151
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Ellegaard KM, Brochet S, Bonilla‐Rosso G, Emery O, Glover N, Hadadi N, Jaron KS, Meer JR, Robinson‐Rechavi M, Sentchilo V, Tagini F, Engel P. Genomic changes underlying host specialization in the bee gut symbiont
Lactobacillus
Firm5. Mol Ecol 2019; 28:2224-2237. [DOI: 10.1111/mec.15075] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Kirsten M. Ellegaard
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Silvia Brochet
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - German Bonilla‐Rosso
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Olivier Emery
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Natasha Glover
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Noushin Hadadi
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Kamil S. Jaron
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Jan R. Meer
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Marc Robinson‐Rechavi
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
| | - Florian Tagini
- Institute of Microbiology, Department of Laboratory Medicine University of Lausanne & Lausanne University Hospital Lausanne Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology University of Lausanne Lausanne Switzerland
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152
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Thankachan D, Fazal A, Francis D, Song L, Webb ME, Seipke RF. A trans-Acting Cyclase Offloading Strategy for Nonribosomal Peptide Synthetases. ACS Chem Biol 2019; 14:845-849. [PMID: 30925045 DOI: 10.1021/acschembio.9b00095] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The terminal step in the biosynthesis of nonribosomal peptides is the hydrolytic release and, frequently, macrocyclization of an aminoacyl-S-thioester by an embedded thioesterase. The surugamide biosynthetic pathway is composed of two nonribosomal peptide synthetase (NRPS) assembly lines in which one produces surugamide A, which is a cyclic octapeptide, and the other produces surugamide F, a linear decapeptide. The terminal module of each system lacks an embedded thioesterase, which led us to question how the peptides are released from the assembly line (and cyclized in the case of surugamide A). We characterized a cyclase belonging to the β-lactamase superfamily in vivo, established that it is a trans-acting release factor for both compounds, and verified this functionality in vitro with a thioester mimic of linear surugamide A. Using bioinformatics, we estimate that ∼11% of filamentous Actinobacteria harbor an NRPS system lacking an embedded thioesterase and instead employ a trans-acting cyclase. This study improves the paradigmatic understanding of how nonribosomal peptides are released from the terminal peptidyl carrier protein and adds a new dimension to the synthetic biology toolkit.
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Affiliation(s)
| | | | | | - Lijiang Song
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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153
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Schorn MA, Jordan PA, Podell S, Blanton JM, Agarwal V, Biggs JS, Allen EE, Moore BS. Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Dysideidae Sponges. mBio 2019; 10:e00821-19. [PMID: 31088928 PMCID: PMC6520454 DOI: 10.1128/mbio.00821-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/09/2019] [Indexed: 01/22/2023] Open
Abstract
Marine sponges are recognized as valuable sources of bioactive metabolites and renowned as petri dishes of the sea, providing specialized niches for many symbiotic microorganisms. Sponges of the family Dysideidae are well documented to be chemically talented, often containing high levels of polyhalogenated compounds, terpenoids, peptides, and other classes of bioactive small molecules. This group of tropical sponges hosts a high abundance of an uncultured filamentous cyanobacterium, Hormoscilla spongeliae Here, we report the comparative genomic analyses of two phylogenetically distinct Hormoscilla populations, which reveal shared deficiencies in essential pathways, hinting at possible reasons for their uncultivable status, as well as differing biosynthetic machinery for the production of specialized metabolites. One symbiont population contains clustered genes for expanded polybrominated diphenylether (PBDE) biosynthesis, while the other instead harbors a unique gene cluster for the biosynthesis of the dysinosin nonribosomal peptides. The hybrid sequencing and assembly approach utilized here allows, for the first time, a comprehensive look into the genomes of these elusive sponge symbionts.IMPORTANCE Natural products provide the inspiration for most clinical drugs. With the rise in antibiotic resistance, it is imperative to discover new sources of chemical diversity. Bacteria living in symbiosis with marine invertebrates have emerged as an untapped source of natural chemistry. While symbiotic bacteria are often recalcitrant to growth in the lab, advances in metagenomic sequencing and assembly now make it possible to access their genetic blueprint. A cell enrichment procedure, combined with a hybrid sequencing and assembly approach, enabled detailed genomic analysis of uncultivated cyanobacterial symbiont populations in two chemically rich tropical marine sponges. These population genomes reveal a wealth of secondary metabolism potential as well as possible reasons for historical difficulties in their cultivation.
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Affiliation(s)
- Michelle A Schorn
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Peter A Jordan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Sheila Podell
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Jessica M Blanton
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Vinayak Agarwal
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jason S Biggs
- University of Guam Marine Laboratory, UoG Station, Mangilao, Guam, USA
| | - Eric E Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, California, USA
- Division of Biological Sciences, University of California, San Diego, California, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
- Center for Microbiome Innovation, University of California, San Diego, California, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, USA
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154
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Twigg FF, Cai W, Huang W, Liu J, Sato M, Perez TJ, Geng J, Dror MJ, Montanez I, Tong TL, Lee H, Zhang W. Identifying the Biosynthetic Gene Cluster for Triacsins with an N-Hydroxytriazene Moiety. Chembiochem 2019; 20:1145-1149. [PMID: 30589194 PMCID: PMC6590916 DOI: 10.1002/cbic.201800762] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 11/05/2022]
Abstract
Triacsins are a family of natural products having in common an N-hydroxytriazene moiety not found in any other known secondary metabolites. Though many studies have examined the biological activity of triacsins in lipid metabolism, their biosynthesis has remained unknown. Here we report the identification of the triacsin biosynthetic gene cluster in Streptomyces aureofaciens ATCC 31442. Bioinformatic analysis of the gene cluster led to the discovery of the tacrolimus producer Streptomyces tsukubaensis NRRL 18488 as a new triacsin producer. In addition to targeted gene disruption to identify necessary genes for triacsin production, stable isotope feeding was performed in vivo to advance the understanding of N-hydroxytriazene biosynthesis.
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Affiliation(s)
- Frederick F Twigg
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Wenlong Cai
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Wei Huang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Joyce Liu
- Department of Bioengineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Michio Sato
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Tynan J Perez
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Jiaxin Geng
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94704, USA
| | - Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Ismael Montanez
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Tate L Tong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Hyunsu Lee
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA, 94704, USA
- Chan Zuckerberg Biohub, 499 Illinois St., San Francisco, CA, 94158, USA
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155
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Gut Symbionts Lactobacillus reuteri R2lc and 2010 Encode a Polyketide Synthase Cluster That Activates the Mammalian Aryl Hydrocarbon Receptor. Appl Environ Microbiol 2019; 85:AEM.01661-18. [PMID: 30389766 PMCID: PMC6498181 DOI: 10.1128/aem.01661-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/24/2018] [Indexed: 12/20/2022] Open
Abstract
Temporary changes in the composition of the microbiota, for example, by oral administration of probiotics, can modulate the host immune system. However, the underlying mechanisms by which probiotics interact with the host are often unknown. Here, we show that Lactobacillus reuteri R2lc and 2010 harbor an orthologous PKS gene cluster that activates the aryl hydrocarbon receptor (AhR). AhR is a ligand-activated transcription factor that plays a key role in a variety of diseases, including amelioration of intestinal inflammation. Understanding the mechanism by which a bacterium modulates the immune system is critical for applying rational selection strategies for probiotic supplementation. Finally, heterologous and/or optimized expression of PKS is a logical next step toward the development of next-generation probiotics to prevent and treat disease. A mechanistic understanding of microbe-host interactions is critical to developing therapeutic strategies for targeted modulation of the host immune system. Different members of the gut symbiont species Lactobacillus reuteri modulate host health by, for example, reduction of intestinal inflammation. Previously, it was shown that L. reuteri activates the aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor that plays an important role in the mucosal immune system, by the production of tryptophan catabolites. Here, we identified a novel pathway by which L. reuteri activates AhR, which is independent of tryptophan metabolism. We screened a library of 36 L. reuteri strains and determined that R2lc and 2010, strains with a pigmented phenotype, are potent AhR activators. By whole-genome sequencing and comparative genomics, we identified genes unique to R2lc and 2010. Our analyses demonstrated that R2lc harbors two genetically distinct polyketide synthase (PKS) clusters, functionally unknown (fun) and pks, each carried by a multicopy plasmid. Inactivation of pks, but not fun, abolished the ability of R2lc to activate AhR. L. reuteri 2010 has a gene cluster homologous to the pks cluster in R2lc with an identical gene organization, which is also responsible for AhR activation. In conclusion, we identified a novel PKS pathway in L. reuteri R2lc and 2010 that is responsible for AhR activation. IMPORTANCE Temporary changes in the composition of the microbiota, for example, by oral administration of probiotics, can modulate the host immune system. However, the underlying mechanisms by which probiotics interact with the host are often unknown. Here, we show that Lactobacillus reuteri R2lc and 2010 harbor an orthologous PKS gene cluster that activates the aryl hydrocarbon receptor (AhR). AhR is a ligand-activated transcription factor that plays a key role in a variety of diseases, including amelioration of intestinal inflammation. Understanding the mechanism by which a bacterium modulates the immune system is critical for applying rational selection strategies for probiotic supplementation. Finally, heterologous and/or optimized expression of PKS is a logical next step toward the development of next-generation probiotics to prevent and treat disease.
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156
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Shi-Kunne X, Jové RDP, Depotter JRL, Ebert MK, Seidl MF, Thomma BPHJ. In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae. FEMS Microbiol Lett 2019; 366:5475643. [PMID: 31004487 PMCID: PMC6502550 DOI: 10.1093/femsle/fnz081] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/23/2019] [Indexed: 01/07/2023] Open
Abstract
Fungi are renowned producers of natural compounds, also known as secondary metabolites (SMs) that display a wide array of biological activities. Typically, the genes that are involved in the biosynthesis of SMs are located in close proximity to each other in so-called secondary metabolite clusters. Many plant-pathogenic fungi secrete SMs during infection in order to promote disease establishment, for instance as cytocoxic compounds. Verticillium dahliae is a notorious plant pathogen that can infect over 200 host plants worldwide. However, the SM repertoire of this vascular pathogen remains mostly uncharted. To unravel the potential of V. dahliae to produce SMs, we performed in silico predictions and in-depth analyses of its secondary metabolite clusters. Using distinctive traits of gene clusters and the conserved signatures of core genes 25 potential SM gene clusters were identified. Subsequently, phylogenetic and comparative genomics analyses were performed, revealing that two putative siderophores, ferricrocin and TAFC, DHN-melanin and fujikurin may belong to the SM repertoire of V. dahliae.
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Affiliation(s)
- Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Roger de Pedro Jové
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands,Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, CB3 0LE Cambridge, United Kingdom
| | - Malaika K Ebert
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands,Corresponding author: Laboratory of Phytopathology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Tel: 0031-317-484536; Fax: 0031-317-483412; E-mail:
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157
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Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi. mSystems 2019; 4:mSystems00012-19. [PMID: 31020039 PMCID: PMC6469955 DOI: 10.1128/msystems.00012-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/16/2019] [Indexed: 01/16/2023] Open
Abstract
Filamentous fungi possess great potential as sources of medicinal bioactive compounds, such as antibiotics, but efficient production is hampered by a limited understanding of how their metabolism is regulated. We investigated the metabolism of six secondary metabolite-producing fungi of the Penicillium genus during nutrient depletion in the stationary phase of batch fermentations and assessed conserved metabolic responses across species using genome-wide transcriptional profiling. A coexpression analysis revealed that expression of biosynthetic genes correlates with expression of genes associated with pathways responsible for the generation of precursor metabolites for secondary metabolism. Our results highlight the main metabolic routes for the supply of precursors for secondary metabolism and suggest that the regulation of fungal metabolism is tailored to meet the demands for secondary metabolite production. These findings can aid in identifying fungal species that are optimized for the production of specific secondary metabolites and in designing metabolic engineering strategies to develop high-yielding fungal cell factories for production of secondary metabolites. IMPORTANCE Secondary metabolites are a major source of pharmaceuticals, especially antibiotics. However, the development of efficient processes of production of secondary metabolites has proved troublesome due to a limited understanding of the metabolic regulations governing secondary metabolism. By analyzing the conservation in gene expression across secondary metabolite-producing fungal species, we identified a metabolic signature that links primary and secondary metabolism and that demonstrates that fungal metabolism is tailored for the efficient production of secondary metabolites. The insight that we provide can be used to develop high-yielding fungal cell factories that are optimized for the production of specific secondary metabolites of pharmaceutical interest.
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158
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Aleti G, Baker JL, Tang X, Alvarez R, Dinis M, Tran NC, Melnik AV, Zhong C, Ernst M, Dorrestein PC, Edlund A. Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease. mBio 2019; 10:e00321-19. [PMID: 30992349 PMCID: PMC6469967 DOI: 10.1128/mbio.00321-19] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/12/2019] [Indexed: 01/03/2023] Open
Abstract
Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world's most common chronic diseases.IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world's most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.
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Affiliation(s)
- Gajender Aleti
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA
| | - Jonathon L Baker
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA
| | - Xiaoyu Tang
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA
| | - Ruth Alvarez
- School of Dentistry, The University of California, Los Angeles, California, USA
| | - Márcia Dinis
- School of Dentistry, The University of California, Los Angeles, California, USA
| | - Nini C Tran
- School of Dentistry, The University of California, Los Angeles, California, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, California, USA
| | - Cuncong Zhong
- Department of Electric Engineering and Computer Science, The University of Kansas, Lawrence, Kansas, USA
| | - Madeleine Ernst
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, California, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, La Jolla, California, USA
| | - Anna Edlund
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, USA
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159
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Koch H, Freese HM, Hahnke RL, Simon M, Wietz M. Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems. Front Microbiol 2019; 10:504. [PMID: 30936857 PMCID: PMC6431674 DOI: 10.3389/fmicb.2019.00504] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/27/2019] [Indexed: 11/16/2022] Open
Abstract
Studying the physiology and genomics of cultured hydrolytic bacteria is a valuable approach to decipher the biogeochemical cycling of marine polysaccharides, major nutrients derived from phytoplankton and macroalgae. We herein describe the profound potential of Alteromonas sp. 76-1, isolated from alginate-enriched seawater at the Patagonian continental shelf, to degrade the algal polysaccharides alginate and ulvan. Phylogenetic analyses indicated that strain 76-1 might represent a novel species, distinguished from its closest relative (Alteromonas naphthalenivorans) by adaptations to their contrasting habitats (productive open ocean vs. coastal sediments). Ecological distinction of 76-1 was particularly manifested in the abundance of carbohydrate-active enzymes (CAZymes), consistent with its isolation from alginate-enriched seawater and elevated abundance of a related OTU in the original microcosm. Strain 76-1 encodes multiple alginate lyases from families PL6, PL7, PL17, and PL18 largely contained in two polysaccharide utilization loci (PUL), which may facilitate the utilization of different alginate structures in nature. Notably, ulvan degradation relates to a 126 Kb plasmid dedicated to polysaccharide utilization, encoding several PL24 and PL25 ulvan lyases and monomer-processing genes. This extensive and versatile CAZyme repertoire allowed substantial growth on polysaccharides, showing comparable doubling times with alginate (2 h) and ulvan (3 h) in relation to glucose (3 h). The finding of homologous ulvanolytic systems in distantly related Alteromonas spp. suggests CAZyme plasmids as effective vehicles for PUL transfer that mediate niche gain. Overall, the demonstrated CAZyme repertoire substantiates the role of Alteromonas in marine polysaccharide degradation and how PUL exchange influences the ecophysiology of this ubiquitous marine taxon.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Heike M. Freese
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Richard L. Hahnke
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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160
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Ravindran A, Sunderrajan S, Pennathur G. Phylogenetic Studies on the Prodigiosin Biosynthetic Operon. Curr Microbiol 2019; 76:597-606. [DOI: 10.1007/s00284-019-01665-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/01/2019] [Indexed: 11/30/2022]
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161
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Li J, Tai C, Deng Z, Zhong W, He Y, Ou HY. VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria. Brief Bioinform 2019; 19:566-574. [PMID: 28077405 DOI: 10.1093/bib/bbw141] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Indexed: 11/13/2022] Open
Abstract
VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands. VRprofile is thus able to co-localize the homologs of these conserved gene clusters using HMMer or BLASTp searches. With the integration of the homologous gene cluster search module with a sequence composition module, VRprofile has exhibited better performance for island-like region predictions than the other widely used methods. In addition, VRprofile also provides an integrated Web interface for aligning and visualizing identified gene clusters with MobilomeDB-archived gene clusters, or a variety set of bacterial genomes. VRprofile might contribute to meet the increasing demands of re-annotations of bacterial variable regions, and aid in the real-time definitions of disease-relevant gene clusters in pathogenic bacteria of interest. VRprofile is freely available at http://bioinfo-mml.sjtu.edu.cn/VRprofile.
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Affiliation(s)
- Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Cui Tai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zixin Deng
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P.R.China
| | - Yongqun He
- Department of microbiology and immunology research, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Hong-Yu Ou
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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162
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He HY, Henderson AC, Du YL, Ryan KS. Two-Enzyme Pathway Links l-Arginine to Nitric Oxide in N-Nitroso Biosynthesis. J Am Chem Soc 2019; 141:4026-4033. [DOI: 10.1021/jacs.8b13049] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hai-Yan He
- Department of Chemistry, University of British Columbia, Vancouver, Canada
| | | | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Katherine S. Ryan
- Department of Chemistry, University of British Columbia, Vancouver, Canada
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163
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Özakin S, Ince E. Genome and metabolome mining of marine obligate Salinisporsatrains to discover new natural products. ACTA ACUST UNITED AC 2019; 43:28-36. [PMID: 30930633 PMCID: PMC6426641 DOI: 10.3906/biy-1807-136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Marine microorganisms are receiving more attention as a promising potential source of new natural products. In the present study, we performed genomic and metabolomic analyses to explore the metabolic potential of the obligate marine actinomycete genus Salinispora. The genomes of thirty Salinispora strains were prospected in search of biosynthetic gene clusters including polyketide synthase (PKS), nonribosomal peptide synthetase (NPRS), terpene, indole, lantibiotics, and siderophores. We determined considerable diversity of natural product biosynthetic gene clusters in their genome. There were a total of 1428 putative gene clusters involved in the biosynthesis of various bioactive natural products. Furthermore, 1509 ketosynthase (KS) and condensation (C) domains were detected by using NapDoS belonging to PKS and NRPS genes, respectively. Metabolic profiling was performed by a nontargeted LC-MS/MS approach combined with spectral networking using Global Natural Product Social Molecular Networking (GNPS). Dereplication and tentative identification of natural products were evaluated for common chemical properties and their associated pathways. Significant bioactive natural products such as lomaiviticin C, 7-OH-staurosporine, staurosporine, and cyanosporaside B were determined. More importantly, an unknown glycosylated compound associated with an NRPS/PKS-I hybrid gene cluster in Salinispora pacifica CNY703 was established through chemical and genomic analyses.
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Affiliation(s)
- Süleyman Özakin
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , La Jolla, California , USA.,Department of Biology, Faculty of Science, Dicle University , Diyarbakır , Turkey
| | - Ebru Ince
- Department of Biology, Faculty of Science, Dicle University , Diyarbakır , Turkey
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164
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Uribe RV, van der Helm E, Misiakou MA, Lee SW, Kol S, Sommer MOA. Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla. Cell Host Microbe 2019; 25:233-241.e5. [PMID: 30737174 DOI: 10.1016/j.chom.2019.01.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/24/2018] [Accepted: 01/02/2019] [Indexed: 01/07/2023]
Abstract
CRISPR-Cas systems in bacteria and archaea provide immunity against bacteriophages and plasmids. To overcome CRISPR immunity, phages have acquired anti-CRISPR genes that reduce CRISPR-Cas activity. Using a synthetic genetic circuit, we developed a high-throughput approach to discover anti-CRISPR genes from metagenomic libraries based on their functional activity rather than sequence homology or genetic context. We identified 11 DNA fragments from soil, animal, and human metagenomes that circumvent Streptococcus pyogenes Cas9 activity in our selection strain. Further in vivo and in vitro characterization of a subset of these hits validated the activity of four anti-CRISPRs. Notably, homologs of some of these anti-CRISPRs were detected in seven different phyla, namely Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Spirochaetes, and Balneolaeota, and have high sequence identity suggesting recent horizontal gene transfer. Thus, anti-CRISPRs against type II-A CRISPR-Cas systems are widely distributed across bacterial phyla, suggesting a more complex ecological role than previously appreciated.
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Affiliation(s)
- Ruben V Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Eric van der Helm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Maria-Anna Misiakou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Sang-Woo Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark.
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165
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Abstract
Natural products have long played a pivotal role in the development of therapeutics for a variety of diseases. Traditionally, soil and marine environments have provided a rich reservoir from which diverse chemical scaffolds could be discovered. Recently, the human microbiome has been recognized as a promising niche from which secondary metabolites with therapeutic potential have begun to be isolated. In this Review, we address how the expansive history of identifying bacterial natural products in other environments is informing the approaches being brought to bear on the study of the human microbiota. We also touch on how these tools can lead to insights about microbe-microbe and host-microbe interactions and help generate biological hypotheses that may lead to developments of new therapeutic modalities.
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166
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Alberti F, Leng DJ, Wilkening I, Song L, Tosin M, Corre C. Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery. Chem Sci 2019; 10:453-463. [PMID: 30746093 PMCID: PMC6335953 DOI: 10.1039/c8sc03814g] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 10/11/2018] [Indexed: 11/21/2022] Open
Abstract
In this study, we report the rapid characterisation of a novel microbial natural product resulting from the rational derepression of a silent gene cluster. A conserved set of five regulatory genes was used as a query to search genomic databases and identify atypical biosynthetic gene clusters (BGCs). A 20-kb BGC from the genetically intractable Streptomyces sclerotialus bacterial strain was captured using yeast-based homologous recombination and introduced into validated heterologous hosts. CRISPR/Cas9-mediated genome editing was then employed to rationally inactivate the key transcriptional repressor and trigger production of an unprecedented class of hybrid natural products exemplified by (2-(benzoyloxy)acetyl)-l-proline, named scleric acid. Subsequent rounds of CRISPR/Cas9-mediated gene deletions afforded a selection of biosynthetic gene mutant strains which led to a plausible biosynthetic pathway for scleric acid assembly. Synthetic standards of scleric acid and a key biosynthetic intermediate were also prepared to confirm the chemical structures we proposed. The assembly of scleric acid involves two unique condensation reactions catalysed by a single NRPS module and an ATP-grasp enzyme that link a proline and a benzoyl residue to each end of a rare hydroxyethyl-ACP intermediate, respectively. Scleric acid was shown to exhibit moderate inhibition activity against Mycobacterium tuberculosis, as well as inhibition of the cancer-associated metabolic enzyme nicotinamide N-methyltransferase (NNMT).
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Affiliation(s)
- Fabrizio Alberti
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences , University of Warwick , Coventry , CV4 7AL , UK . ;
- Department of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
| | - Daniel J Leng
- Department of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
| | - Ina Wilkening
- Department of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
| | - Lijiang Song
- Department of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
| | - Manuela Tosin
- Department of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
| | - Christophe Corre
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences , University of Warwick , Coventry , CV4 7AL , UK . ;
- Department of Chemistry , University of Warwick , Coventry , CV4 7AL , UK
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167
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Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann JH, Dittmar T, Freese HM, Becher D, Simon M, Wietz M. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. THE ISME JOURNAL 2019; 13:92-103. [PMID: 30116038 PMCID: PMC6298977 DOI: 10.1038/s41396-018-0252-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 11/08/2022]
Abstract
Algal polysaccharides are an important bacterial nutrient source and central component of marine food webs. However, cellular and ecological aspects concerning the bacterial degradation of polysaccharide mixtures, as presumably abundant in natural habitats, are poorly understood. Here, we contextualize marine polysaccharide mixtures and their bacterial utilization in several ways using the model bacterium Alteromonas macleodii 83-1, which can degrade multiple algal polysaccharides and contributes to polysaccharide degradation in the oceans. Transcriptomic, proteomic and exometabolomic profiling revealed cellular adaptations of A. macleodii 83-1 when degrading a mix of laminarin, alginate and pectin. Strain 83-1 exhibited substrate prioritization driven by catabolite repression, with initial laminarin utilization followed by simultaneous alginate/pectin utilization. This biphasic phenotype coincided with pronounced shifts in gene expression, protein abundance and metabolite secretion, mainly involving CAZymes/polysaccharide utilization loci but also other functional traits. Distinct temporal changes in exometabolome composition, including the alginate/pectin-specific secretion of pyrroloquinoline quinone, suggest that substrate-dependent adaptations influence chemical interactions within the community. The ecological relevance of cellular adaptations was underlined by molecular evidence that common marine macroalgae, in particular Saccharina and Fucus, release mixtures of alginate and pectin-like rhamnogalacturonan. Moreover, CAZyme microdiversity and the genomic predisposition towards polysaccharide mixtures among Alteromonas spp. suggest polysaccharide-related traits as an ecophysiological factor, potentially relating to distinct 'carbohydrate utilization types' with different ecological strategies. Considering the substantial primary productivity of algae on global scales, these insights contribute to the understanding of bacteria-algae interactions and the remineralization of chemically diverse polysaccharide pools, a key step in marine carbon cycling.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Alexandra Dürwald
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Beatriz Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Silvia Vidal-Melgosa
- MARUM-MPI Bridge Group for Marine Glycobiology, University of Bremen, Bremen, Germany
| | - Jan-Hendrik Hehemann
- MARUM-MPI Bridge Group for Marine Glycobiology, University of Bremen, Bremen, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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168
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Versluis D, Nijsse B, Naim MA, Koehorst JJ, Wiese J, Imhoff JF, Schaap PJ, van Passel MWJ, Smidt H, Sipkema D. Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio. Genome Biol Evol 2018; 10:125-142. [PMID: 29319806 PMCID: PMC5765558 DOI: 10.1093/gbe/evx271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2017] [Indexed: 12/19/2022] Open
Abstract
Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesized that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV, and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin, and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival, for example through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges.
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Affiliation(s)
- Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Bart Nijsse
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Mohd Azrul Naim
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Jutta Wiese
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Johannes F Imhoff
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, The Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands.,National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, The Netherlands
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169
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Elder JR, Paul NC, Burin R, Guard J, Shah DH. Genomic organization and role of SPI-13 in nutritional fitness of Salmonella. Int J Med Microbiol 2018; 308:1043-1052. [PMID: 30466554 DOI: 10.1016/j.ijmm.2018.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/21/2018] [Accepted: 10/10/2018] [Indexed: 02/07/2023] Open
Abstract
Salmonella pathogenicity island 13 (SPI-13) contributes to the virulence of Salmonella. The majority of the SPI-13 genes encode proteins putatively involved in bacterial metabolism, however, their functions largely remain uncharacterized. It is currently unknown if SPI-13 contributes to metabolic fitness of Salmonella and, if so, what are the metabolic substrates for the protein encoded by genes within SPI-13. We employed Phenotype Microarray (Biolog, USA) to compare the metabolic properties of SPI-13 deficient mutant (ΔSPI-13) and the WT parent strain of non-typhoidal Salmonella enterica sub sp. enterica serovar Enteritidis (S. Enteritidis). The results of Phenotype Microarray revealed that SPI-13 is required for efficient utilization of two micronutrients, namely, d-glucuronic acid (DGA) and tyramine (TYR), as sole sources of carbon and/or nitrogen. By systematic deletion of the individual gene(s), we identified specific genes within SPI-13 that are required for efficient utilization of DGA (SEN2977-80) and TYR (SEN2967 and SEN2971-72) as sole nutrient sources. The results show that SPI-13 mediated DGA and TYR metabolic pathways afford nutritional fitness to S. Enteritidis. Comparative genomics analysis of the SPI-13 locus from 247 Salmonella strains belonging to 57 different serovars revealed that SPI-13 genes specifically involved in the metabolism of DGA and TYR are highly conserved in Salmonella enterica. Because DGA and TYR are naturally present as metabolic byproducts in the gastrointestinal tract and other host tissues, we propose a metabolic model that shows that the role of SPI-13 mediated DGA and TYR metabolism in the nutritional fitness of Salmonella is likely linked to nutritional virulence of this pathogen.
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Affiliation(s)
- Jacob R Elder
- Department of Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, 99164-7040, USA
| | - Narayan C Paul
- Department of Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, 99164-7040, USA
| | - Raquel Burin
- Department of Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, 99164-7040, USA
| | - Jean Guard
- Egg Quality and Safety Research Unit, Agriculture Research Service, United StatesDepartment of Agriculture, Athens, GA, 30605, USA
| | - Devendra H Shah
- Department of Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington, 99164-7040, USA; Paul Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, 99164-7040, USA.
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170
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Amiri Moghaddam J, Dávila-Céspedes A, Kehraus S, Crüsemann M, Köse M, Müller CE, König GM. Cyclopropane-Containing Fatty Acids from the Marine Bacterium Labrenzia sp. 011 with Antimicrobial and GPR84 Activity. Mar Drugs 2018; 16:md16100369. [PMID: 30297608 PMCID: PMC6213206 DOI: 10.3390/md16100369] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 11/23/2022] Open
Abstract
Bacteria of the family Rhodobacteraceae are widespread in marine environments and known to colonize surfaces, such as those of e.g., oysters and shells. The marine bacterium Labrenzia sp. 011 is here investigated and it was found to produce two cyclopropane-containing medium-chain fatty acids (1, 2), which inhibit the growth of a range of bacteria and fungi, most effectively that of a causative agent of Roseovarius oyster disease (ROD), Pseudoroseovarius crassostreae DSM 16950. Additionally, compound 2 acts as a potent partial, β-arrestin-biased agonist at the medium-chain fatty acid-activated orphan G-protein coupled receptor GPR84, which is highly expressed on immune cells. The genome of Labrenzia sp. 011 was sequenced and bioinformatically compared with those of other Labrenzia spp. This analysis revealed several cyclopropane fatty acid synthases (CFAS) conserved in all Labrenzia strains analyzed and a putative gene cluster encoding for two distinct CFASs is proposed as the biosynthetic origin of 1 and 2.
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Affiliation(s)
| | | | - Stefan Kehraus
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
| | - Meryem Köse
- Pharmaceutical Institute, Pharmaceutical Chemistry I, An der Immenburg 4, D-53121 Bonn, Germany.
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical Chemistry I, An der Immenburg 4, D-53121 Bonn, Germany.
| | - Gabriele Maria König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
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171
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Abstract
Bacterial pathogens cause plant diseases that threaten the global food supply. To control diseases, it is important to understand how pathogenic bacteria evade plant defense and promote infection. We identify from the phytopathogen Pseudomonas syringae a small-molecule virulence factor—phevamine A. Both the chemical structure and mode of action of phevamine A are different from known bacterial phytotoxins. Phevamine A promotes bacterial growth by suppressing plant immune responses, including both early (the generation of reactive oxygen species) and late (the deposition of cell wall reinforcing callose in leaves and leaf cell death) markers. This work uncovers a widely distributed, small-molecule virulence factor and shows the power of a multidisciplinary approach to identify small molecules important for plant infection. Bacterial plant pathogens cause significant crop damage worldwide. They invade plant cells by producing a variety of virulence factors, including small-molecule toxins and phytohormone mimics. Virulence of the model pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) is regulated in part by the sigma factor HrpL. Our study of the HrpL regulon identified an uncharacterized, three-gene operon in Pto that is controlled by HrpL and related to the Erwinia hrp-associated systemic virulence (hsv) operon. Here, we demonstrate that the hsv operon contributes to the virulence of Pto on Arabidopsis thaliana and suppresses bacteria-induced immune responses. We show that the hsv-encoded enzymes in Pto synthesize a small molecule, phevamine A. This molecule consists of l-phenylalanine, l-valine, and a modified spermidine, and is different from known small molecules produced by phytopathogens. We show that phevamine A suppresses a potentiation effect of spermidine and l-arginine on the reactive oxygen species burst generated upon recognition of bacterial flagellin. The hsv operon is found in the genomes of divergent bacterial genera, including ∼37% of P. syringae genomes, suggesting that phevamine A is a widely distributed virulence factor in phytopathogens. Our work identifies a small-molecule virulence factor and reveals a mechanism by which bacterial pathogens overcome plant defense. This work highlights the power of omics approaches in identifying important small molecules in bacteria–host interactions.
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172
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Tomek MB, Maresch D, Windwarder M, Friedrich V, Janesch B, Fuchs K, Neumann L, Nimeth I, Zwickl NF, Dohm JC, Everest-Dass A, Kolarich D, Himmelbauer H, Altmann F, Schäffer C. A General Protein O-Glycosylation Gene Cluster Encodes the Species-Specific Glycan of the Oral Pathogen Tannerella forsythia: O-Glycan Biosynthesis and Immunological Implications. Front Microbiol 2018; 9:2008. [PMID: 30210478 PMCID: PMC6120980 DOI: 10.3389/fmicb.2018.02008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
The cell surface of the oral pathogen Tannerella forsythia is heavily glycosylated with a unique, complex decasaccharide that is O-glycosidically linked to the bacterium’s abundant surface (S-) layer, as well as other proteins. The S-layer glycoproteins are virulence factors of T. forsythia and there is evidence that protein O-glycosylation underpins the bacterium’s pathogenicity. To elucidate the protein O-glycosylation pathway, genes suspected of encoding pathway components were first identified in the genome sequence of the ATCC 43037 type strain, revealing a 27-kb gene cluster that was shown to be polycistronic. Using a gene deletion approach targeted at predicted glycosyltransferases (Gtfs) and methyltransferases encoded in this gene cluster, in combination with mass spectrometry of the protein-released O-glycans, we show that the gene cluster encodes the species-specific part of the T. forsythia ATCC 43037 decasaccharide and that this is assembled step-wise on a pentasaccharide core. The core was previously proposed to be conserved within the Bacteroidetes phylum, to which T. forsythia is affiliated, and its biosynthesis is encoded elsewhere on the bacterial genome. Next, to assess the prevalence of protein O-glycosylation among Tannerella sp., the publicly available genome sequences of six T. forsythia strains were compared, revealing gene clusters of similar size and organization as found in the ATCC 43037 type strain. The corresponding region in the genome of a periodontal health-associated Tannerella isolate showed a different gene composition lacking most of the genes commonly found in the pathogenic strains. Finally, we investigated whether differential cell surface glycosylation impacts T. forsythia’s overall immunogenicity. Release of proinflammatory cytokines by dendritic cells (DCs) upon stimulation with defined Gtf-deficient mutants of the type strain was measured and their T cell-priming potential post-stimulation was explored. This revealed that the O-glycan is pivotal to modulating DC effector functions, with the T. forsythia-specific glycan portion suppressing and the pentasaccharide core activating a Th17 response. We conclude that complex protein O-glycosylation is a hallmark of pathogenic T. forsythia strains and propose it as a valuable target for the design of novel antimicrobials against periodontitis.
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Affiliation(s)
- Markus B Tomek
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Daniel Maresch
- Division of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Markus Windwarder
- Division of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Valentin Friedrich
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Bettina Janesch
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Kristina Fuchs
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Laura Neumann
- Division of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Irene Nimeth
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Nikolaus F Zwickl
- Bioinformatics Group, Department of Biotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Juliane C Dohm
- Bioinformatics Group, Department of Biotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Arun Everest-Dass
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Heinz Himmelbauer
- Bioinformatics Group, Department of Biotechnology, Universität für Bodenkultur Wien, Vienna, Austria
| | - Friedrich Altmann
- Division of Biochemistry, Department of Chemistry, Universität für Bodenkultur Wien, Vienna, Austria
| | - Christina Schäffer
- NanoGlycobiology Unit, Department of NanoBiotechnology, Universität für Bodenkultur Wien, Vienna, Austria
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173
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Kim MC, Machado H, Jang KH, Trzoss L, Jensen PR, Fenical W. Integration of Genomic Data with NMR Analysis Enables Assignment of the Full Stereostructure of Neaumycin B, a Potent Inhibitor of Glioblastoma from a Marine-Derived Micromonospora. J Am Chem Soc 2018; 140:10775-10784. [PMID: 30085661 DOI: 10.1021/jacs.8b04848] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microbial metabolites known as the macrolides are some of the most successful natural products used to treat infectious and immune diseases. Describing the structures of these complex metabolites, however, is often extremely difficult due to the presence of multiple stereogenic centers inherent in this class of polyketide-derived metabolites. With the availability of genome sequence data and a better understanding of the molecular genetics of natural product biosynthesis, it is now possible to use bioinformatic approaches in tandem with spectroscopic tools to assign the full stereostructures of these complex metabolites. In our quest to discover and develop new agents for the treatment of cancer, we observed the production of a highly cytotoxic macrolide, neaumycin B, by a marine-derived actinomycete bacterium of the genus Micromonospora. Neaumycin B is a complex polycyclic macrolide possessing 19 asymmetric centers, usually requiring selective degradation, crystallization, derivatization, X-ray diffraction analysis, synthesis, or other time-consuming approaches to assign the complete stereostructure. As an alternative approach, we sequenced the genome of the producing strain and identified the neaumycin gene cluster ( neu). By integrating the known stereospecificities of biosynthetic enzymes with comprehensive NMR analysis, the full stereostructure of neaumycin B was confidently assigned. This approach exemplifies how mining gene cluster information while integrating NMR-based structure data can achieve rapid, efficient, and accurate stereostructural assignments for complex macrolides.
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Affiliation(s)
- Min Cheol Kim
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Henrique Machado
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Kyoung Hwa Jang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Lynnie Trzoss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Center for Microbiome Innovation , University of California, San Diego , La Jolla , California 92093-0204 , United States
| | - William Fenical
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093-0204 , United States.,Moores Comprehensive Cancer Center , University of California, San Diego , La Jolla , California 92093-0204 , United States
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174
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Wasil Z, Kuhnert E, Simpson TJ, Cox RJ. Oryzines A & B, Maleidride Congeners from Aspergillus oryzae and Their Putative Biosynthesis. J Fungi (Basel) 2018; 4:jof4030096. [PMID: 30104550 PMCID: PMC6162547 DOI: 10.3390/jof4030096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/24/2023] Open
Abstract
Aspergillus oryzae is traditionally used in East Asia for the production of food and brewing. In addition, it has been developed into a suitable host for the heterologous expression of natural product biosynthetic genes and gene clusters, enabling the functional analysis of the encoded enzymes. A. oryzae shares a 99.5% genome homology with Aspergillus flavus, but their secondary metabolomes differ significantly and various compounds unique to A. oryzae have been reported. While using A. oryzae as a host for heterologous expression experiments we discovered two new metabolites in extracts of A. oryzae M-2-3 with an unusual maleidride backbone, which were named oryzine A and B. Their structures were elucidated by high resolution mass spectrometry (HRMS) and nuclear magnetic resonance (NMR) analysis. Their structural relationships with known maleidrides implied involvement of a citrate synthase (CS) and a polyketide (PKS) or fatty acid synthase (FAS) in their biosynthesis. Analysis of the A. oryzae genome revealed a single putative biosynthetic gene cluster (BGC) consistent with the hypothetical biosynthesis of the oryzines. These findings increase knowledge of the chemical potential of A. oryzae and are the first attempt to link a novel product of this fungus with genomic data.
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Affiliation(s)
- Zahida Wasil
- University of Bristol, School of Chemistry, Cantock's Close, Bristol BS8 1TS, UK.
| | - Eric Kuhnert
- Leibniz Universität Hannover, Biomolekulares Wirkstoffzentrum und Institut für Organische Chemie, Schneiderberg 38, 30167 Hannover, Germany.
| | - Thomas J Simpson
- University of Bristol, School of Chemistry, Cantock's Close, Bristol BS8 1TS, UK.
| | - Russell J Cox
- Leibniz Universität Hannover, Biomolekulares Wirkstoffzentrum und Institut für Organische Chemie, Schneiderberg 38, 30167 Hannover, Germany.
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175
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Zhang J, Li X, Deng Z, Ou HY. Comparative Analysis of CRISPR Loci Found in Streptomyces Genome Sequences. Interdiscip Sci 2018; 10:848-853. [DOI: 10.1007/s12539-018-0301-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 07/03/2018] [Accepted: 07/10/2018] [Indexed: 12/24/2022]
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176
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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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177
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Gilbert MK, Mack BM, Moore GG, Downey DL, Lebar MD, Joardar V, Losada L, Yu J, Nierman WC, Bhatnagar D. Whole genome comparison of Aspergillus flavus L-morphotype strain NRRL 3357 (type) and S-morphotype strain AF70. PLoS One 2018; 13:e0199169. [PMID: 29966003 PMCID: PMC6028093 DOI: 10.1371/journal.pone.0199169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 06/01/2018] [Indexed: 01/03/2023] Open
Abstract
Aspergillus flavus is a saprophytic fungus that infects corn, peanuts, tree nuts and other agriculturally important crops. Once the crop is infected the fungus has the potential to secrete one or more mycotoxins, the most carcinogenic of which is aflatoxin. Aflatoxin contaminated crops are deemed unfit for human or animal consumption, which results in both food and economic losses. Within A. flavus, two morphotypes exist: the S strains (small sclerotia) and L strains (large sclerotia). Significant morphological and physiological differences exist between the two morphotypes. For example, the S-morphotypes produces sclerotia that are smaller (< 400 μm), greater in quantity, and contain higher concentrations of aflatoxin than the L-morphotypes (>400 μm). The morphotypes also differ in pigmentation, pH homeostasis in culture and the number of spores produced. Here we report the first full genome sequence of an A. flavus S morphotype, strain AF70. We provide a comprehensive comparison of the A. flavus S-morphotype genome sequence with a previously sequenced genome of an L-morphotype strain (NRRL 3357), including an in-depth analysis of secondary metabolic clusters and the identification SNPs within their aflatoxin gene clusters.
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Affiliation(s)
- Matthew K. Gilbert
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Brian M. Mack
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
| | - Geromy G. Moore
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
| | - Darlene L. Downey
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
| | - Matthew D. Lebar
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
| | - Vinita Joardar
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Liliana Losada
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - JiuJiang Yu
- Food Quality Laboratory, USDA, Beltsville, Maryland, United States of America
| | - William C. Nierman
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Deepak Bhatnagar
- Food and Feed Safety Unit, USDA, New Orleans, Louisiana, United States of America
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178
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Global evolution of glycosylated polyene macrolide antibiotic biosynthesis. Mol Phylogenet Evol 2018; 127:239-247. [PMID: 29885934 DOI: 10.1016/j.ympev.2018.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/04/2018] [Indexed: 11/22/2022]
Abstract
Antibiotics are the most marvelous evolutionary products of microbes to obtain competitive advantage and maintain ecological balance. However, the origination and development of antibiotics has yet to be explicitly investigated. Due to diverse structures and similar biosynthesis, glycosylated polyene macrolides (gPEMs) were chosen to explore antibiotic evolution. A total of 130 candidate and 38 transitional gPEM clusters were collected from actinomycetes genomes, providing abundant references for phenotypic gaps in gPEM evolution. The most conserved parts of gPEM biosynthesis were found and used for phylogeny construction. On this basis, we proposed ancestral gPEM clusters at different evolutionary stages and interpreted the possible evolutionary histories in detail. The results revealed that gPEMs evolved from small rings to large rings and continuously increased structural diversity through acquiring, discarding and exchanging genes from different evolutionary origins, as well as co-evolution of functionally related proteins. The combination of horizontal gene transfers, environmental effects and host preference resulted in the diversity and worldwide distribution of gPEMs. This study is not only a useful exploration on antibiotic evolution but also an inspiration for diversity and biogeographic investigations on antibiotics in the era of Big Data.
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179
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Hoogendoorn K, Barra L, Waalwijk C, Dickschat JS, van der Lee TAJ, Medema MH. Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium. Front Microbiol 2018; 9:1158. [PMID: 29922257 PMCID: PMC5996196 DOI: 10.3389/fmicb.2018.01158] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/14/2018] [Indexed: 11/13/2022] Open
Abstract
Plant pathogenic fungi in the Fusarium genus cause severe damage to crops, resulting in great financial losses and health hazards. Specialized metabolites synthesized by these fungi are known to play key roles in the infection process, and to provide survival advantages inside and outside the host. However, systematic studies of the evolution of specialized metabolite-coding potential across Fusarium have been scarce. Here, we apply a combination of bioinformatic approaches to identify biosynthetic gene clusters (BGCs) across publicly available genomes from Fusarium, to group them into annotated families and to study gain/loss events of BGC families throughout the history of the genus. Comparison with MIBiG reference BGCs allowed assignment of 29 gene cluster families (GCFs) to pathways responsible for the production of known compounds, while for 57 GCFs, the molecular products remain unknown. Comparative analysis of BGC repertoires using ancestral state reconstruction raised several new hypotheses on how BGCs contribute to Fusarium pathogenicity or host specificity, sometimes surprisingly so: for example, a gene cluster for the biosynthesis of hexadehydro-astechrome was identified in the genome of the biocontrol strain Fusarium oxysporum Fo47, while being absent in that of the tomato pathogen F. oxysporum f.sp. lycopersici. Several BGCs were also identified on supernumerary chromosomes; heterologous expression of genes for three terpene synthases encoded on the Fusarium poae supernumerary chromosome and subsequent GC/MS analysis showed that these genes are functional and encode enzymes that each are able to synthesize koraiol; this observed functional redundancy supports the hypothesis that localization of copies of BGCs on supernumerary chromosomes provides freedom for evolutionary innovations to occur, while the original function remains conserved. Altogether, this systematic overview of biosynthetic diversity in Fusarium paves the way for targeted natural product discovery based on automated identification of species-specific pathways as well as for connecting species ecology to the taxonomic distributions of BGCs.
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Affiliation(s)
- Koen Hoogendoorn
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands.,Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Lena Barra
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Cees Waalwijk
- Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
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180
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Huang YY, Martínez-del Campo A, Balskus EP. Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity. Gut Microbes 2018; 9:437-451. [PMID: 29405826 PMCID: PMC6219649 DOI: 10.1080/19490976.2018.1435244] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ1-pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.
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Affiliation(s)
- Yolanda Y. Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA,CONTACT Emily P. Balskus Commense Inc., 100 Edwin H. Land Blvd, Cambridge, MA 02142
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181
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Adamek M, Alanjary M, Sales-Ortells H, Goodfellow M, Bull AT, Winkler A, Wibberg D, Kalinowski J, Ziemert N. Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species. BMC Genomics 2018; 19:426. [PMID: 29859036 PMCID: PMC5984834 DOI: 10.1186/s12864-018-4809-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 05/21/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary. RESULTS Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis' strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes. CONCLUSIONS Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.
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Affiliation(s)
- Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Mohammad Alanjary
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Helena Sales-Ortells
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Michael Goodfellow
- School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU UK
| | - Alan T. Bull
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Anika Winkler
- Universität Bielefeld, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Daniel Wibberg
- Universität Bielefeld, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Jörn Kalinowski
- Universität Bielefeld, Center for Biotechnology (CeBiTec), Bielefeld, Germany
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
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182
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Spohn M, Edenhart S, Alanjary M, Ziemert N, Wibberg D, Kalinowski J, Niedermeyer THJ, Stegmann E, Wohlleben W. Identification of a novel aminopolycarboxylic acid siderophore gene cluster encoding the biosynthesis of ethylenediaminesuccinic acid hydroxyarginine (EDHA). Metallomics 2018; 10:722-734. [PMID: 29667664 DOI: 10.1039/c8mt00009c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The mechanism of siderophore-mediated iron supply enhances fitness and survivability of microorganisms under iron limited growth conditions. One class of naturally occurring ionophores is the small aminopolycarboxylic acids (APCAs). Although they are structurally related to the most famous anthropogenic chelating agent, ethylenediaminetetraacetate (EDTA), they have been largely neglected by the scientific community. Here, we demonstrate the detection of APCA gene clusters by a computational screening of a nucleotide database. This genome mining approach enabled the discovery of a yet unknown APCA gene cluster in well-described actinobacterial strains, either known for their potential to produce valuable secondary metabolites (Streptomyces avermitilis) or for their pathogenic lifestyle (Streptomyces scabies, Corynebacterium pseudotuberculosis, Corynebacterium ulcerans and Nocardia brasiliensis). The herein identified gene cluster was shown to encode the biosynthesis of APCA, ethylenediaminesuccinic acid hydroxyarginine (EDHA). Detailed and comparatively performed production and transcriptional profiling of EDHA and its biosynthesis genes showed strict iron-responsive biosynthesis.
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Affiliation(s)
- Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen, Microbiology/Biotechnology, University of Tuebingen, Tuebingen, Germany.
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183
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Alex A, Antunes A. Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts. PLoS One 2018; 13:e0194368. [PMID: 29775460 PMCID: PMC5959193 DOI: 10.1371/journal.pone.0194368] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 03/01/2018] [Indexed: 11/18/2022] Open
Abstract
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.
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Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail: (AA); (AA)
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail: (AA); (AA)
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184
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Biosynthetic pathway for furanosteroid demethoxyviridin and identification of an unusual pregnane side-chain cleavage. Nat Commun 2018; 9:1838. [PMID: 29743477 PMCID: PMC5943271 DOI: 10.1038/s41467-018-04298-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/18/2018] [Indexed: 01/16/2023] Open
Abstract
Furanosteroids, represented by wortmannin, viridin, and demethoxyviridin, are a special group of fungal-derived, highly oxygenated steroids featured by an extra furan ring. They are well-known nanomolar-potency inhibitors of phosphatidylinositol 3-kinase and widely used in biological studies. Despite their importance, the biosyntheses of these molecules are poorly understood. Here, we report the identification of the biosynthetic gene cluster for demethoxyviridin, consisting of 19 genes, and among them 15 biosynthetic genes, including six cytochrome P450 monooxygenase genes, are deleted. As a result, 14 biosynthetic intermediates are isolated, and the biosynthetic pathway for demethoxyviridin is elucidated. Notably, the pregnane side-chain cleavage requires three enzymes: flavin-dependent Baeyer-Villiger monooxygenase, esterase, and dehydrogenase, in sharp contrast to the single cytochrome P450-mediated process in mammalian cells. Structure–activity analyses of these obtained biosynthetic intermediates reveal that the 3-keto group, the C1β–OH, and the aromatic ring C are important for the inhibition of phosphatidylinositol 3-kinase. Demethoxyviridin is a fungal steroid that inhibits a phosphatidylinositol 3-kinase, an enzyme contributing to tumor progression. Here, the authors elucidate the biosynthetic route that leads to the formation of demethoxyviridin in fungi.
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185
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Steglich M, Hofmann JD, Helmecke J, Sikorski J, Spröer C, Riedel T, Bunk B, Overmann J, Neumann-Schaal M, Nübel U. Convergent Loss of ABC Transporter Genes From Clostridioides difficile Genomes Is Associated With Impaired Tyrosine Uptake and p-Cresol Production. Front Microbiol 2018; 9:901. [PMID: 29867812 PMCID: PMC5951980 DOI: 10.3389/fmicb.2018.00901] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
We report the frequent, convergent loss of two genes encoding the substrate-binding protein and the ATP-binding protein of an ATP-binding cassette (ABC) transporter from the genomes of unrelated Clostridioides difficile strains. This specific genomic deletion was strongly associated with the reduced uptake of tyrosine and phenylalanine and production of derived Stickland fermentation products, including p-cresol, suggesting that the affected ABC transporter had been responsible for the import of aromatic amino acids. In contrast, the transporter gene loss did not measurably affect bacterial growth or production of enterotoxins. Phylogenomic analysis of publically available genome sequences indicated that this transporter gene deletion had occurred multiple times in diverse clonal lineages of C. difficile, with a particularly high prevalence in ribotype 027 isolates, where 48 of 195 genomes (25%) were affected. The transporter gene deletion likely was facilitated by the repetitive structure of its genomic location. While at least some of the observed transporter gene deletions are likely to have occurred during the natural life cycle of C. difficile, we also provide evidence for the emergence of this mutation during long-term laboratory cultivation of reference strain R20291.
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Affiliation(s)
- Matthias Steglich
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Julia D Hofmann
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Julia Helmecke
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ulrich Nübel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
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186
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Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes. Appl Environ Microbiol 2018; 84:AEM.02828-17. [PMID: 29500259 PMCID: PMC5930311 DOI: 10.1128/aem.02828-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/21/2018] [Indexed: 01/23/2023] Open
Abstract
Bicyclomycin (BCM) is a clinically promising antibiotic that is biosynthesized by Streptomyces cinnamoneus DSM 41675. BCM is structurally characterized by a core cyclo(l-Ile-l-Leu) 2,5-diketopiperazine (DKP) that is extensively oxidized. Here, we identify the BCM biosynthetic gene cluster, which shows that the core of BCM is biosynthesized by a cyclodipeptide synthase, and the oxidative modifications are introduced by five 2-oxoglutarate-dependent dioxygenases and one cytochrome P450 monooxygenase. The discovery of the gene cluster enabled the identification of BCM pathways encoded by the genomes of hundreds of Pseudomonas aeruginosa isolates distributed globally, and heterologous expression of the pathway from P. aeruginosa SCV20265 demonstrated that the product is chemically identical to BCM produced by S. cinnamoneus. Overall, putative BCM gene clusters have been found in at least seven genera spanning Actinobacteria and Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria). This represents a rare example of horizontal gene transfer of an intact biosynthetic gene cluster across such distantly related bacteria, and we show that these gene clusters are almost always associated with mobile genetic elements. IMPORTANCE Bicyclomycin is the only natural product antibiotic that selectively inhibits the transcription termination factor Rho. This mechanism of action, combined with its proven biological safety and its activity against clinically relevant Gram-negative bacterial pathogens, makes it a very promising antibiotic candidate. Here, we report the identification of the bicyclomycin biosynthetic gene cluster in the known bicyclomycin-producing organism Streptomyces cinnamoneus, which will enable the engineered production of new bicyclomycin derivatives. The identification of this gene cluster also led to the discovery of hundreds of bicyclomycin pathways encoded in highly diverse bacteria, including in the opportunistic pathogen Pseudomonas aeruginosa. This wide distribution of a complex biosynthetic pathway is very unusual and provides an insight into how a pathway for an antibiotic can be transferred between diverse bacteria.
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187
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Lebar MD, Cary JW, Majumdar R, Carter-Wientjes CH, Mack BM, Wei Q, Uka V, De Saeger S, Diana Di Mavungu J. Identification and functional analysis of the aspergillic acid gene cluster in Aspergillus flavus. Fungal Genet Biol 2018; 116:14-23. [PMID: 29674152 DOI: 10.1016/j.fgb.2018.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 04/04/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
Abstract
Aspergillus flavus can colonize important food staples and produce aflatoxins, a group of toxic and carcinogenic secondary metabolites. Previous in silico analysis of the A. flavus genome revealed 56 gene clusters predicted to be involved in the biosynthesis of secondary metabolites. A. flavus secondary metabolites produced during infection of maize seed are of particular interest, especially with respect to their roles in the biology of the fungus. A predicted nonribosomal peptide synthetase-like (NRPS-like) gene, designated asaC (AFLA_023020), present in the uncharacterized A. flavus secondary metabolite gene cluster 11 was previously shown to be expressed during the earliest stages of maize kernel infection. Cluster 11 is composed of six additional genes encoding a number of putative decorating enzymes as well as a transporter and transcription factor. We generated knock-out mutants of the seven predicted cluster 11 genes. LC-MS analysis of extracts from knockout mutants of these genes showed that they were responsible for the synthesis of the previously characterized antimicrobial mycotoxin aspergillic acid. Extracts of the asaC mutant showed no production of aspergillic acid or its precursors. Knockout of the cluster 11 P450 oxidoreductase afforded a pyrazinone metabolite, the aspergillic acid precursor deoxyaspergillic acid. The formation of hydroxyaspergillic acid was abolished in a desaturase/hydroxylase mutant. The hydroxamic acid functional group in aspergillic acid allows the molecule to bind to iron resulting in the production of a red pigment in A. flavus identified previously as ferriaspergillin. A reduction of aflatoxin B1 and cyclopiazonic acid that correlated with reduced fungal growth was observed in maize kernel infection assays when aspergillic acid biosynthesis in A. flavus is halted.
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Affiliation(s)
- Matthew D Lebar
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA.
| | - Jeffrey W Cary
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA
| | | | | | - Brian M Mack
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA
| | - Qijian Wei
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA
| | - Valdet Uka
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sarah De Saeger
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - José Diana Di Mavungu
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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188
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Jenul C, Sieber S, Daeppen C, Mathew A, Lardi M, Pessi G, Hoepfner D, Neuburger M, Linden A, Gademann K, Eberl L. Biosynthesis of fragin is controlled by a novel quorum sensing signal. Nat Commun 2018; 9:1297. [PMID: 29602945 PMCID: PMC5878181 DOI: 10.1038/s41467-018-03690-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 03/05/2018] [Indexed: 11/23/2022] Open
Abstract
Members of the diazeniumdiolate class of natural compounds show potential for drug development because of their antifungal, antibacterial, antiviral, and antitumor activities. Yet, their biosynthesis has remained elusive to date. Here, we identify a gene cluster directing the biosynthesis of the diazeniumdiolate compound fragin in Burkholderia cenocepacia H111. We provide evidence that fragin is a metallophore and that metal chelation is the molecular basis of its antifungal activity. A subset of the fragin biosynthetic genes is involved in the synthesis of a previously undescribed cell-to-cell signal molecule, valdiazen. RNA-Seq analyses reveal that valdiazen controls fragin biosynthesis and affects the expression of more than 100 genes. Homologs of the valdiazen biosynthesis genes are found in various bacteria, suggesting that valdiazen-like compounds may constitute a new class of signal molecules. We use structural information, in silico prediction of enzymatic functions and biochemical data to propose a biosynthesis route for fragin and valdiazen. Fragin is a diazeniumdiolate metabolite with antifungal activity, produced by some bacteria. Here, Jenul et al. show that metal chelation is the molecular basis of fragin’s antifungal activity, and that a gene cluster directing fragin biosynthesis is also involved in the synthesis of a signal molecule.
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Affiliation(s)
- Christian Jenul
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.,Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Christophe Daeppen
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.,Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Anugraha Mathew
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Dominic Hoepfner
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Markus Neuburger
- Department of Chemistry, University of Basel, 4056, Basel, Switzerland
| | - Anthony Linden
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, 8057, Zurich, Switzerland.
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
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189
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Aspergillus flavus Secondary Metabolites: More than Just Aflatoxins. Food Saf (Tokyo) 2018; 6:7-32. [PMID: 32231944 DOI: 10.14252/foodsafetyfscj.2017024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/09/2018] [Indexed: 11/21/2022] Open
Abstract
Aspergillus flavus is best known for producing the family of potent carcinogenic secondary metabolites known as aflatoxins. However, this opportunistic plant and animal pathogen also produces numerous other secondary metabolites, many of which have also been shown to be toxic. While about forty of these secondary metabolites have been identified from A. flavus cultures, analysis of the genome has predicted the existence of at least 56 secondary metabolite gene clusters. Many of these gene clusters are not expressed during growth of the fungus on standard laboratory media. This presents researchers with a major challenge of devising novel strategies to manipulate the fungus and its genome so as to activate secondary metabolite gene expression and allow identification of associated cluster metabolites. In this review, we discuss the genetic, biochemical and bioinformatic methods that are being used to identify previously uncharacterized secondary metabolite gene clusters and their associated metabolites. It is important to identify as many of these compounds as possible to determine their bioactivity with respect to fungal development, survival, virulence and especially with respect to any potential synergistic toxic effects with aflatoxin.
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190
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Baars O, Morel FMM, Zhang X. The purple non-sulfur bacterium Rhodopseudomonas palustris produces novel petrobactin-related siderophores under aerobic and anaerobic conditions. Environ Microbiol 2018; 20:1667-1676. [PMID: 29473283 DOI: 10.1111/1462-2920.14078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 01/20/2018] [Accepted: 02/17/2018] [Indexed: 11/28/2022]
Abstract
Many bacteria produce siderophores to bind and take up Fe(III), an essential trace metal with extremely low solubility in oxygenated environments at circumneutral pH. The purple non-sulfur bacterium Rhodopseudomonas palustris str. CGA009 is a metabolically versatile model organism with high iron requirements that is able to grow under aerobic and anaerobic conditions. Siderophore biosynthesis has been predicted by genomic analysis, however, siderophore structures were not identified. Here, we elucidate the structure of two novel siderophores from R. palustris: rhodopetrobactin A and B. Rhodopetrobactins are structural analogues of the known siderophore petrobactin in which the Fe chelating moieties are conserved, including two 3,4-dihydroxybenzoate and a citrate substructure. In the place of two spermidine linker groups in petrobactin, rhodopetrobactins contain two 4,4'-diaminodibutylamine groups of which one or both are acetylated at the central amine. We analyse siderophore production under different growth modes and show that rhodopetrobactins are produced in response to Fe limitation under aerobic as well as under anaerobic conditions. Evaluation of the chemical characteristics of rhodopetrobactins indicates that they are well suited to support Fe acquisition under variable oxygen and light conditions.
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Affiliation(s)
- Oliver Baars
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - François M M Morel
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
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191
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Abstract
The terminal alkyne is a readily derivatized functionality valued for its diverse applications in material synthesis, pharmaceutical science, and chemical biology. The synthetic biology routes to terminal alkynes are highly desired and yet underexplored. Some marine natural products contain a terminal alkyne functionality, and the discovery of the biosynthetic gene clusters for jamaicamide B and carmabin A marked the beginning of a new era in the understanding and engineering of terminal alkyne biosynthesis. In this chapter, we will overview recent advances in understanding the biosynthetic machinery for terminal alkyne synthesis. We will first describe how to elucidate terminal alkyne biosynthetic mechanism through heterologous expression, purification, and in vitro biochemical assays of individual pathway proteins. This will be followed by the description of an in vivo reporting system for the characterization of a membrane-bound bifunctional desaturase/acetylenase involved in terminal alkyne formation. The chapter will also cover the strategies for discovering additional protein homologs for terminal alkyne synthesis from microbes as well as the applications of click chemistry to identify and quantify terminal alkyne-bearing metabolites from microbial cultures. We will conclude this chapter with current challenges and future directions in this field.
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Affiliation(s)
- Xuejun Zhu
- University of California, Berkeley, CA, United States
| | - Wenjun Zhang
- University of California, Berkeley, CA, United States; Chan Zuckerberg Biohub, San Francisco, CA, United States.
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192
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Complete Genome Sequence of a Ciprofloxacin-Resistant Salmonella enterica subsp. enterica Serovar Kentucky Sequence Type 198 Strain, PU131, Isolated from a Human Patient in Washington State. GENOME ANNOUNCEMENTS 2018; 6:6/9/e00125-18. [PMID: 29496839 PMCID: PMC5834327 DOI: 10.1128/genomea.00125-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Strains of the ciprofloxacin-resistant (Cipr) Salmonella enterica subsp. enterica serovar Kentucky sequence type 198 (ST198) have rapidly and extensively disseminated globally to become a major food safety and public health concern. Here, we report the complete genome sequence of a CiprS. Kentucky ST198 strain, PU131, isolated from a human patient in Washington State (USA).
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193
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Casini A, Chang FY, Eluere R, King AM, Young EM, Dudley QM, Karim A, Pratt K, Bristol C, Forget A, Ghodasara A, Warden-Rothman R, Gan R, Cristofaro A, Borujeni AE, Ryu MH, Li J, Kwon YC, Wang H, Tatsis E, Rodriguez-Lopez C, O’Connor S, Medema MH, Fischbach MA, Jewett MC, Voigt C, Gordon DB. A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology. J Am Chem Soc 2018; 140:4302-4316. [DOI: 10.1021/jacs.7b13292] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Arturo Casini
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Fang-Yuan Chang
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Andrew M. King
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Eric M. Young
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Quentin M. Dudley
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty Karim
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Anthony Forget
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amar Ghodasara
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Robert Warden-Rothman
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Rui Gan
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander Cristofaro
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amin Espah Borujeni
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Min-Hyung Ryu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Jian Li
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Yong-Chan Kwon
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - He Wang
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Evangelos Tatsis
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - Sarah O’Connor
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Michael A. Fischbach
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Bioengineering and Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, California 94305, United States
| | - Michael C. Jewett
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher Voigt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - D. Benjamin Gordon
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
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194
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Schwarz FM, Schuchmann K, Müller V. Hydrogenation of CO 2 at ambient pressure catalyzed by a highly active thermostable biocatalyst. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:237. [PMID: 30186365 PMCID: PMC6119302 DOI: 10.1186/s13068-018-1236-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/22/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Replacing fossil fuels as energy carrier requires alternatives that combine sustainable production, high volumetric energy density, easy and fast refueling for mobile applications, and preferably low risk of hazard. Molecular hydrogen (H2) has been considered as promising alternative; however, practical application is struggling because of the low volumetric energy density and the explosion hazard when stored in large amounts. One way to overcome these limitations is the transient conversion of H2 into other chemicals with increased volumetric energy density and lower risk hazard, for example so-called liquid organic hydrogen carriers such as formic acid/formate that is obtained by hydrogenation of CO2. Many homogenous and heterogenous chemical catalysts have been described in the past years, however, often requiring high pressures and temperatures. Recently, the first biocatalyst for this reaction has been described opening the route to a biotechnological alternative for this conversion. RESULTS The hydrogen-dependent CO2 reductase (HDCR) is a highly active biocatalyst for storing H2 in the form of formic acid/formate by reversibly catalyzing the hydrogenation of CO2. We report the identification, isolation, and characterization of the first thermostable HDCR operating at temperatures up to 70 °C. The enzyme was isolated from the thermophilic acetogenic bacterium Thermoanaerobacter kivui and displays exceptionally high activities in both reaction directions, substantially exceeding known chemical catalysts. CO2 hydrogenation is catalyzed at mild conditions with a turnover frequency of 9,556,000 h-1 (specific activity of 900 µmol formate min-1 mg-1) and the reverse reaction, H2 + CO2 release from formate, is catalyzed with a turnover frequency of 9,892,000 h-1 (930 µmol H2 min-1 mg-1). The HDCR of T. kivui consists of a [FeFe] hydrogenase subunit putatively coupled to a tungsten-dependent CO2 reductase/formate dehydrogenase subunit by an array of iron-sulfur clusters. CONCLUSIONS The discovery of the first thermostable HDCR provides a promising biological alternative for a chemically challenging reaction and might serve as model for the better understanding of catalysts able to efficiently reduce CO2. The catalytic activity for reversible CO2 hydrogenation of this enzyme is the highest activity known for bio- and chemical catalysts and requiring only ambient temperatures and pressures. The thermostability provides more flexibility regarding the process parameters for a biotechnological application.
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Affiliation(s)
- Fabian M. Schwarz
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Kai Schuchmann
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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195
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Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery. J Ind Microbiol Biotechnol 2017; 45:615-619. [PMID: 29255991 DOI: 10.1007/s10295-017-1993-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/26/2017] [Indexed: 10/18/2022]
Abstract
The rapid increase of publicly available microbial genome sequences has highlighted the presence of hundreds of thousands of biosynthetic gene clusters (BGCs) encoding valuable secondary metabolites. The experimental characterization of new BGCs is extremely laborious and struggles to keep pace with the in silico identification of potential BGCs. Therefore, the prioritisation of promising candidates among computationally predicted BGCs represents a pressing need. Here, we propose an output ordering and prioritisation system (OOPS) which helps sorting identified BGCs by a wide variety of custom-weighted biological and biochemical criteria in a flexible and user-friendly interface. OOPS facilitates a judicious prioritisation of BGCs using G+C content, coding sequence length, gene number, cluster self-similarity and codon bias parameters, as well as enabling the user to rank BGCs based upon BGC type, novelty, and taxonomic distribution. Effective prioritisation of BGCs will help to reduce experimental attrition rates and improve the breadth of bioactive metabolites characterized.
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196
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Bignell E, Cairns TC, Throckmorton K, Nierman WC, Keller NP. Secondary metabolite arsenal of an opportunistic pathogenic fungus. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2016.0023. [PMID: 28080993 DOI: 10.1098/rstb.2016.0023] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2016] [Indexed: 12/31/2022] Open
Abstract
Aspergillus fumigatus is a versatile fungus able to successfully exploit diverse environments from mammalian lungs to agricultural waste products. Among its many fitness attributes are dozens of genetic loci containing biosynthetic gene clusters (BGCs) producing bioactive small molecules (often referred to as secondary metabolites or natural products) that provide growth advantages to the fungus dependent on environment. Here we summarize the current knowledge of these BGCs-18 of which can be named to product-their expression profiles in vivo, and which BGCs may enhance virulence of this opportunistic human pathogen. Furthermore, we find extensive evidence for the presence of many of these BGCs, or similar BGCs, in distantly related genera including the emerging pathogen Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats, and suggest such BGCs may be predictive of pathogenic potential in other fungi.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Elaine Bignell
- Manchester Fungal Infection Group, Institute of Inflammation and Repair, 2.24 Core Technology Facility, Grafton Street, Manchester, M13 9NT, UK
| | - Timothy C Cairns
- Department of Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kurt Throckmorton
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
| | | | - Nancy P Keller
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA, .,Department of Medical Microbiology, University of Wisconsin, Madison, WI 53706, USA
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197
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Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 2017; 551:648-652. [PMID: 29168502 DOI: 10.1038/nature24661] [Citation(s) in RCA: 722] [Impact Index Per Article: 103.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 10/25/2017] [Indexed: 12/30/2022]
Abstract
The human gut microbiota produces dozens of metabolites that accumulate in the bloodstream, where they can have systemic effects on the host. Although these small molecules commonly reach concentrations similar to those achieved by pharmaceutical agents, remarkably little is known about the microbial metabolic pathways that produce them. Here we use a combination of genetics and metabolic profiling to characterize a pathway from the gut symbiont Clostridium sporogenes that generates aromatic amino acid metabolites. Our results reveal that this pathway produces twelve compounds, nine of which are known to accumulate in host serum. All three aromatic amino acids (tryptophan, phenylalanine and tyrosine) serve as substrates for the pathway, and it involves branching and alternative reductases for specific intermediates. By genetically manipulating C. sporogenes, we modulate serum levels of these metabolites in gnotobiotic mice, and show that in turn this affects intestinal permeability and systemic immunity. This work has the potential to provide the basis of a systematic effort to engineer the molecular output of the gut bacterial community.
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Affiliation(s)
- Dylan Dodd
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Matthew H Spitzer
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anthony Le
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Tina M Cowan
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michael A Fischbach
- California Institute for Quantitative Bioscience and Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco 94143, California, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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198
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Frattaruolo L, Lacret R, Cappello AR, Truman AW. A Genomics-Based Approach Identifies a Thioviridamide-Like Compound with Selective Anticancer Activity. ACS Chem Biol 2017; 12:2815-2822. [PMID: 28968491 DOI: 10.1021/acschembio.7b00677] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Thioviridamide is a structurally novel ribosomally synthesized and post-translational modified peptide (RiPP) produced by Streptomyces olivoviridis NA005001. It is characterized by a structure that features a series of thioamide groups and possesses potent antiproliferative activity in cancer cell lines. Its unusual structure allied to its promise as an anticancer compound led us to investigate the diversity of thioviridamide-like pathways across sequenced bacterial genomes. We have isolated and characterized three diverse members of this family of natural products. This characterization is supported by transformation-associated recombination cloning and heterologous expression of one of these compounds, thiostreptamide S4. Our work provides an insight into the diversity of this rare class of compound and indicates that the unusual N-terminus of thioviridamide is not introduced biosynthetically but is instead introduced during acetone extraction. A detailed analysis of the biological activity of one of the newly discovered compounds, thioalbamide, indicates that it is highly cytotoxic to cancer cells, while exhibiting significantly less activity toward a noncancerous epithelial cell line.
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Affiliation(s)
- Luca Frattaruolo
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom
- Department
of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Rodney Lacret
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom
| | - Anna Rita Cappello
- Department
of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Andrew W. Truman
- Department
of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom
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199
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Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology. mSystems 2017; 2:mSystems00040-17. [PMID: 29152584 PMCID: PMC5686519 DOI: 10.1128/msystems.00040-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/03/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs. By comparing these BGCs to one another as well as a curated set of known specialized metabolite BGCs, we discovered that the majority of Bacillus natural products are comprised of a small set of highly conserved, well-distributed, known natural product compounds. Most of these metabolites have important roles influencing the physiology and development of Bacillus species. We identified, in addition to these characterized compounds, many unique, weakly conserved BGCs scattered across the genus that are predicted to encode unknown natural products. Many of these "singleton" BGCs appear to have been acquired via horizontal gene transfer. Based on this large-scale characterization of metabolite production in the Bacilli, we go on to connect the alkylpyrones, natural products that are highly conserved but previously biologically uncharacterized, to a role in Bacillus physiology: inhibiting spore development. IMPORTANCEBacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus's metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial group can make. We discovered that the majority of the specialized metabolites produced by Bacillus species are highly conserved, known compounds with important signaling roles in the physiology and development of this bacterium. Additionally, there is significant unique biosynthetic machinery distributed across the genus that might lead to new, unknown metabolites with diverse biological functions. Inspired by the findings of our genomic analysis, we speculate that the highly conserved alkylpyrones might have an important biological activity within this genus. We go on to validate this prediction by demonstrating that these natural products are developmental signals in Bacillus and act by inhibiting sporulation.
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200
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Joynt R, Seipke RF. A phylogenetic and evolutionary analysis of antimycin biosynthesis. MICROBIOLOGY-SGM 2017; 164:28-39. [PMID: 29111964 PMCID: PMC5883857 DOI: 10.1099/mic.0.000572] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Streptomyces species and other Actinobacteria are ubiquitous in diverse environments worldwide and are the source of, or inspiration for, the majority of antibiotics. The genomic era has enhanced biosynthetic understanding of these valuable chemical entities and has also provided a window into the diversity and distribution of natural product biosynthetic gene clusters. Antimycin is an inhibitor of mitochondrial cytochrome c reductase and more recently was shown to inhibit Bcl-2/Bcl-XL-related anti-apoptotic proteins commonly overproduced by cancerous cells. Here we identify 73 putative antimycin biosynthetic gene clusters (BGCs) in publicly available genome sequences of Actinobacteria and classify them based on the presence or absence of cluster-situated genes antP and antQ, which encode a kynureninase and a phosphopantetheinyl transferase (PPTase), respectively. The majority of BGCs possess either both antP and antQ (L-form) or neither (S-form), while a minority of them lack either antP or antQ (IQ- or IP-form, respectively). We also evaluate the biogeographical distribution and phylogenetic relationships of antimycin producers and BGCs. We show that antimycin BGCs occur on five of the seven continents and are frequently isolated from plants and other higher organisms. We also provide evidence for two distinct phylogenetic clades of antimycin producers and gene clusters, which delineate S-form from L- and I-form BGCs. Finally, our findings suggest that the ancestral antimycin producer harboured an L-form gene cluster which was primarily propagated by vertical transmission and subsequently diversified into S-, IQ- and IP-form biosynthetic pathways.
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Affiliation(s)
- Rebecca Joynt
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
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