1
|
Maurer JJ, Cheng Y, Pedroso A, Thompson KK, Akter S, Kwan T, Morota G, Kinstler S, Porwollik S, McClelland M, Escalante-Semerena JC, Lee MD. Peeling back the many layers of competitive exclusion. Front Microbiol 2024; 15:1342887. [PMID: 38591029 PMCID: PMC11000858 DOI: 10.3389/fmicb.2024.1342887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 04/10/2024] Open
Abstract
Baby chicks administered a fecal transplant from adult chickens are resistant to Salmonella colonization by competitive exclusion. A two-pronged approach was used to investigate the mechanism of this process. First, Salmonella response to an exclusive (Salmonella competitive exclusion product, Aviguard®) or permissive microbial community (chicken cecal contents from colonized birds containing 7.85 Log10Salmonella genomes/gram) was assessed ex vivo using a S. typhimurium reporter strain with fluorescent YFP and CFP gene fusions to rrn and hilA operon, respectively. Second, cecal transcriptome analysis was used to assess the cecal communities' response to Salmonella in chickens with low (≤5.85 Log10 genomes/g) or high (≥6.00 Log10 genomes/g) Salmonella colonization. The ex vivo experiment revealed a reduction in Salmonella growth and hilA expression following co-culture with the exclusive community. The exclusive community also repressed Salmonella's SPI-1 virulence genes and LPS modification, while the anti-virulence/inflammatory gene avrA was upregulated. Salmonella transcriptome analysis revealed significant metabolic disparities in Salmonella grown with the two different communities. Propanediol utilization and vitamin B12 synthesis were central to Salmonella metabolism co-cultured with either community, and mutations in propanediol and vitamin B12 metabolism altered Salmonella growth in the exclusive community. There were significant differences in the cecal community's stress response to Salmonella colonization. Cecal community transcripts indicated that antimicrobials were central to the type of stress response detected in the low Salmonella abundance community, suggesting antagonism involved in Salmonella exclusion. This study indicates complex community interactions that modulate Salmonella metabolism and pathogenic behavior and reduce growth through antagonism may be key to exclusion.
Collapse
Affiliation(s)
- John J. Maurer
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ying Cheng
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Adriana Pedroso
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Kasey K. Thompson
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Shamima Akter
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Tiffany Kwan
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Gota Morota
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Sydney Kinstler
- School of Animal Sciences, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | | | - Margie D. Lee
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| |
Collapse
|
2
|
Guo L, Wambui J, Wang C, Muchaamba F, Fernandez-Cantos MV, Broos J, Tasara T, Kuipers OP, Stephan R. Cesin, a short natural variant of nisin, displays potent antimicrobial activity against major pathogens despite lacking two C-terminal macrocycles. Microbiol Spectr 2023; 11:e0531922. [PMID: 37754751 PMCID: PMC10581189 DOI: 10.1128/spectrum.05319-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 08/06/2023] [Indexed: 09/28/2023] Open
Abstract
Nisin is a widely used lantibiotic owing to its potent antimicrobial activity and its food-grade status. Its mode of action includes cell wall synthesis inhibition and pore formation, which are attributed to the lipid II binding and pore-forming domains, respectively. We discovered cesin, a short natural variant of nisin, produced by the psychrophilic anaerobe Clostridium estertheticum. Unlike other natural nisin variants, cesin lacks the two terminal macrocycles constituting the pore-forming domain. The current study aimed at heterologous expression and characterization of the antimicrobial activity and physicochemical properties of cesin. Following the successful heterologous expression of cesin in Lactococcus lactis, the lantibiotic demonstrated a broad and potent antimicrobial profile comparable to that of nisin. Determination of its mode of action using lipid II and lipoteichoic acid binding assays linked the potent antimicrobial activity to lipid II binding and electrostatic interactions with teichoic acids. Fluorescence microscopy showed that cesin lacks pore-forming ability in its natural form. Stability tests have shown the lantibiotic is highly stable at different pH values and temperature conditions, but that it can be degraded by trypsin. However, a bioengineered analog, cesin R15G, overcame the trypsin degradation, while keeping full antimicrobial activity. This study shows that cesin is a novel (small) nisin variant that efficiently kills target bacteria by inhibiting cell wall synthesis without pore formation. IMPORTANCE The current increase in antibiotic-resistant pathogens necessitates the discovery and application of novel antimicrobials. In this regard, we recently discovered cesin, which is a short natural variant of nisin produced by the psychrophilic Clostridium estertheticum. However, its suitability as an antimicrobial compound was in doubt due to its structural resemblance to nisin(1-22), a bioengineered short variant of nisin with low antimicrobial activity. Here, we show by heterologous expression, purification, and characterization that the potency of cesin is not only much higher than that of nisin(1-22), but that it is even comparable to the full-length nisin, despite lacking two C-terminal rings that are essential for nisin's activity. We show that cesin is a suitable scaffold for bioengineering to improve its applicability, such as resistance to trypsin. This study demonstrates the suitability of cesin for future application in food and/or for health as a potent and stable antimicrobial compound.
Collapse
Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Joseph Wambui
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Chenhui Wang
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| |
Collapse
|
3
|
Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
Collapse
Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
| |
Collapse
|
4
|
Pahalagedara ASNW, Jauregui R, Maclean P, Altermann E, Flint S, Palmer J, Brightwell G, Gupta TB. Culture and genome-based analysis of four soil Clostridium isolates reveal their potential for antimicrobial production. BMC Genomics 2021; 22:686. [PMID: 34548019 PMCID: PMC8456703 DOI: 10.1186/s12864-021-08005-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Soil bacteria are a major source of specialized metabolites including antimicrobial compounds. Yet, one of the most diverse genera of bacteria ubiquitously present in soil, Clostridium, has been largely overlooked in bioactive compound discovery. As Clostridium spp. thrive in extreme environments with their metabolic mechanisms adapted to the harsh conditions, they are likely to synthesize molecules with unknown structures, properties, and functions. Therefore, their potential to synthesize small molecules with biological activities should be of great interest in the search for novel antimicrobial compounds. The current study focused on investigating the antimicrobial potential of four soil Clostridium isolates, FS01, FS2.2 FS03, and FS04, using a genome-led approach, validated by culture-based methods. RESULTS Conditioned/spent media from all four Clostridium isolates showed varying levels of antimicrobial activity against indicator microorganism; all four isolates significantly inhibited the growth of Pseudomonas aeruginosa. FS01, FS2.2, and FS04 were active against Bacillus mycoides and FS03 reduced the growth of Bacillus cereus. Phylogenetic analysis together with DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and functional genome distribution (FGD) analyses confirmed that FS01, FS2.2, and FS04 belong to the species Paraclostridium bifermentans, Clostridium cadaveris, and Clostridium senegalense respectively, while FS03 may represent a novel species of the genus Clostridium. Bioinformatics analysis using antiSMASH 5.0 predicted the presence of eight biosynthetic gene clusters (BGCs) encoding for the synthesis of ribosomally synthesized post-translationally modified peptides (RiPPs) and non-ribosomal peptides (NRPs) in four genomes. All predicted BGCs showed no similarity with any known BGCs suggesting novelty of the molecules from those predicted gene clusters. In addition, the analysis of genomes for putative virulence factors revealed the presence of four putative Clostridium toxin related genes in FS01 and FS2.2 genomes. No genes associated with the main Clostridium toxins were identified in the FS03 and FS04 genomes. CONCLUSIONS The presence of BGCs encoding for uncharacterized RiPPs and NRPSs in the genomes of antagonistic Clostridium spp. isolated from farm soil indicated their potential to produce novel secondary metabolites. This study serves as a basis for the identification and characterization of potent antimicrobials from these soil Clostridium spp. and expands the current knowledge base, encouraging future research into bioactive compound production in members of the genus Clostridium.
Collapse
Affiliation(s)
- Amila S N W Pahalagedara
- Food System Integrity team, Hopkirk Research Institute, AgResearch Ltd, Massey University, 4474, Palmerston North, New Zealand
- School of Food and Advanced Technology, Massey University, 4442, Palmerston North, New Zealand
- Data Science team, Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Ruy Jauregui
- Data Science team, Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Paul Maclean
- Data Science team, Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Eric Altermann
- Food System Integrity team, Hopkirk Research Institute, AgResearch Ltd, Massey University, 4474, Palmerston North, New Zealand
- School of Food and Advanced Technology, Massey University, 4442, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, 4442, Palmerston North, New Zealand
- Data Science team, Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Jon Palmer
- School of Food and Advanced Technology, Massey University, 4442, Palmerston North, New Zealand
- Data Science team, Grasslands Research Centre, AgResearch Ltd, Palmerston North, New Zealand
| | - Gale Brightwell
- Food System Integrity team, Hopkirk Research Institute, AgResearch Ltd, Massey University, 4474, Palmerston North, New Zealand
- School of Food and Advanced Technology, Massey University, 4442, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Tanushree Barua Gupta
- Food System Integrity team, Hopkirk Research Institute, AgResearch Ltd, Massey University, 4474, Palmerston North, New Zealand.
- School of Food and Advanced Technology, Massey University, 4442, Palmerston North, New Zealand.
| |
Collapse
|
5
|
Neuwirth T, Letzel AC, Tank C, Ishida K, Cyrulies M, Schmölz L, Lorkowski S, Hertweck C. Induced Production, Synthesis, and Immunomodulatory Action of Clostrisulfone, a Diarylsulfone from Clostridium acetobutylicum. Chemistry 2020; 26:15855-15858. [PMID: 32996646 PMCID: PMC7756337 DOI: 10.1002/chem.202003500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/29/2020] [Indexed: 01/25/2023]
Abstract
The anaerobe Clostridium acetobutylicum belongs to the most important industrially used bacteria. Whereas genome mining points to a high potential for secondary metabolism in C. acetobutylicum, the functions of most biosynthetic gene clusters are cryptic. We report that the addition of supra‐physiological concentrations of cysteine triggered the formation of a novel natural product, clostrisulfone (1). Its structure was fully elucidated by NMR, MS and the chemical synthesis of a reference compound. Clostrisulfone is the first reported natural product with a diphenylsulfone scaffold. A biomimetic synthesis suggests that pentamethylchromanol‐derived radicals capture sulfur dioxide to form 1. In a cell‐based assay using murine macrophages a biphasic and dose‐dependent regulation of the LPS‐induced release of nitric oxide was observed in the presence of 1.
Collapse
Affiliation(s)
- Toni Neuwirth
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Anne-Catrin Letzel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Cedric Tank
- BioPilotPlant, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Michael Cyrulies
- BioPilotPlant, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Lisa Schmölz
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Straße 25, 07743, Jena, Germany
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Straße 25, 07743, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| |
Collapse
|
6
|
Roman D, Raguž L, Keiff F, Meyer F, Barthels F, Schirmeister T, Kloss F, Beemelmanns C. Modular Solid-Phase Synthesis of Antiprotozoal Barnesin Derivatives. Org Lett 2020; 22:3744-3748. [PMID: 32212714 DOI: 10.1021/acs.orglett.0c00723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we applied and optimized a solid support (SP)-based Horner-Wadsworth-Emmons reagent to prepare SP-bound vinylogous amino acids. Subsequent SP-based peptide synthesis, global deprotection, and chemical modifications yielded 14 lipodipeptides carrying vinylogous amino acids, including the natural product barnesin A (1). Biological evaluation revealed that several synthesized derivatives show micromolar to nanomolar inhibitory activity against papain-like cysteine proteases, human cathepsin L, and rhodesain.
Collapse
Affiliation(s)
- Dávid Roman
- Leibniz Institute for Natural-Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Luka Raguž
- Leibniz Institute for Natural-Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraβe 11a, 07745 Jena, Germany
| | - François Keiff
- Leibniz Institute for Natural-Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Florian Meyer
- Leibniz Institute for Natural-Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Florian Kloss
- Leibniz Institute for Natural-Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraβe 11a, 07745 Jena, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural-Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstraβe 11a, 07745 Jena, Germany
| |
Collapse
|
7
|
New perspectives on the treatment of mycobacterial infections using antibiotics. Appl Microbiol Biotechnol 2020; 104:4197-4209. [PMID: 32185432 DOI: 10.1007/s00253-020-10513-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/22/2020] [Accepted: 02/28/2020] [Indexed: 12/13/2022]
Abstract
More than 100 years have passed since the discovery of Mycobacterium tuberculosis, in 1882, as the pathogen that causes tuberculosis (TB). However, globally, TB is still one of the leading causes of death by infectious diseases. In 2018, approximately 10.0 million people were diagnosed with TB owing to the development of advanced strategies by M. tuberculosis to resist antibiotics, including the development of a dormant state. The World Health Organization (WHO) and the Sustainable Development Goals (SDGs) are dedicated to ending TB by 2030. However, the development of strategies to discover new TB drugs and new therapies is crucial for the achievement of this goal. Unfortunately, the rapid occurrence of multidrug-resistant strains of M. tuberculosis has worsened the current situation, thereby warranting prioritized discovery of new anti-TB drugs and the development of new treatment regimens in academia and the pharmaceutical industry. In this mini review, we provide a brief overview of the current research and development pipeline for new anti-TB drugs and present our perspective of TB drug innovation. The data presented herein may enable the introduction of more effective medicines and therapeutic regimens into the market.Key Points• The Updated Global New TB Drug Pipelines are briefly summarized.• Novel strategies for the discovery of new TB drugs, including novel sources, bioinformatics, and synthetic biology strategies, are discussed.• New therapeutic options, including living therapeutics and phage therapy, are proposed.
Collapse
|
8
|
An anaerobic bacterium host system for heterologous expression of natural product biosynthetic gene clusters. Nat Commun 2019; 10:3665. [PMID: 31413323 PMCID: PMC6694145 DOI: 10.1038/s41467-019-11673-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Anaerobic bacteria represent an overlooked rich source of biological and chemical diversity. Due to the challenge of cultivation and genetic intractability, assessing the capability of their biosynthetic gene clusters (BGCs) for secondary metabolite production requires an efficient heterologous expression system. However, this kind of host system is still unavailable. Here, we use the facultative anaerobe Streptococcus mutans UA159 as a heterologous host for the expression of BGCs from anaerobic bacteria. A natural competence based large DNA fragment cloning (NabLC) technique was developed, which can move DNA fragments up to 40-kb directly and integrate a 73.7-kb BGC to the genome of S. mutans UA159 via three rounds of NabLC cloning. Using this system, we identify an anti-infiltration compound, mutanocyclin, from undefined BGCs from human oral bacteria. We anticipate this host system will be useful for heterologous expression of BGCs from anaerobic bacteria. Anaerobic bacteria represent a rich source of biological and chemical diversity but are difficult to cultivate and there is a lack of heterologous expression systems. Here the authors develop an expression system based on S. mutans UA159 for biosynthetic gene clusters from anaerobic bacteria.
Collapse
|
9
|
Schieferdecker S, Shabuer G, Letzel AC, Urbansky B, Ishida-Ito M, Ishida K, Cyrulies M, Dahse HM, Pidot S, Hertweck C. Biosynthesis of Diverse Antimicrobial and Antiproliferative Acyloins in Anaerobic Bacteria. ACS Chem Biol 2019; 14:1490-1497. [PMID: 31243958 DOI: 10.1021/acschembio.9b00228] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Metabolic profiling and genome mining revealed that anaerobic bacteria have the potential to produce acyloin natural products. In addition to sattazolin A and B, three new sattazolin congeners and a novel acyloin named clostrocyloin were isolated from three strains of Clostridium beijerinckii, a bacterium used for industrial solvent production. Bioactivity profiling showed that the sattazolin derivatives possess antimicrobial activities against mycobacteria and pseudomonads with only low cytotoxicity. Clostrocyloin was found to be mainly active against fungi. The thiamine diphosphate (ThDP)-dependent sattazolin-producing synthase was identified in silico and characterized both in vivo and in in vitro enzyme assays. A related acyloin synthase from the clostrocyloin producer was shown to be responsible for the production of the acyloin core of clostrocyloin. The biotransformation experiments provided first insights into the substrate scope of the clostrocyloin synthase and revealed biosynthetic intermediates.
Collapse
Affiliation(s)
- Sebastian Schieferdecker
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gulimila Shabuer
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Anne-Catrin Letzel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Barbara Urbansky
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Michael Cyrulies
- BioPilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sacha Pidot
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Victoria 3010, Australia
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
| |
Collapse
|
10
|
Bains W, Petkowski JJ, Sousa-Silva C, Seager S. Trivalent Phosphorus and Phosphines as Components of Biochemistry in Anoxic Environments. ASTROBIOLOGY 2019; 19:885-902. [PMID: 30896974 DOI: 10.1089/ast.2018.1958] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phosphorus is an essential element for all life on Earth, yet trivalent phosphorus (e.g., in phosphines) appears to be almost completely absent from biology. Instead phosphorus is utilized by life almost exclusively as phosphate, apart from a small contingent of other pentavalent phosphorus compounds containing structurally similar chemical groups. In this work, we address four previously stated arguments as to why life does not explore trivalent phosphorus: (1) precedent (lack of confirmed instances of trivalent phosphorus in biochemicals suggests that life does not have the means to exploit this chemistry), (2) thermodynamic limitations (synthesizing trivalent phosphorus compounds is too energetically costly), (3) stability (phosphines are too reactive and readily oxidize in an oxygen (O2)-rich atmosphere), and (4) toxicity (the trivalent phosphorus compounds are broadly toxic). We argue that the first two of these arguments are invalid, and the third and fourth arguments only apply to the O2-rich environment of modern Earth. Specifically, both the reactivity and toxicity of phosphines are specific to aerobic life and strictly dependent on O2-rich environment. We postulate that anaerobic life persisting in anoxic (O2-free) environments may exploit trivalent phosphorus chemistry much more extensively. We review the production of trivalent phosphorus compounds by anaerobic organisms, including phosphine gas and an alkyl phosphine, phospholane. We suggest that the failure to find more such compounds in modern terrestrial life may be a result of the strong bias of the search for natural products toward aerobic organisms. We postulate that a more thorough identification of metabolites of the anaerobic biosphere could reveal many more trivalent phosphorus compounds. We conclude with a discussion of the implications of our work for the origin and early evolution of life, and suggest that trivalent phosphorus compounds could be valuable markers for both extraterrestrial life and the Shadow Biosphere on Earth.
Collapse
Affiliation(s)
| | - Janusz Jurand Petkowski
- 2Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Clara Sousa-Silva
- 2Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Sara Seager
- 2Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- 3Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts
- 4Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, Cambridge, Massachusetts
| |
Collapse
|
11
|
Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
Collapse
Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| |
Collapse
|
12
|
Adamek M, Alanjary M, Ziemert N. Applied evolution: phylogeny-based approaches in natural products research. Nat Prod Rep 2019; 36:1295-1312. [DOI: 10.1039/c9np00027e] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here we highlight how phylogenetic analyses can be used to facilitate natural product discovery and structure elucidation.
Collapse
Affiliation(s)
- Martina Adamek
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
| | | | - Nadine Ziemert
- Applied Natural Products Genome Mining
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen (IMIT)
- University of Tuebingen
- 72076 Tuebingen
- Germany
| |
Collapse
|
13
|
Li JS, Barber CC, Zhang W. Natural products from anaerobes. J Ind Microbiol Biotechnol 2018; 46:375-383. [PMID: 30284140 DOI: 10.1007/s10295-018-2086-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/25/2018] [Indexed: 12/27/2022]
Abstract
Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode unexpected biosynthetic potential for natural products, however, chemical data on natural products from the anaerobic world are extremely limited. Here, we review the current body of work on natural products isolated from strictly anaerobic microbes, including recent genome mining efforts to discover polyketides and non-ribosomal peptides from anaerobes. These known natural products of anaerobes have demonstrated interesting molecular scaffolds, biosynthetic logic, and/or biological activities, making anaerobes a promising reservoir for future natural product discovery.
Collapse
Affiliation(s)
- Jeffrey S Li
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Colin Charles Barber
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| |
Collapse
|
14
|
Ueoka R, Bhushan A, Probst SI, Bray WM, Lokey RS, Linington RG, Piel J. Genome-Based Identification of a Plant-Associated Marine Bacterium as a Rich Natural Product Source. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Agneya Bhushan
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Silke I. Probst
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Walter M. Bray
- Chemistry & Biochemistry Department; University of California Santa Cruz; 1156 High Street 95064 Santa Cruz California USA
| | - R. Scott Lokey
- Chemistry & Biochemistry Department; University of California Santa Cruz; 1156 High Street 95064 Santa Cruz California USA
| | - Roger G. Linington
- Department of Chemistry; Simon Fraser University; 8888 University Drive Bumaby BC V5A 1S6 Canada
| | - Jörn Piel
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| |
Collapse
|
15
|
Ueoka R, Bhushan A, Probst SI, Bray WM, Lokey RS, Linington RG, Piel J. Genome-Based Identification of a Plant-Associated Marine Bacterium as a Rich Natural Product Source. Angew Chem Int Ed Engl 2018; 57:14519-14523. [PMID: 30025185 DOI: 10.1002/anie.201805673] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/12/2018] [Indexed: 01/14/2023]
Abstract
The large number of sequenced bacterial genomes provides the opportunity to bioinformatically identify rich natural product sources among previously neglected microbial groups. Testing this discovery strategy, unusually high biosynthetic potential was suggested for the Oceanospirillales member Gynuella sunshinyii, a Gram-negative marine bacterium from the rhizosphere of the halophilic plant Carex scabrifolia. Its genome contains numerous unusual biosynthetic gene clusters for diverse types of metabolites. Genome-guided isolation yielded representatives of four different natural product classes, of which only alteramide A was known. Cytotoxic lacunalides were identified as products of a giant trans-acyltransferase polyketide synthase gene cluster, one of six present in this strain. Cytological profiling against HeLa cells suggested that lacunalide A disrupts CDK signaling in the cell cycle. In addition, chemical studies on model compounds were conducted, suggesting the structurally unusual ergoynes as products of a conjugated diyne-thiourea cyclization reaction.
Collapse
Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Agneya Bhushan
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Silke I Probst
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Walter M Bray
- Chemistry & Biochemistry Department, University of California Santa Cruz, 1156 High Street, 95064, Santa Cruz, California, USA
| | - R Scott Lokey
- Chemistry & Biochemistry Department, University of California Santa Cruz, 1156 High Street, 95064, Santa Cruz, California, USA
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Bumaby, BC, V5A 1S6, Canada
| | - Jörn Piel
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| |
Collapse
|
16
|
Rischer M, Raguž L, Guo H, Keiff F, Diekert G, Goris T, Beemelmanns C. Biosynthesis, Synthesis, and Activities of Barnesin A, a NRPS-PKS Hybrid Produced by an Anaerobic Epsilonproteobacterium. ACS Chem Biol 2018; 13:1990-1995. [PMID: 29901979 DOI: 10.1021/acschembio.8b00445] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the wealth of physiological knowledge and plentiful genomes available, only few natural products of anaerobic bacteria have been identified until today and even less have been linked to their biosynthetic gene cluster. Here, we analyzed a unique NRPS-PKS hybrid gene cluster from an anaerobic Epsilonproteobacterium ( Sulfurospirillum barnesii). Phylogenetic analysis of key biosynthetic genes, gene expression studies, and comparative metabolomics resulted in the identification of the first anoxically biosynthesized NRPS-PKS hybrid metabolite: a lipo-dipeptide with a vinylogous side chain, called barnesin A. The absolute structure was verified by a modular total synthesis, and barnesin and derivatives were found to have antimicrobial activity, as well as selective and nanomolar inhibitory activity, against pharmacological important cysteine proteases, such as cathepsin B.
Collapse
Affiliation(s)
- Maja Rischer
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Luka Raguž
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Francois Keiff
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology−Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| |
Collapse
|
17
|
Khan RA. Natural products chemistry: The emerging trends and prospective goals. Saudi Pharm J 2018; 26:739-753. [PMID: 29991919 PMCID: PMC6036106 DOI: 10.1016/j.jsps.2018.02.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023] Open
Abstract
The role and contributions of natural products chemistry in advancements of the physical and biological sciences, its interdisciplinary domains, and emerging of new avenues by providing novel applications, constructive inputs, thrust, comprehensive understanding, broad perspective, and a new vision for future is outlined. The developmental prospects in bio-medical, health, nutrition, and other interrelated sciences along with some of the emerging trends in the subject area are also discussed as part of the current review of the basic and core developments, innovation in techniques, advances in methodology, and possible applications with their effects on the sciences in general and natural products chemistry in particular. The overview of the progress and ongoing developments in broader areas of the natural products chemistry discipline, its role and concurrent economic and scientific implications, contemporary objectives, future prospects as well as impending goals are also outlined. A look at the natural products chemistry in providing scientific progress in various disciplines is deliberated upon.
Collapse
Affiliation(s)
- Riaz A. Khan
- Department of Medicinal Chemistry, Qassim University, Qassim 51452, Saudi Arabia
- Manav Rachna International University, National Capital Region, Faridabad, HR 121 004, India
| |
Collapse
|
18
|
Patakova P, Kolek J, Sedlar K, Koscova P, Branska B, Kupkova K, Paulova L, Provaznik I. Comparative analysis of high butanol tolerance and production in clostridia. Biotechnol Adv 2018; 36:721-738. [DOI: 10.1016/j.biotechadv.2017.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022]
|
19
|
Kenney GE, Dassama LMK, Pandelia ME, Gizzi AS, Martinie RJ, Gao P, DeHart CJ, Schachner LF, Skinner OS, Ro SY, Zhu X, Sadek M, Thomas PM, Almo SC, Bollinger JM, Krebs C, Kelleher NL, Rosenzweig AC. The biosynthesis of methanobactin. Science 2018; 359:1411-1416. [PMID: 29567715 DOI: 10.1126/science.aap9437] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/07/2018] [Indexed: 11/02/2022]
Abstract
Metal homeostasis poses a major challenge to microbes, which must acquire scarce elements for core metabolic processes. Methanobactin, an extensively modified copper-chelating peptide, was one of the earliest natural products shown to enable microbial acquisition of a metal other than iron. We describe the core biosynthetic machinery responsible for the characteristic posttranslational modifications that grant methanobactin its specificity and affinity for copper. A heterodimer comprising MbnB, a DUF692 family iron enzyme, and MbnC, a protein from a previously unknown family, performs a dioxygen-dependent four-electron oxidation of the precursor peptide (MbnA) to install an oxazolone and an adjacent thioamide, the characteristic methanobactin bidentate copper ligands. MbnB and MbnC homologs are encoded together and separately in many bacterial genomes, suggesting functions beyond their roles in methanobactin biosynthesis.
Collapse
Affiliation(s)
- Grace E Kenney
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Laura M K Dassama
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | | | - Anthony S Gizzi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ryan J Martinie
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peng Gao
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Caroline J DeHart
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Luis F Schachner
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Owen S Skinner
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Soo Y Ro
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Xiao Zhu
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Monica Sadek
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - J Martin Bollinger
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neil L Kelleher
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C Rosenzweig
- Department of Molecular Biosciences and Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
| |
Collapse
|
20
|
van Geelen L, Meier D, Rehberg N, Kalscheuer R. (Some) current concepts in antibacterial drug discovery. Appl Microbiol Biotechnol 2018; 102:2949-2963. [PMID: 29455386 DOI: 10.1007/s00253-018-8843-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 12/30/2022]
Abstract
The rise of multidrug resistance in bacteria rendering pathogens unresponsive to many clinical drugs is widely acknowledged and considered a critical global healthcare issue. There is broad consensus that novel antibacterial chemotherapeutic options are extremely urgently needed. However, the development pipeline of new antibacterial drug lead structures is poorly filled and not commensurate with the scale of the problem since the pharmaceutical industry has shown reduced interest in antibiotic development in the past decades due to high economic risks and low profit expectations. Therefore, academic research institutions have a special responsibility in finding novel treatment options for the future. In this mini review, we want to provide a broad overview of the different approaches and concepts that are currently pursued in this research field.
Collapse
Affiliation(s)
- Lasse van Geelen
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225, Dusseldorf, Germany
| | - Dieter Meier
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225, Dusseldorf, Germany
| | - Nidja Rehberg
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225, Dusseldorf, Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, 40225, Dusseldorf, Germany.
| |
Collapse
|
21
|
The industrial anaerobe Clostridium acetobutylicum uses polyketides to regulate cellular differentiation. Nat Commun 2017; 8:1514. [PMID: 29138399 PMCID: PMC5686105 DOI: 10.1038/s41467-017-01809-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/17/2017] [Indexed: 11/24/2022] Open
Abstract
Polyketides are an important class of bioactive small molecules valued not only for their diverse therapeutic applications, but also for their role in controlling interesting biological phenotypes in their producing organisms. While numerous polyketides are known to be derived from aerobic organisms, only a single family of polyketides has been identified from anaerobic organisms. Here we uncover a family of polyketides native to the anaerobic bacterium Clostridium acetobutylicum, an organism well-known for its historical use as an industrial producer of the organic solvents acetone, butanol, and ethanol. Through mutational analysis and chemical complementation assays, we demonstrate that these polyketides act as chemical triggers of sporulation and granulose accumulation in this strain. This study represents a significant addition to the body of work demonstrating the existence and importance of polyketides in anaerobes, and showcases a strategy of manipulating the secondary metabolism of an organism to improve traits relevant for industrial applications. Polyketides are secondary metabolites mainly found in aerobic organisms with wide applications in medicine and agriculture. Here, the authors uncover new polyketides native to the anaerobic bacterium Clostridium acetobutylicum and show their role in triggering sporulation and granulose accumulation.
Collapse
|
22
|
Why new antibiotics are not obviously useful now. Int J Antimicrob Agents 2017; 49:549-553. [DOI: 10.1016/j.ijantimicag.2016.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/08/2016] [Accepted: 11/12/2016] [Indexed: 01/22/2023]
|
23
|
Mamo G. Anaerobes as Sources of Bioactive Compounds and Health Promoting Tools. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 156:433-464. [PMID: 27432247 DOI: 10.1007/10_2016_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aerobic microorganisms have been sources of medicinal agents for several decades and an impressive variety of drugs have been isolated from their cultures, studied and formulated to treat or prevent diseases. On the other hand, anaerobes, which are believed to be the oldest life forms on earth and evolved remarkably diverse physiological functions, have largely been neglected as sources of bioactive compounds. However, results obtained from the limited research done so far show that anaerobes are capable of producing a range of interesting bioactive compounds that can promote human health. In fact, some of these bioactive compounds are found to be novel in their structure and/or mode of action.Anaerobes play health-promoting roles through their bioactive products as well as application of whole cells. The bioactive compounds produced by these microorganisms include antimicrobial agents and substances such as immunomodulators and vitamins. Bacteriocins produced by anaerobes have been in use as preservatives for about 40 years. Because these substances are effective at low concentrations, encounter relatively less resistance from bacteria and are safe to use, there is a growing interest in these antimicrobial agents. Moreover, several antibiotics have been reported from the cultures of anaerobes. Closthioamide and andrimid produced by Clostridium cellulolyticum and Pantoea agglomerans, respectively, are examples of novel antibiotics of anaerobe origin. The discovery of such novel bioactive compounds is expected to encourage further studies which can potentially lead to tapping of the antibiotic production potential of this fascinating group of microorganisms.Anaerobes are widely used in preparation of fermented foods and beverages. During the fermentation processes, these organisms produce a number of bioactive compounds including anticancer, antihypertensive and antioxidant substances. The well-known health promoting effect of fermented food is mostly due to these bioactive compounds. In addition to their products, whole cell anaerobes have very interesting applications for enhancing the quality of life. Probiotic anaerobes have been on the market for many years and are receiving growing acceptance as health promoters. Gut anaerobes have been used to treat patients suffering from severe Clostridium difficile infection syndromes including diarrhoea and colitis which cannot be treated by other means. Whole cell anaerobes are also studied to detect and cure cancer. In recent years, evidence is emerging that anaerobes constituting the microbiome are linked to our overall health. A dysfunctional microbiome is believed to be the cause of many diseases including cancer, allergy, infection, obesity, diabetes and several other disorders. Maintaining normal microflora is believed to alleviate some of these serious health problems. Indeed, the use of probiotics and prebiotics which favourably change the number and composition of the gut microflora is known to render a health promoting effect. Our interaction with the microbiome anaerobes is complex. In fact, not only our lives but also our identities are more closely linked to the anaerobic microbial world than we may possibly imagine. We are just at the beginning of unravelling the secret of association between the microbiome and human body, and a clear understanding of the association may bring a paradigm shift in the way we diagnose and treat diseases and disorders. This chapter highlights some of the work done on bioactive compounds and whole cell applications of the anaerobes that foster human health and improve the quality of life.
Collapse
Affiliation(s)
- Gashaw Mamo
- Biotechnology, Center for Chemistry & Chemical Engineering, Lund University, 221 00, Lund, Sweden.
| |
Collapse
|
24
|
Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes - a review. Nat Prod Rep 2016; 33:988-1005. [PMID: 27272205 DOI: 10.1039/c6np00025h] [Citation(s) in RCA: 404] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.
Collapse
Affiliation(s)
- Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tuebingen, Germany.
| | | | | |
Collapse
|
25
|
Letzel AC, Pidot SJ, Hertweck C. Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria. BMC Genomics 2014; 15:983. [PMID: 25407095 PMCID: PMC4289311 DOI: 10.1186/1471-2164-15-983] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/23/2014] [Indexed: 02/04/2023] Open
Abstract
Background Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a diverse group of biologically active bacterial molecules. Due to the conserved genomic arrangement of many of the genes involved in their synthesis, these secondary metabolite biosynthetic pathways can be predicted from genome sequence data. To date, however, despite the myriad of sequenced genomes covering many branches of the bacterial phylogenetic tree, such an analysis for a broader group of bacteria like anaerobes has not been attempted. Results We investigated a collection of 211 complete and published genomes, focusing on anaerobic bacteria, whose potential to encode RiPPs is relatively unknown. We showed that the presence of RiPP-genes is widespread among anaerobic representatives of the phyla Actinobacteria, Proteobacteria and Firmicutes and that, collectively, anaerobes possess the ability to synthesize a broad variety of different RiPP classes. More than 25% of anaerobes are capable of producing RiPPs either alone or in conjunction with other secondary metabolites, such as polyketides or non-ribosomal peptides. Conclusion Amongst the analyzed genomes, several gene clusters encode uncharacterized RiPPs, whilst others show similarity with known RiPPs. These include a number of potential class II lanthipeptides; head-to-tail cyclized peptides and lactococcin 972-like RiPP. This study presents further evidence in support of anaerobic bacteria as an untapped natural products reservoir. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-983) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology HKI, Beutenbergstr, 11a, Jena 07745, Germany.
| |
Collapse
|
26
|
Kloss F, Chiriac AI, Hertweck C. Mapping of the Modular Closthioamide Architecture Reveals Crucial Motifs of Polythioamide Antibiotics. Chemistry 2014; 20:15451-8. [DOI: 10.1002/chem.201403836] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 12/20/2022]
|
27
|
Recent advances in genome-based polyketide discovery. Curr Opin Biotechnol 2014; 29:107-15. [DOI: 10.1016/j.copbio.2014.03.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/11/2014] [Accepted: 03/14/2014] [Indexed: 11/27/2022]
|
28
|
Pidot S, Ishida K, Cyrulies M, Hertweck C. Discovery of Clostrubin, an Exceptional Polyphenolic Polyketide Antibiotic from a Strictly Anaerobic Bacterium. Angew Chem Int Ed Engl 2014; 53:7856-9. [DOI: 10.1002/anie.201402632] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 01/09/2023]
|
29
|
Pidot S, Ishida K, Cyrulies M, Hertweck C. Discovery of Clostrubin, an Exceptional Polyphenolic Polyketide Antibiotic from a Strictly Anaerobic Bacterium. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
30
|
Pidot SJ, Coyne S, Kloss F, Hertweck C. Antibiotics from neglected bacterial sources. Int J Med Microbiol 2014; 304:14-22. [DOI: 10.1016/j.ijmm.2013.08.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
31
|
Cloning and heterologous expression of the thioviridamide biosynthesis gene cluster from Streptomyces olivoviridis. Appl Environ Microbiol 2013; 79:7110-3. [PMID: 23995943 DOI: 10.1128/aem.01978-13] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thioviridamide is a unique peptide antibiotic containing five thioamide bonds from Streptomyces olivoviridis. Draft genome sequencing revealed a gene (the tvaA gene) encoding the thioviridamide precursor peptide. The thioviridamide biosynthesis gene cluster was identified by heterologous production of thioviridamide in Streptomyces lividans.
Collapse
|
32
|
Kloss F, Pidot S, Goerls H, Friedrich T, Hertweck C. Formation of a Dinuclear Copper(I) Complex from theClostridium-Derived Antibiotic Closthioamide. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304714] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
33
|
Kloss F, Pidot S, Goerls H, Friedrich T, Hertweck C. Formation of a dinuclear copper(I) complex from the Clostridium-derived antibiotic closthioamide. Angew Chem Int Ed Engl 2013; 52:10745-8. [PMID: 24039060 DOI: 10.1002/anie.201304714] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Florian Kloss
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Dept. of Biomolecular Chemistry, Beutenbergstr. 11a, 07745 Jena (Germany)
| | | | | | | | | |
Collapse
|
34
|
Ahrendt T, Miltenberger M, Haneburger I, Kirchner F, Kronenwerth M, Brachmann AO, Hilbi H, Bode HB. Biosynthesis of the natural fluorophore legioliulin from legionella. Chembiochem 2013; 14:1415-8. [PMID: 23821465 DOI: 10.1002/cbic.201300373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Indexed: 11/07/2022]
Abstract
Let it shine: The biosynthesis of the UV fluorophore legioliulin (1) from Legionella spp. was elucidated and the phenylalanine ammonium lyase LglD responsible for the formation of the starter unit cinnamic acid was biochemically characterized. Additionally, two novel derivatives differing in the starter unit have been identified by mutasynthesis experiments.
Collapse
Affiliation(s)
- Tilman Ahrendt
- Merck Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | | | | | | | | | | | | | | |
Collapse
|
35
|
|
36
|
Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models. PLoS One 2013; 8:e62136. [PMID: 23637983 PMCID: PMC3630128 DOI: 10.1371/journal.pone.0062136] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 03/19/2013] [Indexed: 01/24/2023] Open
Abstract
There is a growing interest in the Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) of microbes, fungi and plants because they can produce bioactive peptides such as antibiotics. The ability to identify the substrate specificity of the enzyme's adenylation (A) and acyl-transferase (AT) domains is essential to rationally deduce or engineer new products. We here report on a Hidden Markov Model (HMM)-based ensemble method to predict the substrate specificity at high quality. We collected a new reference set of experimentally validated sequences. An initial classification based on alignment and Neighbor Joining was performed in line with most of the previously published prediction methods. We then created and tested single substrate specific HMMs and found that their use improved the correct identification significantly for A as well as for AT domains. A major advantage of the use of HMMs is that it abolishes the dependency on multiple sequence alignment and residue selection that is hampering the alignment-based clustering methods. Using our models we obtained a high prediction quality for the substrate specificity of the A domains similar to two recently published tools that make use of HMMs or Support Vector Machines (NRPSsp and NRPS predictor2, respectively). Moreover, replacement of the single substrate specific HMMs by ensembles of models caused a clear increase in prediction quality. We argue that the superiority of the ensemble over the single model is caused by the way substrate specificity evolves for the studied systems. It is likely that this also holds true for other protein domains. The ensemble predictor has been implemented in a simple web-based tool that is available at http://www.cmbi.ru.nl/NRPS-PKS-substrate-predictor/.
Collapse
|