribosomal peptides formed by cyanobacteria. These oligopeptides are potent inhibitors of protease; thus, they can be used for drug development and the control of mosquitoes. They also play a key ecological role in the defense of cyanobacteria against microcrustaceans. The purpose of this review is to systematically identify the key characteristics of microviridins, including its chemical structure and biosynthesis, as well as its biotechnological and ecological significance.
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24
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Witthohn M, Strieth D, Eggert S, Kins S, Ulber R, Muffler K. Heterologous production of a cyanobacterial bacteriocin with potent antibacterial activity. CURRENT RESEARCH IN BIOTECHNOLOGY 2021. [DOI: 10.1016/j.crbiot.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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25
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Yount NY, Weaver DC, de Anda J, Lee EY, Lee MW, Wong GCL, Yeaman MR. Discovery of Novel Type II Bacteriocins Using a New High-Dimensional Bioinformatic Algorithm. Front Immunol 2020; 11:1873. [PMID: 33013838 PMCID: PMC7494827 DOI: 10.3389/fimmu.2020.01873] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/13/2020] [Indexed: 12/28/2022] Open
Abstract
Antimicrobial compounds first arose in prokaryotes by necessity for competitive self-defense. In this light, prokaryotes invented the first host defense peptides. Among the most well-characterized of these peptides are class II bacteriocins, ribosomally-synthesized polypeptides produced chiefly by Gram-positive bacteria. In the current study, a tensor search protocol-the BACIIα algorithm-was created to identify and classify bacteriocin sequences with high fidelity. The BACIIα algorithm integrates a consensus signature sequence, physicochemical and genomic pattern elements within a high-dimensional query tool to select for bacteriocin-like peptides. It accurately retrieved and distinguished virtually all families of known class II bacteriocins, with an 86% specificity. Further, the algorithm retrieved a large set of unforeseen, putative bacteriocin peptide sequences. A recently-developed machine-learning classifier predicted the vast majority of retrieved sequences to induce negative Gaussian curvature in target membranes, a hallmark of antimicrobial activity. Prototypic bacteriocin candidate sequences were synthesized and demonstrated potent antimicrobial efficacy in vitro against a broad spectrum of human pathogens. Therefore, the BACIIα algorithm expands the scope of prokaryotic host defense bacteriocins and enables an innovative bioinformatics discovery strategy. Understanding how prokaryotes have protected themselves against microbial threats over eons of time holds promise to discover novel anti-infective strategies to meet the challenge of modern antibiotic resistance.
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Affiliation(s)
- Nannette Y. Yount
- Division of Infectious Diseases, Los Angeles County Harbor-UCLA Medical Center, Torrance, CA, United States
- Division of Molecular Medicine, Los Angeles County Harbor-UCLA Medical Center, Torrance, CA, United States
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
| | - David C. Weaver
- Department of Mathematics, University of California, Berkeley, Berkeley, CA, United States
| | - Jaime de Anda
- Departments of Bioengineering, Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- The California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ernest Y. Lee
- Departments of Bioengineering, Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- The California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Michelle W. Lee
- Departments of Bioengineering, Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- The California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gerard C. L. Wong
- Departments of Bioengineering, Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States
- The California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Michael R. Yeaman
- Division of Infectious Diseases, Los Angeles County Harbor-UCLA Medical Center, Torrance, CA, United States
- Division of Molecular Medicine, Los Angeles County Harbor-UCLA Medical Center, Torrance, CA, United States
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
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26
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Bösch NM, Borsa M, Greczmiel U, Morinaka BI, Gugger M, Oxenius A, Vagstad AL, Piel J. Landornamides: Antiviral Ornithine‐Containing Ribosomal Peptides Discovered through Genome Mining. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Nina M. Bösch
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Mariana Borsa
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Ute Greczmiel
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Brandon I. Morinaka
- Department of Pharmacy National University of Singapore 18 Science Drive 4 Singapore 117543 Singapore
| | - Muriel Gugger
- Institut Pasteur Collection des Cyanobactéries Département de Microbiologie 75015 Paris France
| | - Annette Oxenius
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Anna L. Vagstad
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jörn Piel
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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27
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Bösch NM, Borsa M, Greczmiel U, Morinaka BI, Gugger M, Oxenius A, Vagstad AL, Piel J. Landornamides: Antiviral Ornithine‐Containing Ribosomal Peptides Discovered through Genome Mining. Angew Chem Int Ed Engl 2020; 59:11763-11768. [DOI: 10.1002/anie.201916321] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/11/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Nina M. Bösch
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Mariana Borsa
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Ute Greczmiel
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Brandon I. Morinaka
- Department of Pharmacy National University of Singapore 18 Science Drive 4 Singapore 117543 Singapore
| | - Muriel Gugger
- Institut Pasteur Collection des Cyanobactéries Département de Microbiologie 75015 Paris France
| | - Annette Oxenius
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Anna L. Vagstad
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jörn Piel
- Institute of Microbiology Eidgenössische Technische Hochschule (ETH) Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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28
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Österholm J, Popin RV, Fewer DP, Sivonen K. Phylogenomic Analysis of Secondary Metabolism in the Toxic Cyanobacterial Genera Anabaena, Dolichospermum and Aphanizomenon. Toxins (Basel) 2020; 12:E248. [PMID: 32290496 PMCID: PMC7232259 DOI: 10.3390/toxins12040248] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 01/20/2023] Open
Abstract
Cyanobacteria produce an array of toxins that pose serious health risks to humans and animals. The closely related diazotrophic genera, Anabaena, Dolichospermum, and Aphanizomenon, frequently form poisonous blooms in lakes and brackish waters around the world. These genera form a complex now termed the Anabaena, Dolichospermum, and Aphanizomenon (ADA) clade and produce a greater array of toxins than any other cyanobacteria group. However, taxonomic confusion masks the distribution of toxin biosynthetic pathways in cyanobacteria. Here we obtained 11 new draft genomes to improve the understanding of toxin production in these genera. Comparison of secondary metabolite pathways in all available 31 genomes for these three genera suggests that the ability to produce microcystin, anatoxin-a, and saxitoxin is associated with specific subgroups. Each toxin gene cluster was concentrated or even limited to a certain subgroup within the ADA clade. Our results indicate that members of the ADA clade encode a variety of secondary metabolites following the phylogenetic clustering of constituent species. The newly sequenced members of the ADA clade show that phylogenetic separation of planktonic Dolichospermum and benthic Anabaena is not complete. This underscores the importance of taxonomic revision of Anabaena, Dolichospermum, and Aphanizomenon genera to reflect current phylogenomic understanding.
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Affiliation(s)
| | | | | | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (J.Ö.); (R.V.P.); (D.P.F.)
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29
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Baindara P, Nallabelli N, Korpole S. Whole genome mining reveals a diverse repertoire of lanthionine synthetases and lanthipeptides among the genus
Paenibacillus. J Appl Microbiol 2019; 128:473-490. [DOI: 10.1111/jam.14495] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 12/16/2022]
Affiliation(s)
- P Baindara
- CSIR‐Institute of Microbial Technology Microbial Type Culture Collection and Gene Bank Chandigarh India
| | - N Nallabelli
- CSIR‐Institute of Microbial Technology Microbial Type Culture Collection and Gene Bank Chandigarh India
| | - S Korpole
- CSIR‐Institute of Microbial Technology Microbial Type Culture Collection and Gene Bank Chandigarh India
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30
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Mareš J, Johansen JR, Hauer T, Zima J, Ventura S, Cuzman O, Tiribilli B, Kaštovský J. Taxonomic resolution of the genus Cyanothece (Chroococcales, Cyanobacteria), with a treatment on Gloeothece and three new genera, Crocosphaera, Rippkaea, and Zehria. JOURNAL OF PHYCOLOGY 2019; 55:578-610. [PMID: 30830691 DOI: 10.1111/jpy.12853] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/06/2018] [Indexed: 06/09/2023]
Abstract
The systematics of single-celled cyanobacteria represents a major challenge due to morphological convergence and application of various taxonomic concepts. The genus Cyanothece is one of the most problematic cases, as the name has been applied to oval-shaped coccoid cyanobacteria lacking sheaths with little regard to their phylogenetic position and details of morphology and ultrastructure. Hereby we analyze an extensive set of complementary genetic and phenotypic evidence to disentangle the relationships among these cyanobacteria. We provide diagnostic characters to separate the known genera Cyanothece, Gloeothece, and Aphanothece, and provide a valid description for Crocosphaera gen. nov. We describe two new genera, Rippkaea and Zehria, to characterize two distinct phylogenetic lineages outside the previously known genera. We further describe 13 new species in total including Cyanothece svehlovae, Gloeothece aequatorialis, G. aurea, G. bryophila, G. citriformis, G. reniformis, Gloeothece tonkinensis, G. verrucosa, Crocosphaera watsonii, C. subtropica, C. chwakensis, Rippkaea orientalis, and Zehria floridana to recognize the intrageneric diversity as rendered by polyphasic analysis. We discuss the close relationship of free-living cyanobacteria from the Crocosphaera lineage to nitrogen-fixing endosymbionts of marine algae. The current study includes several experimental strains (Crocosphaera and "Cyanothece") important for the study of diazotrophy and the global oceanic nitrogen cycle, and provides evidence suggesting ancestral N2 -fixing capability in the chroococcalean lineage.
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Affiliation(s)
- Jan Mareš
- Institute of Hydrobiology, Biology Centre, The Czech Academy of Sciences, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Jeffrey R Johansen
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
- John Carroll University, Department of Biology, University Heights, Ohio, 44118, USA
| | - Tomáš Hauer
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982, Třeboň, Czech Republic
| | - Jan Zima
- Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982, Třeboň, Czech Republic
- Department of Parasitology, Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice
| | - Stefano Ventura
- Firenze Unit, Institute of Ecosystem Study, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Oana Cuzman
- Institute for the Conservation and Valorization of Cultural Heritage, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Bruno Tiribilli
- Firenze Unit, Institute for Complex Systems, National Research Council of Italy, via Madonna del Piano 10, I-500 19, Sesto Fiorentino, Italy
| | - Jan Kaštovský
- Department of Botany, University of South Bohemia, Faculty of Science, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
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31
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Chu WL, Phang SM. Bioactive Compounds from Microalgae and Their Potential Applications as Pharmaceuticals and Nutraceuticals. GRAND CHALLENGES IN ALGAE BIOTECHNOLOGY 2019. [DOI: 10.1007/978-3-030-25233-5_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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Cabello-Yeves PJ, Picazo A, Camacho A, Callieri C, Rosselli R, Roda-Garcia JJ, Coutinho FH, Rodriguez-Valera F. Ecological and genomic features of two widespread freshwater picocyanobacteria. Environ Microbiol 2018; 20:3757-3771. [PMID: 30117250 DOI: 10.1111/1462-2920.14377] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/08/2018] [Indexed: 12/15/2022]
Abstract
We present two genomes of widespread freshwater picocyanobacteria isolated by extinction dilution from a Spanish oligotrophic reservoir. Based on microscopy and genomic properties, both picocyanobacteria were tentatively designated Synechococcus lacustris Tous, formerly described as a metagenome assembled genome (MAG) from the same habitat, and Cyanobium usitatum Tous, described here for the first time. Both strains were purified in unicyanobacterial cultures, and their genomes were sequenced. They are broadly distributed in freshwater systems; the first seems to be a specialist on temperate reservoirs (Tous, Amadorio, Dexter, Lake Lanier, Sparkling), and the second appears to also be abundant in cold environments including ice-covered lakes such as Lake Baikal, Lake Erie or the brackish Baltic Sea. Having complete genomes provided access to the flexible genome that does not assemble in MAGs. We found several genomic islands in both genomes, within which there were genes for nitrogen acquisition, transporters for a wide set of compounds and biosynthesis of phycobilisomes in both strains. Some of these regions of low coverage in metagenomes also included antimicrobial compounds, transposases and phage defence systems, including a novel type III CRISPR-Cas phage defence system that was only detected in Synechococcus lacustris Tous.
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Affiliation(s)
- Pedro J Cabello-Yeves
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | | | - Riccardo Rosselli
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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33
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BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously. G3-GENES GENOMES GENETICS 2018; 8:2167-2172. [PMID: 29789313 PMCID: PMC6027881 DOI: 10.1534/g3.118.200220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
One of the most commonly used tools to compare protein or DNA sequences against databases is BLAST. We introduce a web tool that allows the performance of BLAST-searches of protein/DNA sequences in whole-genome sequenced bacteria/archaea, and displays a large amount of BLAST-results simultaneously. The circular bacterial replicons are projected as horizontal lines with fixed length of 360, representing the degrees of a circle. A coordinate system is created with length of the replicon along the x-axis and the number of replicon used on the y-axis. When a query sequence matches with a gene/protein of a particular replicon, the BLAST-results are depicted as an "x,y" position in a specially adapted plot. This tool allows the visualization of the results from the whole data to a particular gene/protein in real time with low computational resources.
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34
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Driscoll CB, Meyer KA, Šulčius S, Brown NM, Dick GJ, Cao H, Gasiūnas G, Timinskas A, Yin Y, Landry ZC, Otten TG, Davis TW, Watson SB, Dreher TW. A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales. HARMFUL ALGAE 2018; 77:93-107. [PMID: 30005805 DOI: 10.1016/j.hal.2018.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N2-fixing heterocysts, and the uptake and incorporation of the major nutrients P, N and S, we identified several gene pathways in the pangenome that may contribute to niche partitioning. Genes for problematic secondary metabolites-cyanotoxins and taste-and-odor compounds-were sporadically present, as were other polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. By contrast, genes predicted to encode the ribosomally generated bacteriocin peptides were found in all genomes.
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Affiliation(s)
- Connor B Driscoll
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Kevin A Meyer
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI 48109-1005, USA
| | - Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Akademijos Str. 2, LT-08412, Vilnius, Lithuania
| | - Nathan M Brown
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Gregory J Dick
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA
| | - Huansheng Cao
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA
| | - Giedrius Gasiūnas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Albertas Timinskas
- Department of Bioinformatics, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Zachary C Landry
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Timothy G Otten
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Timothy W Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43402, USA
| | - Susan B Watson
- Environment and Climate Change Canada, Canada Centre for Inland Waters, Burlington, ON L7S 1A1, Canada
| | - Theo W Dreher
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
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35
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ATPase activity regulation by leader peptide processing of ABC transporter maturation and secretion protein, NukT, for lantibiotic nukacin ISK-1. Appl Microbiol Biotechnol 2017; 102:763-772. [DOI: 10.1007/s00253-017-8645-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/09/2017] [Accepted: 11/12/2017] [Indexed: 10/18/2022]
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36
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Carson DA, Barkema HW, Naushad S, De Buck J. Bacteriocins of Non-aureus Staphylococci Isolated from Bovine Milk. Appl Environ Microbiol 2017; 83:e01015-17. [PMID: 28667105 PMCID: PMC5561277 DOI: 10.1128/aem.01015-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/23/2017] [Indexed: 12/24/2022] Open
Abstract
Non-aureus staphylococci (NAS), the bacteria most commonly isolated from the bovine udder, potentially protect the udder against infection by major mastitis pathogens due to bacteriocin production. In this study, we determined the inhibitory capability of 441 bovine NAS isolates (comprising 26 species) against bovine Staphylococcus aureus Furthermore, inhibiting isolates were tested against a human methicillin-resistant S. aureus (MRSA) isolate using a cross-streaking method. We determined the presence of bacteriocin clusters in NAS whole genomes using genome mining tools, BLAST, and comparison of genomes of closely related inhibiting and noninhibiting isolates and determined the genetic organization of any identified bacteriocin biosynthetic gene clusters. Forty isolates from 9 species (S. capitis, S. chromogenes, S. epidermidis, S. pasteuri, S. saprophyticus, S. sciuri, S. simulans, S. warneri, and S. xylosus) inhibited growth of S. aureus in vitro, 23 isolates of which, from S. capitis, S. chromogenes, S. epidermidis, S. pasteuri, S. simulans, and S. xylosus, also inhibited MRSA. One hundred five putative bacteriocin gene clusters encompassing 6 different classes (lanthipeptides, sactipeptides, lasso peptides, class IIa, class IIc, and class IId) in 95 whole genomes from 16 species were identified. A total of 25 novel bacteriocin precursors were described. In conclusion, NAS from bovine mammary glands are a source of potential bacteriocins, with >21% being possible producers, representing potential for future characterization and prospective clinical applications.IMPORTANCE Mastitis (particularly infections caused by Staphylococcus aureus) costs Canadian dairy producers $400 million/year and is the leading cause of antibiotic use on dairy farms. With increasing antibiotic resistance and regulations regarding use, there is impetus to explore bacteriocins (bacterially produced antimicrobial peptides) for treatment and prevention of bacterial infections. We examined the ability of 441 NAS bacteria from Canadian bovine milk samples to inhibit growth of S. aureus in the laboratory. Overall, 9% inhibited growth of S. aureus and 58% of those also inhibited MRSA. In NAS whole-genome sequences, we identified >21% of NAS as having bacteriocin genes. Our study represents a foundation to further explore NAS bacteriocins for clinical use.
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Affiliation(s)
- Domonique A Carson
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Sohail Naushad
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jeroen De Buck
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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37
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Collins FWJ, O'Connor PM, O'Sullivan O, Gómez-Sala B, Rea MC, Hill C, Ross RP. Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome. Sci Rep 2017; 7:3481. [PMID: 28615683 PMCID: PMC5471241 DOI: 10.1038/s41598-017-03339-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/20/2017] [Indexed: 11/09/2022] Open
Abstract
Lactobacilli constitute a large genus of Gram-positive lactic acid bacteria which have widespread roles ranging from gut commensals to starters in fermented foods. A combination of in silico and laboratory-based screening allowed us to determine the overall bacteriocin producing potential of representative strains of each species of the genus. The genomes of 175 lactobacilli and 38 associated species were screened for the presence of antimicrobial producing genes and combined with screening for antimicrobial activity against a range of indicators. There also appears to be a link between the strains' environment and bacteriocin production, with those from the animal and human microbiota encoding over twice as many bacteriocins as those from other sources. Five novel bacteriocins were identified belonging to differing bacteriocin classes, including two-peptide bacteriocins (muricidin and acidocin X) and circular bacteriocins (paracyclicin). In addition, there was a clear clustering of helveticin type bacteriolysins in the Lactobacillus acidophilus group of species. This combined in silico and in vitro approach to screening has demonstrated the true diversity and complexity of bacteriocins across the genus. It also highlights their biological importance in terms of communication and competition between closely related strains in diverse complex microbial environments.
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Affiliation(s)
- Fergus W J Collins
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Paula M O'Connor
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Mary C Rea
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- Teagasc Food Research Centre, Teagasc Moorepark, Fermoy, Cork, Ireland. .,APC Microbiome Institute, University College Cork, Cork, Ireland. .,School of Microbiology, University College Cork, Cork, Ireland.
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38
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Abstract
INTRODUCTION The effectiveness of lantibiotics against MDR pathogens and the progression of agents MU1140, NAI-107, NVB302 and duramycin into pre-clinical and clinical trials have highlighted their potential in the fight against bacterial resistance. The number of known lantibiotics and knowledge of their biosynthetic pathways has increased in recent years due to higher quality genomic data being delivered by next generation sequencing technologies combined with the development of specific genome mining tools, enabling the prediction of lantibiotic clusters. Areas covered: In this review, the author describes how the increase of high quality genomic data has increased the discovery of novel lantibiotics. Expert opinion: Novel apparatus such as the iChip enabling the isolation of uncultable bacteria will undoubtedly increase the identification rate of novel antimicrobial peptides including lantibiotics. The ability to then assess the lantibiotic clusters via recombinant production or synthesis using a high throughput method is one of the next challenges for developing these agents into the clinical environment.
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Aharonovich D, Sher D. Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals. THE ISME JOURNAL 2016; 10:2892-2906. [PMID: 27128996 PMCID: PMC5148192 DOI: 10.1038/ismej.2016.70] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/16/2016] [Accepted: 03/22/2016] [Indexed: 11/08/2022]
Abstract
Interactions between marine microorganisms may determine the dynamics of microbial communities. Here, we show that two strains of the globally abundant marine cyanobacterium Prochlorococcus, MED4 and MIT9313, which belong to two different ecotypes, differ markedly in their response to co-culture with a marine heterotrophic bacterium, Alteromonas macleodii strain HOT1A3. HOT1A3 enhanced the growth of MIT9313 at low cell densities, yet inhibited it at a higher concentration, whereas it had no effect on MED4 growth. The early transcriptomic responses of Prochlorococcus cells after 20 h in co-culture showed no evidence of nutrient starvation, whereas the expression of genes involved in photosynthesis, protein synthesis and stress responses typically decreased in MED4 and increased in MIT313. Differential expression of genes involved in outer membrane modification, efflux transporters and, in MIT9313, lanthipeptides (prochlorosins) suggests that Prochlorococcus mount a specific response to the presence of the heterotroph in the cultures. Intriguingly, many of the differentially-expressed genes encoded short proteins, including two new families of co-culture responsive genes: CCRG-1, which is found across the Prochlorococcus lineage and CCRG-2, which contains a sequence motif involved in the export of prochlorosins and other bacteriocin-like peptides, and are indeed released from the cells into the media.
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Affiliation(s)
- Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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40
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Liu L, Hao T, Xie Z, Horsman GP, Chen Y. Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans. Sci Rep 2016; 6:37479. [PMID: 27869143 PMCID: PMC5116633 DOI: 10.1038/srep37479] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/28/2016] [Indexed: 11/09/2022] Open
Abstract
Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as "poor" sources of natural products.
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Affiliation(s)
- Liwei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Hao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhoujie Xie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, N2L3C5, Canada
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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41
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Liaimer A, Jensen JB, Dittmann E. A Genetic and Chemical Perspective on Symbiotic Recruitment of Cyanobacteria of the Genus Nostoc into the Host Plant Blasia pusilla L. Front Microbiol 2016; 7:1693. [PMID: 27847500 PMCID: PMC5088731 DOI: 10.3389/fmicb.2016.01693] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/10/2016] [Indexed: 12/04/2022] Open
Abstract
Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction showed a remarkable local diversity among isolates assigned to several Nostoc clades. An extensive web of negative allelopathic interactions was recorded at an agricultural site, but not at the undisturbed natural site. The cell extracts of the cyanobacteria did not show antimicrobial activities, but four isolates were shown to be cytotoxic to human cells. The secondary metabolite profiles of the isolates were mapped by MALDI-TOF MS, and the most prominent ions were further analyzed by Q-TOF for MS/MS aided identification. Symbiotic isolates produced a great variety of small peptide-like substances, most of which lack any record in the databases. Among identified compounds we found microcystin and nodularin variants toxic to eukaryotic cells. Microcystin producing chemotypes were dominating as symbiotic recruits but not in the free-living community. In addition, we were able to identify several novel aeruginosins and banyaside-like compounds, as well as nostocyclopeptides and nosperin.
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Affiliation(s)
- Anton Liaimer
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of NorwayTromsø, Norway
| | - John B. Jensen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of NorwayTromsø, Norway
| | - Elke Dittmann
- Department of Microbiology, Institute for Biochemistry and Biology, University of PotsdamPotsdam, Germany
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42
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Parnasa R, Nagar E, Sendersky E, Reich Z, Simkovsky R, Golden S, Schwarz R. Small secreted proteins enable biofilm development in the cyanobacterium Synechococcus elongatus. Sci Rep 2016; 6:32209. [PMID: 27558743 PMCID: PMC4997328 DOI: 10.1038/srep32209] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/03/2016] [Indexed: 11/18/2022] Open
Abstract
Small proteins characterized by a double-glycine (GG) secretion motif, typical of secreted bacterial antibiotics, are encoded by the genomes of diverse cyanobacteria, but their functions have not been investigated to date. Using a biofilm-forming mutant of Synechococcus elongatus PCC 7942 and a mutational approach, we demonstrate the involvement of four small secreted proteins and their GG-secretion motifs in biofilm development. These proteins are denoted EbfG1-4 (enable biofilm formation with a GG-motif). Furthermore, the conserved cysteine of the peptidase domain of the Synpcc7942_1133 gene product (dubbed PteB for peptidase transporter essential for biofilm) is crucial for biofilm development and is required for efficient secretion of the GG-motif containing proteins. Transcriptional profiling of ebfG1-4 indicated elevated transcript levels in the biofilm-forming mutant compared to wild type (WT). However, these transcripts decreased, acutely but transiently, when the mutant was cultured in extracellular fluids from a WT culture, and biofilm formation was inhibited. We propose that WT cells secrete inhibitor(s) that suppress transcription of ebfG1-4, whereas secretion of the inhibitor(s) is impaired in the biofilm-forming mutant, leading to synthesis and secretion of EbfG1-4 and supporting the formation of biofilms.
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Affiliation(s)
- Rami Parnasa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Ziv Reich
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Golden
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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43
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Coutinho FH, Dutilh BE, Thompson CC, Thompson FL. Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features. Arch Microbiol 2016; 198:973-986. [PMID: 27339259 DOI: 10.1007/s00203-016-1256-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/23/2016] [Accepted: 06/07/2016] [Indexed: 01/24/2023]
Abstract
Members of the recently proposed genus Parasynechococcus (Cyanobacteria) are extremely abundant throughout the global ocean and contribute significantly to global primary productivity. However, the taxonomy of these organisms remains poorly characterized. The aim of this study was to propose a new taxonomic framework for Parasynechococcus based on a genomic taxonomy approach that incorporates genomic, physiological and ecological data. Through in silico DNA-DNA hybridization, average amino acid identity, dinucleotide signatures and phylogenetic reconstruction, a total of 15 species of Parasynechococcus could be delineated. Each species was then described on the basis of their gene content, light and nutrient utilization strategies, geographical distribution patterns throughout the oceans and response to environmental parameters.
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Affiliation(s)
- F H Coutinho
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - B E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - C C Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - F L Thompson
- Instituto de Biologia (IB), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- COPPE, SAGE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
- CCS, IB, BIOMAR, Laboratório de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho. S/N, BLOCO A (Anexo) A3 - sl 102, Rio de Janeiro, RJ, 21941-599, Brazil.
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44
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Mazard S, Penesyan A, Ostrowski M, Paulsen IT, Egan S. Tiny Microbes with a Big Impact: The Role of Cyanobacteria and Their Metabolites in Shaping Our Future. Mar Drugs 2016; 14:E97. [PMID: 27196915 PMCID: PMC4882571 DOI: 10.3390/md14050097] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 01/12/2023] Open
Abstract
Cyanobacteria are among the first microorganisms to have inhabited the Earth. Throughout the last few billion years, they have played a major role in shaping the Earth as the planet we live in, and they continue to play a significant role in our everyday lives. Besides being an essential source of atmospheric oxygen, marine cyanobacteria are prolific secondary metabolite producers, often despite the exceptionally small genomes. Secondary metabolites produced by these organisms are diverse and complex; these include compounds, such as pigments and fluorescent dyes, as well as biologically-active compounds with a particular interest for the pharmaceutical industry. Cyanobacteria are currently regarded as an important source of nutrients and biofuels and form an integral part of novel innovative energy-efficient designs. Being autotrophic organisms, cyanobacteria are well suited for large-scale biotechnological applications due to the low requirements for organic nutrients. Recent advances in molecular biology techniques have considerably enhanced the potential for industries to optimize the production of cyanobacteria secondary metabolites with desired functions. This manuscript reviews the environmental role of marine cyanobacteria with a particular focus on their secondary metabolites and discusses current and future developments in both the production of desired cyanobacterial metabolites and their potential uses in future innovative projects.
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Affiliation(s)
- Sophie Mazard
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia.
| | - Anahit Penesyan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia.
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia.
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney NSW 2109, Australia.
| | - Suhelen Egan
- Centre for Marine Bio-Innovation and School of Biological Earth and Environmental Sciences, University of New South Wales, Sydney NSW 2052, Australia.
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45
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Dittmann E, Gugger M, Sivonen K, Fewer DP. Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria. Trends Microbiol 2016; 23:642-652. [PMID: 26433696 DOI: 10.1016/j.tim.2015.07.008] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/07/2015] [Accepted: 07/17/2015] [Indexed: 10/23/2022]
Abstract
Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with intricate chemical structures and potent biological activities. The bulk of these natural products are known from just a handful of genera. Recent efforts have elucidated the mechanisms underpinning the biosynthesis of a diverse array of natural products from cyanobacteria. Many of the biosynthetic mechanisms are unique to cyanobacteria or rarely described from other organisms. Advances in genome sequence technology have precipitated a deluge of genome sequences for cyanobacteria. This makes it possible to link known natural products to biosynthetic gene clusters but also accelerates the discovery of new natural products through genome mining. These studies demonstrate that cyanobacteria encode a huge variety of cryptic gene clusters for the production of natural products, and the known chemical diversity is likely to be just a fraction of the true biosynthetic capabilities of this fascinating and ancient group of organisms.
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Affiliation(s)
- Elke Dittmann
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, Golm, Germany
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Kaarina Sivonen
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - David P Fewer
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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46
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Zhang G, Li J, Zhu T, Gu Q, Li D. Advanced tools in marine natural drug discovery. Curr Opin Biotechnol 2016; 42:13-23. [PMID: 26954946 DOI: 10.1016/j.copbio.2016.02.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 01/10/2023]
Abstract
Marine natural products (MNPs) remain promising drug sources with several marine-derived drugs having been successfully approved. Nevertheless, it is never a smooth sailing to seek bioactive compounds from marine environments, during which many challenges are need to be faced to, for example, discovering unique marine resources, reviving unculturable organisms outside the marine environment, distinguishing novel compounds from the known ones, and disclosing the function of MNPs and optimizing their pharmacological use. Herein we review some advanced techniques and methodologies that can be employed to deal with above challenges with the intent of inspiring the forthcoming efforts in MNPs discovery pipelines.
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Affiliation(s)
- Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Jing Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
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47
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Otten TG, Paerl HW. Health Effects of Toxic Cyanobacteria in U.S. Drinking and Recreational Waters: Our Current Understanding and Proposed Direction. Curr Environ Health Rep 2016; 2:75-84. [PMID: 26231244 DOI: 10.1007/s40572-014-0041-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cyanobacterial-derived water quality impairment issues are a growing concern worldwide. In addition to their ecological impacts, these organisms are prolific producers of bioactive secondary metabolites, many of which are known human intoxicants. To date only a handful of these compounds have been thoroughly studied and their toxicological risks estimated. While there are currently no national guidelines in place to deal with this issue, it is increasingly likely that within the next several years guidelines will be implemented. The intent of this review is to survey all relevant literature pertaining to cyanobacterial harmful algal bloom secondary metabolites, to inform a discussion on how best to manage this global public health threat.
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Affiliation(s)
- Timothy G Otten
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA,
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48
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Micallef ML, D'Agostino PM, Sharma D, Viswanathan R, Moffitt MC. Genome mining for natural product biosynthetic gene clusters in the Subsection V cyanobacteria. BMC Genomics 2015; 16:669. [PMID: 26335778 PMCID: PMC4558948 DOI: 10.1186/s12864-015-1855-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 08/17/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Cyanobacteria are well known for the production of a range of secondary metabolites. Whilst recent genome sequencing projects has led to an increase in the number of publically available cyanobacterial genomes, the secondary metabolite potential of many of these organisms remains elusive. Our study focused on the 11 publically available Subsection V cyanobacterial genomes, together with the draft genomes of Westiella intricata UH strain HT-29-1 and Hapalosiphon welwitschii UH strain IC-52-3, for their genetic potential to produce secondary metabolites. The Subsection V cyanobacterial genomes analysed in this study are reported to produce a diverse range of natural products, including the hapalindole-family of compounds, microcystin, hapalosin, mycosporine-like amino acids and hydrocarbons. RESULTS A putative gene cluster for the cyclic depsipeptide hapalosin, known to reverse P-glycoprotein multiple drug resistance, was identified within three Subsection V cyanobacterial genomes, including the producing cyanobacterium H. welwitschii UH strain IC-52-3. A number of orphan NRPS/PKS gene clusters and ribosomally-synthesised and post translationally-modified peptide gene clusters (including cyanobactin, microviridin and bacteriocin gene clusters) were identified. Furthermore, gene clusters encoding the biosynthesis of mycosporine-like amino acids, scytonemin, hydrocarbons and terpenes were also identified and compared. CONCLUSIONS Genome mining has revealed the diversity, abundance and complex nature of the secondary metabolite potential of the Subsection V cyanobacteria. This bioinformatic study has identified novel biosynthetic enzymes which have not been associated with gene clusters of known classes of natural products, suggesting that these cyanobacteria potentially produce structurally novel secondary metabolites.
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Affiliation(s)
- Melinda L Micallef
- School of Science and Health, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia.
| | - Paul M D'Agostino
- School of Science and Health, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, 2052, Australia.
| | - Deepti Sharma
- Department of Chemistry, Case Western Reserve University, 2740 Millis Science Center, Adelbert Road, Cleveland, OH, 44106, USA.
| | - Rajesh Viswanathan
- Department of Chemistry, Case Western Reserve University, 2740 Millis Science Center, Adelbert Road, Cleveland, OH, 44106, USA.
| | - Michelle C Moffitt
- School of Science and Health, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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49
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Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes. Appl Environ Microbiol 2015; 81:7290-304. [PMID: 26253660 DOI: 10.1128/aem.01223-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/02/2015] [Indexed: 11/20/2022] Open
Abstract
Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides.
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50
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Raja R, Hemaiswarya S, Ganesan V, Carvalho IS. Recent developments in therapeutic applications of Cyanobacteria. Crit Rev Microbiol 2015; 42:394-405. [PMID: 25629310 DOI: 10.3109/1040841x.2014.957640] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The cyanobacteria (blue-green algae) are photosynthetic prokaryotes having applications in human health with numerous biological activities and as a dietary supplement. It is used as a food supplement because of its richness in nutrients and digestibility. Many cyanobacteria (Microcystis sp, Anabaena sp, Nostoc sp, Oscillatoria sp., etc.) produce a great variety of secondary metabolites with potent biological activities. Cyanobacteria produce biologically active and chemically diverse compounds belonging to cyclic peptides, lipopeptides, fatty acid amides, alkaloids and saccharides. More than 50% of the marine cyanobacteria are potentially exploitable for extracting bioactive substances which are effective in killing cancer cells by inducing apoptotic death. Their role as anti-viral, anti-tumor, antimicrobial, anti-HIV and a food additive have also been well established. However, such products are at different stages of clinical trials and only a few compounds have reached to the market.
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Affiliation(s)
- Rathinam Raja
- a Food Science Lab, Meditbio, Faculty of Sciences and Technology , University of Algarve , Faro , Portugal and
| | - Shanmugam Hemaiswarya
- a Food Science Lab, Meditbio, Faculty of Sciences and Technology , University of Algarve , Faro , Portugal and
| | | | - Isabel S Carvalho
- a Food Science Lab, Meditbio, Faculty of Sciences and Technology , University of Algarve , Faro , Portugal and
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