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Thetsana C, Kobayashi R, Manadee K, Kodani S. Isolation and structure determination of a new depsipeptide crocapeptin C from the myxobacterium Melittangium boletus. Nat Prod Res 2024:1-7. [PMID: 38270086 DOI: 10.1080/14786419.2024.2308719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
A new cyclic depsipeptide, crocapeptin C (1), containing 3-amino-6-hydroxy-2-piperidone (Ahp) was isolated from the methanol extract of the myxobacterium Melittangium boletus. The chemical structure of crocapeptin C (1) was determined through NMR and ESI-MS analysis. The stereochemistries of the constituent amino acids in crocapeptin C (1) were determined using the advanced Marfey's method and ROESY spectrum data. Crocapeptin C (1) exhibited potent inhibitory activity against chymotrypsin with an IC50 value of 0.5 µM.
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Affiliation(s)
- Chanaphat Thetsana
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Ryo Kobayashi
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kanitta Manadee
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Shinya Kodani
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
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2
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Kamada S, Wakabayashi R, Naganuma T. Phylogenetic Revisit to a Review on Predatory Bacteria. Microorganisms 2023; 11:1673. [PMID: 37512846 PMCID: PMC10385382 DOI: 10.3390/microorganisms11071673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.
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Affiliation(s)
- Saki Kamada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Ryoka Wakabayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
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3
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Wei X, Moreno-Hagelsieb G, Glick BR, Doxey AC. Comparative analysis of adenylate isopentenyl transferase genes in plant growth-promoting bacteria and plant pathogenic bacteria. Heliyon 2023; 9:e13955. [PMID: 36938451 PMCID: PMC10018469 DOI: 10.1016/j.heliyon.2023.e13955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 03/09/2023] Open
Abstract
Cytokinin is a major phytohormone that has been used in agriculture as a plant-growth stimulating compound since its initial discovery in the 1960s. Isopentenyl transferase (IPT) is a rate-limiting enzyme for cytokinin biosynthesis, which is produced by plants as well as bacteria including both plant pathogenic species and plant growth-promoting bacteria (PGPB). It has been hypothesized that there may be differences in IPT function between plant pathogens and PGPB. However, a comprehensive comparison of IPT genes between plant pathogenic and PGPB species has not been performed. Here, we performed a global comparison of IPT genes across bacteria, analyzing their DNA sequences, codon usage, phyletic distribution, promoter structure and genomic context. We found that adenylate type IPT genes are highly specific to plant-associated bacteria and subdivide into two major clades: clade A, largely composed of proteobacterial plant pathogens; and clade B, largely composed of actinomycete PGPB species. Besides these phylogenetic differences, we identified several genomic features that suggest differences in IPT regulation between pathogens and PGPB. Pathogen-associated IPTs tended to occur in predicted virulence loci, whereas PGPB-associated IPTs tended to co-occur with other genes involved in cytokinin metabolism and degradation. Pathogen-associated IPTs also showed elevated gene copy numbers, significant deviation in codon usage patterns, and extended promoters, suggesting differences in regulation and activity levels. Our results are consistent with the hypothesis that differences in IPT regulation and activity exist between plant pathogens and PGPB, which determine their effect on plant host phenotypes through the control of cytokinin levels.
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Affiliation(s)
- Xin Wei
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | | | - Bernard R. Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Corresponding author.
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4
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Ye X, Liu W, Ma S, Chen X, Qiao Y, Zhao Y, Fan Q, Li X, Dong C, Fang X, Huan M, Han J, Huang Y, Cui Z, Li Z. Expression and characterization of 1,4-α-glucan branching enzyme from Microvirga sp. MC18 and its application in the preparation of slowly digestible starch. Protein Expr Purif 2021; 185:105898. [PMID: 33962003 DOI: 10.1016/j.pep.2021.105898] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/25/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
Nutraceuticals containing modified starch with increased content of slowly-digestible starch (SDS) may reduce the prevalence of obesity, diabetes and cardiovascular diseases due to its slow digestion rate. Enzymatic methods for the preparation of modified starch have attracted increasing attention because of their low environmental impact, safety and specificity. In this study, the efficient glucan branching enzyme McGBE from Microvirga sp. MC18 was identified, and its relevant properties as well as its potential for industrial starch modification were evaluated. The purified McGBE exhibited the highest specificity for potato starch, with a maximal specific activity of 791.21 U/mg. A time-dependent increase in the content of α-1,6 linkages from 3.0 to 6.0% was observed in McGBE-modified potato starch. The proportion of shorter chains (degree of polymerization, DP < 13) increased from 29.2 to 63.29% after McGBE treatment, accompanied by a reduction of the medium length chains (DP 13-24) from 52.30 to 35.99% and longer chains (DP > 25) from 18.51 to 0.72%. The reduction of the storage modulus (G') and retrogradation enthalpy (ΔHr) of potato starch with increasing treatment time demonstrated that McGBE could inhibit the short- and long-term retrogradation of starch. Under the optimal conditions, the SDS content of McGBE-modified potato starch increased by 65.8% compared to native potato starch. These results suggest that McGBE has great application potential for the preparation of modified starch with higher SDS content that is resistant to retrogradation.
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Affiliation(s)
- Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Liu
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiyun Ma
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaopei Chen
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Qiao
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuqiang Zhao
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qiwen Fan
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xu Li
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chaonan Dong
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodong Fang
- Guangzhou Hanyun Pharmaceutical Technology Co. Ltd., Guangzhou, 510000, China
| | - Minghui Huan
- Microbial Research Institute of Liaoning Province, Chaoyang, 122000, China
| | - Jian Han
- College of Agriculture, Xinjiang Agricultural University, XinJiang, 830052, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China.
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5
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Tiwari A, Kaweewan I, Miyake Y, Hemmi H, Kodani S. Isolation and structure determination of new chymotrypsin inhibitory peptides streptopeptolins B and C. Nat Prod Res 2019; 35:2700-2706. [DOI: 10.1080/14786419.2019.1663514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ankit Tiwari
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Issara Kaweewan
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Yuto Miyake
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hikaru Hemmi
- Food Research Institute, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
- Academic Institute, Shizuoka University, Shizuoka, Japan
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A Highly Polymorphic Receptor Governs Many Distinct Self-Recognition Types within the Myxococcales Order. mBio 2019; 10:mBio.02751-18. [PMID: 30755513 PMCID: PMC6372800 DOI: 10.1128/mbio.02751-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Many biological species distinguish self from nonself by using different mechanisms. Higher animals recognize close kin via complex processes that often involve the five senses, cognition, and learning, whereas some microbes achieve self-recognition simply through the activity of a single genetic locus. Here we describe a single locus, traA, in myxobacteria that governs cell-cell recognition within natural populations. We found that traA is widespread across the order Myxococcales. TraA is highly polymorphic among diverse myxobacterial isolates, and such polymorphisms determine selectivity in self-recognition. Through bioinformatic and experimental analyses, we showed that traA governs many distinct recognition groups within Myxococcales. This report provides an example in which a single locus influences social recognition across a wide phylogenetic range of natural populations. Self-recognition underlies sociality in many group-living organisms. In bacteria, cells use various strategies to recognize kin to form social groups and, in some cases, to transition into multicellular life. One strategy relies on a single genetic locus that encodes a variable phenotypic tag (“greenbeard”) for recognizing other tag bearers. Previously, we discovered a polymorphic cell surface receptor called TraA that directs self-identification through homotypic interactions in the social bacterium Myxococcus xanthus. Recognition by TraA leads to cellular resource sharing in a process called outer membrane exchange (OME). A second gene in the traA operon, traB, is also required for OME but is not involved in recognition. Our prior studies of TraA identified only six recognition groups among closely related M. xanthus isolates. Here we hypothesize that the number of traA polymorphisms and, consequently, the diversity of recognition in wild isolates are much greater. To test this hypothesis, we expand the scope of TraA characterization to the order Myxococcales. From genomic sequences within the three suborders of Myxococcales, we identified 90 traA orthologs. Sequence analyses and functional characterization of traAB loci suggest that OME is well maintained among diverse myxobacterial taxonomic groups. Importantly, TraA orthologs are highly polymorphic within their variable domain, the region that confers selectivity in self-recognition. We experimentally defined 10 distinct recognition groups and, based on phylogenetic and experimental analyses, predicted >60 recognition groups among the 90 traA alleles. Taken together, our findings revealed a widespread greenbeard locus that mediates the diversity of self-recognition across the order Myxococcales.
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7
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Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, Poehlein A, Ziemert N, König GM, Schäberle TF. Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites. Sci Rep 2018; 8:16600. [PMID: 30413766 PMCID: PMC6226438 DOI: 10.1038/s41598-018-34954-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/29/2018] [Indexed: 01/14/2023] Open
Abstract
Comparative genomic/metabolomic analysis is a powerful tool to disclose the potential of microbes for the biosynthesis of novel specialized metabolites. In the group of marine myxobacteria only a limited number of isolated species and sequenced genomes is so far available. However, the few compounds isolated thereof so far show interesting bioactivities and even novel chemical scaffolds; thereby indicating a huge potential for natural product discovery. In this study, all marine myxobacteria with accessible genome data (n = 5), including Haliangium ochraceum DSM 14365, Plesiocystis pacifica DSM 14875, Enhygromyxa salina DSM 15201 and the two newly sequenced species Enhygromyxa salina SWB005 and SWB007, were analyzed. All of these accessible genomes are large (~10 Mb), with a relatively small core genome and many unique coding sequences in each strain. Genome analysis revealed a high variety of biosynthetic gene clusters (BGCs) between the strains and several resistance models and essential core genes indicated the potential to biosynthesize antimicrobial molecules. Polyketides (PKs) and terpenes represented the majority of predicted specialized metabolite BGCs and contributed to the highest share between the strains. BGCs coding for non-ribosomal peptides (NRPs), PK/NRP hybrids and ribosomally synthesized and post-translationally modified peptides (RiPPs) were mostly strain specific. These results were in line with the metabolomic analysis, which revealed a high diversity of the chemical features between the strains. Only 6-11% of the metabolome was shared between all the investigated strains, which correlates to the small core genome of these bacteria (13-16% of each genome). In addition, the compound enhygrolide A, known from E. salina SWB005, was detected for the first time and structurally elucidated from Enhygromyxa salina SWB006. The here acquired data corroborate that these microorganisms represent a most promising source for the detection of novel specialized metabolites.
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Affiliation(s)
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Mohammad Alanjary
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Henrik Harms
- German Center for Infection Research (DZIF) Partner Site Cologne/Bonn, Bonn, Germany.,Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anja Poehlein
- Department of Genomics and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August-University Göttingen, Göttingen, Germany
| | - Nadine Ziemert
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.
| | - Till F Schäberle
- German Center for Infection Research (DZIF) Partner Site Cologne/Bonn, Bonn, Germany. .,Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany. .,Department of Bioresources of the Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.
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8
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In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides. BMC Genomics 2018; 19:757. [PMID: 30340510 PMCID: PMC6194562 DOI: 10.1186/s12864-018-5151-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/08/2018] [Indexed: 11/23/2022] Open
Abstract
Background An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability to reside and thrive in its current environment. Similar to external signaling molecules, cytoplasmic signals are also sensed by methyl-accepting chemotaxis proteins (MCPs) via diverse ligand binding domains. Myxobacteria are complex soil-dwelling social microbes that can perform a variety of physiologic and metabolic activities ranging from gliding motility, sporulation, biofilm formation, carotenoid and secondary metabolite biosynthesis, predation, and slime secretion. To live such complex lifestyles, they have evolved efficient signal transduction systems with numerous one- and two-component regulatory system along with a large array of chemosensory systems to perceive and integrate both external and internal cues. Results Here we report the in silico characterization of a putative energy taxis cluster, Cc-5, which is present in only one amongst 34 known and sequenced myxobacterial genomes, Corallococcus coralloides. In addition, we propose that this energy taxis cluster is involved in oxygen sensing, suggesting that C. coralloides can sense (either directly or indirectly) and then respond to changing concentrations of molecular oxygen. Conclusions This hypothesis is based on the presence of a unique MCP encoded in this gene cluster that contains two different oxygen-binding sensor domains, PAS and globin. In addition, the two monooxygenases encoded in this cluster may contribute to aerobic respiration via ubiquinone biosynthesis, which is part of the cytochrome bc1 complex. Finally, we suggest that this cluster was acquired from Actinobacteria, Gammaproteobacteria or Cyanobacteria. Overall, this in silico study has identified a potentially innovative and evolved mechanism of energy taxis in only one of the myxobacteria, C. coralloides. Electronic supplementary material The online version of this article (10.1186/s12864-018-5151-6) contains supplementary material, which is available to authorized users.
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9
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Kodani S, Komaki H, Hemmi H, Miyake Y, Kaweewan I, Dohra H. Streptopeptolin, a Cyanopeptolin-Type Peptide from Streptomyces olivochromogenes. ACS OMEGA 2018; 3:8104-8110. [PMID: 30087936 PMCID: PMC6072256 DOI: 10.1021/acsomega.8b01042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Cyanopeptolin-type peptides are cyclic depsipeptides that commonly have 3-amino-6-hydroxy-2-piperidone (Ahp) unit in the molecules. So far, cyanopeptolin-type peptides have been isolated as protease inhibitors from a wide variety of cyanobacteria. In the course of screening for new peptides, a new peptide streptopeptolin, which had the similar structure to cyanopeptolin, was isolated from the extract of Streptomyces olivochromogenes NBRC 3561. Streptopeptolin is the first cyanopeptolin-type peptide isolated from actinobacteria. The structure of streptopeptolin was determined by the analysis of electrospray ionization mass spectrometry and NMR to be cyclic depsipeptide containing unusual amino acids, Ahp, and N-methyl tyrosine. As a result of protease inhibition test, streptopeptolin showed inhibitory activity against chymotrypsin. The whole genome sequence data of S. olivochromogenes revealed the biosynthetic gene cluster for streptopeptolin, which encoded a nonribosomal peptide synthetase. We proposed a biosynthetic pathway of streptopeptolin based on bioinformatics analysis.
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Affiliation(s)
- Shinya Kodani
- Academic
Institute, Graduate School of Integrated Science and Technology, Graduate School of
Science and Technology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Hisayuki Komaki
- Biological
Resource Center, National Institute of Technology
and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hikaru Hemmi
- Food
Research
Institute, National Agriculture and Food
Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yuto Miyake
- Academic
Institute, Graduate School of Integrated Science and Technology, Graduate School of
Science and Technology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Issara Kaweewan
- Academic
Institute, Graduate School of Integrated Science and Technology, Graduate School of
Science and Technology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Hideo Dohra
- Academic
Institute, Graduate School of Integrated Science and Technology, Graduate School of
Science and Technology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
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10
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Sharma G, Burrows LL, Singer M. Diversity and Evolution of Myxobacterial Type IV Pilus Systems. Front Microbiol 2018; 9:1630. [PMID: 30072980 PMCID: PMC6060248 DOI: 10.3389/fmicb.2018.01630] [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: 02/13/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022] Open
Abstract
Type IV pili (T4P) are surface-exposed protein fibers that play key roles in the bacterial life cycle via surface attachment/adhesion, biofilm formation, motility, and development. The order Myxococcales (myxobacteria) are members of the class Deltaproteobacteria and known for their large genome size and complex social behaviors, including gliding motility, fruiting body formation, biofilm production, and prey hunting. Myxococcus xanthus, the best-characterized member of the order, relies on the appropriate expression of 17 type IVa (T4aP) genes organized in a single cluster plus additional genes (distributed throughout the genome) for social motility and development. Here, we compared T4aP genes organization within the myxobacteria to understand their evolutionary origins and diversity. We found that T4aP genes are organized as large clusters in suborder Cystobacterineae, whereas in other two suborders Sorangiineae and Nannocystineae, these genes are dispersed throughout the genome. Based on the genomic organization, the phylogeny of conserved proteins, and synteny studies among 28 myxobacterial and 66 Proteobacterial genomes, we propose an evolutionary model for the origin of myxobacterial T4aP genes independently from other orders in class Deltaproteobacteria. Considering a major role for T4P, this study further proposes the origins and evolution of social motility in myxobacteria and provides a foundation for understanding how complex-behavioral traits, such as gliding motility, multicellular development, etc., might have evolved in this diverse group of complex organisms.
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Affiliation(s)
- Gaurav Sharma
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada
| | - Mitchell Singer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
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11
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Panter F, Krug D, Baumann S, Müller R. Self-resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria. Chem Sci 2018; 9:4898-4908. [PMID: 29910943 PMCID: PMC5982219 DOI: 10.1039/c8sc01325j] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/01/2018] [Indexed: 01/14/2023] Open
Abstract
There is astounding discrepancy between the genome-inscribed production capacity and the set of known secondary metabolite classes from many microorganisms as detected under laboratory cultivation conditions. Genome-mining techniques are meant to fill this gap, but in order to favor discovery of structurally novel as well as bioactive compounds it is crucial to amend genomics-based strategies with selective filtering principles. In this study, we followed a self-resistance guided approach aiming at the discovery of inhibitors of topoisomerase, known as valid target in both cancer and antibiotic therapy. A common host self-defense mechanism against such inhibitors in bacteria is mediated by so-called pentapeptide repeat proteins (PRP). Genes encoding the biosynthetic machinery for production of an alleged topoisomerase inhibitor were found on the basis of their collocation adjacent to a predicted PRP in the genome of the myxobacterium Pyxidicoccus fallax An d48, but to date no matching compound has been reported from this bacterium. Activation of this peculiar polyketide synthase type-II gene cluster in the native host as well as its heterologous expression led to the structure elucidation of new natural products that were named pyxidicyclines and provided an insight into their biosynthesis. Subsequent topoisomerase inhibition assays showed strong affinity to - and inhibition of - unwinding topoisomerases such as E. coli topoisomerase IV and human topoisomerase I by pyxidicyclines as well as precise selectivity, since E. coli topoisomerase II (gyrase) was not inhibited at concentrations up to 50 μg ml-1.
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Affiliation(s)
- Fabian Panter
- Department Microbial Natural Products , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research (HZI) , Department of Pharmaceutical Biotechnology , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany .
| | - Daniel Krug
- Department Microbial Natural Products , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research (HZI) , Department of Pharmaceutical Biotechnology , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany .
| | - Sascha Baumann
- Department Microbial Natural Products , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research (HZI) , Department of Pharmaceutical Biotechnology , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany .
| | - Rolf Müller
- Department Microbial Natural Products , Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Centre for Infection Research (HZI) , Department of Pharmaceutical Biotechnology , Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany .
- German Centre for Infection Research , partner-site Hannover/Braunschweig , Germany
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12
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Premnath P, Reck M, Wittstein K, Stadler M, Wagner-Döbler I. Screening for inhibitors of mutacin synthesis in Streptococcus mutans using fluorescent reporter strains. BMC Microbiol 2018; 18:24. [PMID: 29580208 PMCID: PMC5870221 DOI: 10.1186/s12866-018-1170-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/20/2018] [Indexed: 01/22/2023] Open
Abstract
Background Within the polymicrobial dental plaque biofilm, bacteria kill competitors by excreting mixtures of bacteriocins, resulting in improved fitness and survival. Inhibiting their bacteriocin synthesis might therefore be a useful strategy to eliminate specific pathogens. We used Streptococcus mutans, a highly acidogenic inhabitant of dental plaque, as a model and searched for natural products that reduced mutacin synthesis. To this end we fused the promoter of mutacin VI to the GFP+ gene and integrated the construct into the genome of S. mutans UA159 by single homologous recombination. Results The resulting reporter strain 423p - gfp + was used to screen 297 secondary metabolites from different sources, mainly myxobacteria and fungi, for their ability to reduce the fluorescence of the fully induced reporter strain by > 50% while growth was almost unaffected (> 90% of control). Seven compounds with different chemical structures and different modes of action were identified. Erinacine C was subsequently validated and shown to inhibit transcription of all three mutacins of S. mutans. The areas of the inhibition zones of the sensor strains S. sanguinis and Lactococcus lactis were reduced by 35% to 61% in comparison to controls in the presence of erinacine C, demonstrating that the amount of active mutacins in the culture supernatants of S. mutans was reduced. Erinacines are cyathane diterpenes that were extracted from cultures of the edible mushroom Hericium erinaceus. They have anti-inflammatory, antimicrobial and neuroprotective effects. For erinacine C, a new biological activity was found here. Conclusions We demonstrate the successful development of a whole-cell fluorescent reporter for the screening of natural compounds and report that erinacine C suppresses mutacin synthesis in S. mutans without affecting cell viability. Electronic supplementary material The online version of this article (10.1186/s12866-018-1170-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Priyanka Premnath
- Helmholtz-Center for Infection Research, Group Microbial Communication, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Michael Reck
- Helmholtz-Center for Infection Research, Group Microbial Communication, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Kathrin Wittstein
- Helmholtz-Center for Infection Research, Department of Microbial Drugs, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Marc Stadler
- Helmholtz-Center for Infection Research, Department of Microbial Drugs, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Irene Wagner-Döbler
- Helmholtz-Center for Infection Research, Group Microbial Communication, Inhoffenstr. 7, 38124, Braunschweig, Germany.
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13
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Hoffmann T, Krug D, Bozkurt N, Duddela S, Jansen R, Garcia R, Gerth K, Steinmetz H, Müller R. Correlating chemical diversity with taxonomic distance for discovery of natural products in myxobacteria. Nat Commun 2018; 9:803. [PMID: 29476047 PMCID: PMC5824889 DOI: 10.1038/s41467-018-03184-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 01/24/2018] [Indexed: 01/22/2023] Open
Abstract
Some bacterial clades are important sources of novel bioactive natural products. Estimating the magnitude of chemical diversity available from such a resource is complicated by issues including cultivability, isolation bias and limited analytical data sets. Here we perform a systematic metabolite survey of ~2300 bacterial strains of the order Myxococcales, a well-established source of natural products, using mass spectrometry. Our analysis encompasses both known and previously unidentified metabolites detected under laboratory cultivation conditions, thereby enabling large-scale comparison of production profiles in relation to myxobacterial taxonomy. We find a correlation between taxonomic distance and the production of distinct secondary metabolite families, further supporting the idea that the chances of discovering novel metabolites are greater by examining strains from new genera rather than additional representatives within the same genus. In addition, we report the discovery and structure elucidation of rowithocin, a myxobacterial secondary metabolite featuring an uncommon phosphorylated polyketide scaffold. It is thought that the chances for discovery of novel natural products increase by screening rare organisms. Here the authors analyse metabolites produced by over 2300 myxobacterial strains and, indeed, find a correlation between taxonomic distance and production of distinct secondary metabolite families.
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Affiliation(s)
- Thomas Hoffmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
| | - Nisa Bozkurt
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Srikanth Duddela
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Rolf Jansen
- Helmholtz Centre for Infection Research (HZI), Department of Microbial Drugs, 38124, Braunschweig, Germany
| | - Ronald Garcia
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany
| | - Klaus Gerth
- Helmholtz Centre for Infection Research (HZI), Department of Microbial Drugs, 38124, Braunschweig, Germany
| | - Heinrich Steinmetz
- Helmholtz Centre for Infection Research (HZI), Department of Microbial Drugs, 38124, Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department of Microbial Natural Products, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany.
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14
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Hoffmann M, Auerbach D, Panter F, Hoffmann T, Dorrestein PC, Müller R. Homospermidine Lipids: A Compound Class Specifically Formed during Fruiting Body Formation of Myxococcus xanthus DK1622. ACS Chem Biol 2018; 13:273-280. [PMID: 29185703 DOI: 10.1021/acschembio.7b00816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The fascinating ability of myxobacteria to form multicellular spore filled fruiting bodies under starvation conditions was widely studied as a model for cooperative microbial behavior. The potential of a life cycle induced change of secondary metabolism, as a means to discover novel natural products, remains largely underexplored. We therefore studied the model organism Myxococcus xanthus DK1622 under submersed and solid cultivation conditions to find putatively life-cycle related compounds by applying statistical analysis on analytical data. Utilizing the advantageous characteristics of LC-MS, LC-MS/MS, and MALDI-MSI allowed the identification of compounds unambiguously associated with myxobacterial fruiting bodies. Our screening effort resulted in the purification and structure elucidation of a novel compound, the homospermidine lipid, from cultures that had undergone the fruiting process. A combination of molecular networking and targeted LC-MS/MS in conjunction with our in-house metabolomics database subsequently revealed alternative producers of the respective compound as well as a number of compounds belonging to the same structural class. Three further members of this compound class were isolated from an alternative producer and structurally elucidated by NMR. Insights into the biosynthesis of this novel compound class was gained by feeding of isotopically labeled substrates and in silico analysis.
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Affiliation(s)
- Michael Hoffmann
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - David Auerbach
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
- Collaborative Mass Spectrometry Innovation Center, Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
| | - Rolf Müller
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
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15
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Surup F, Viehrig K, Rachid S, Plaza A, Maurer CK, Hartmann RW, Müller R. Crocadepsins-Depsipeptides from the Myxobacterium Chondromyces crocatus Found by a Genome Mining Approach. ACS Chem Biol 2018; 13:267-272. [PMID: 29220569 DOI: 10.1021/acschembio.7b00900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Analysis of the genome sequence of the myxobacterium Chondromyces crocatus Cm c5 revealed the presence of numerous cryptic megasynthetase gene clusters, one of which we here assign to two previously unknown chlorinated metabolites by a comparative gene inactivation and secondary metabolomics approach. Structure elucidation of these compounds revealed a unique cyclic depsipeptide skeleton featuring β- and δ-amide bonds of aspartic acid and 3-methyl ornithine moieties, respectively. Insights into their biosynthesis were obtained by targeted gene inactivation and feeding experiments employing isotope-labeled precursors. The compounds were produced ubiquitously by the species Chondromyces crocatus and were found to inhibit the carbon storage regulator-RNA interaction.
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Affiliation(s)
- Frank Surup
- Helmholtz Center
for Infection Research (HZI), Department Microbial Drugs, Inhoffenstraβe
7, 38124 Braunschweig, Germany
- German Centre for Infection Research Association (DZIF), partner site Hannover-Braunschweig, Inhoffenstraβe 7, 38124 Braunschweig, Germany
| | - Konrad Viehrig
- Helmholtz Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Center for Infection Research
and Pharmaceutical Biotechnology, Saarland University, Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Shwan Rachid
- Helmholtz Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Center for Infection Research
and Pharmaceutical Biotechnology, Saarland University, Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Alberto Plaza
- Helmholtz Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Center for Infection Research
and Pharmaceutical Biotechnology, Saarland University, Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Christine K. Maurer
- Department of Drug Design & Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research Association (DZIF), partner site Hannover-Braunschweig, Inhoffenstraβe 7, 38124 Braunschweig, Germany
| | - Rolf W. Hartmann
- Department of Drug Design & Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research Association (DZIF), partner site Hannover-Braunschweig, Inhoffenstraβe 7, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Center
for Infection Research (HZI), Department Microbial Drugs, Inhoffenstraβe
7, 38124 Braunschweig, Germany
- Helmholtz Institute for Pharmaceutical
Research Saarland (HIPS), Helmholtz Center for Infection Research
and Pharmaceutical Biotechnology, Saarland University, Campus, Building C2.3, 66123 Saarbrücken, Germany
- German Centre for Infection Research Association (DZIF), partner site Hannover-Braunschweig, Inhoffenstraβe 7, 38124 Braunschweig, Germany
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16
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Li Z, Ji K, Zhou J, Ye X, Wang T, Luo X, Huang Y, Cao H, Cui Z, Kong Y. A debranching enzyme IsoM of Corallococcus sp. strain EGB with potential in starch processing. Int J Biol Macromol 2017; 105:1300-1309. [DOI: 10.1016/j.ijbiomac.2017.07.153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 01/30/2023]
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17
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Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713. GENOME ANNOUNCEMENTS 2017; 5:5/45/e01262-17. [PMID: 29122879 PMCID: PMC5679812 DOI: 10.1128/genomea.01262-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The formation of spore-filled fruiting bodies in response to starvation represents a hallmark of many members of the order Myxococcales. Here, we present the complete 9.9-Mb genome of the fruiting type strain Melittangium boletus DSM 14713, the first member of this genus to have its genome sequenced.
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18
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Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71. GENOME ANNOUNCEMENTS 2017; 5:5/43/e01227-17. [PMID: 29074673 PMCID: PMC5658511 DOI: 10.1128/genomea.01227-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In response to starvation, members of the order Myxococcales form morphologically very different fruiting bodies. To determine whether fruiting myxobacteria share a common genetic program that leads to fruiting body formation, we sequenced and assembled the genome of Nannocystis exedens DSM 71 as two contigs with a total GC content of 72%.
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19
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Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655. GENOME ANNOUNCEMENTS 2017; 5:5/43/e01196-17. [PMID: 29074667 PMCID: PMC5658505 DOI: 10.1128/genomea.01196-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Among myxobacteria, the genus Cystobacter is known not only for fruiting body formation but also for formation of secondary metabolites, such as cystobactamids and cystothiazols. Here, we present the complete genome sequence of the Cystobacter fuscus strain DSM 52655, which comprises 12,349,744 bp and 9,836 putative protein-coding sequences.
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20
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Yasir M. Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota. Braz J Microbiol 2017; 49:248-257. [PMID: 29108974 PMCID: PMC5913830 DOI: 10.1016/j.bjm.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 05/29/2017] [Accepted: 08/15/2017] [Indexed: 02/01/2023] Open
Abstract
In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.
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Affiliation(s)
- Muhammad Yasir
- King Abdulaziz University, King Fahd Medical Research Center, Special Infectious Agents Unit, Jeddah, Saudi Arabia.
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21
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Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing. GENOME ANNOUNCEMENTS 2017; 5:5/40/e01127-17. [PMID: 28983009 PMCID: PMC5629066 DOI: 10.1128/genomea.01127-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Members of the Myxococcales order initiate a developmental program in response to starvation that culminates in formation of spore-filled fruiting bodies. To investigate the genetic basis for fruiting body formation, we present the complete 8.9-Mb genome sequence of Myxococcus macrosporus strain DSM 14697, generated using the PacBio sequencing platform.
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22
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Bihelovic F, Stichnoth D, Surup F, Müller R, Trauner D. Total Synthesis of Crocagin A. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Filip Bihelovic
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
- Present address: Faculty of Chemistry; University of Belgrade; Studentski trg 12-16 11158 Belgrade Serbia
| | - Desiree Stichnoth
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Frank Surup
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Dirk Trauner
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
- Department of Chemistry; New York University; 100 Washington Square East New York USA
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23
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Bihelovic F, Stichnoth D, Surup F, Müller R, Trauner D. Total Synthesis of Crocagin A. Angew Chem Int Ed Engl 2017; 56:12848-12851. [DOI: 10.1002/anie.201612641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 07/19/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Filip Bihelovic
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
- Present address: Faculty of Chemistry; University of Belgrade; Studentski trg 12-16 11158 Belgrade Serbia
| | - Desiree Stichnoth
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Frank Surup
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Dirk Trauner
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
- Department of Chemistry; New York University; 100 Washington Square East New York USA
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Affiliation(s)
- Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Birte Abt
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
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Abstract
With the advent of very rapid and cheap genome analyses and the linkage of these plus microbial metabolomics to potential compound structures came the realization that there was an immense sea of novel agents to be mined and tested. In addition, it is now recognized that there is significant microbial involvement in many natural products isolated from “nominally non-microbial sources”. This short review covers the current screening methods that have evolved and one might even be tempted to say “devolved” in light of the realization that target-based screens had problems when the products entered clinical testing, with off-target effects being the major ones. Modern systems include, but are not limited to, screening in cell lines utilizing very modern techniques (a high content screen) that are designed to show interactions within cells when treated with an “agent”. The underlying principle(s) used in such systems dated back to unpublished attempts in the very early 1980s by the pharmaceutical industry to show toxic interactions within animal cells by using automated light microscopy. Though somewhat successful, the technology was not adequate for any significant commercialization. Somewhat later, mammalian cell lines that were “genetically modified” to alter signal transduction cascades, either up or down, and frequently linked to luciferase readouts, were then employed in a 96-well format. In the case of microbes, specific resistance parameters were induced in isogenic cell lines from approximately the mid-1970s. In the latter two cases, comparisons against parent and sibling cell lines were used in order that a rapid determination of potential natural product “hits” could be made. Obviously, all of these assay systems could also be, and were, used for synthetic molecules. These methods and their results have led to a change in what the term “screening for bioactivity” means. In practice, versions of phenotypic screening are returning, but in a dramatically different scientific environment from the 1970s, as I hope to demonstrate in the short article that follows.
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Chemische Struktur und Biosynthese der Crocagine, polycyclischer Peptide ribosomalen Ursprungs ausChondromyces crocatus. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Viehrig K, Surup F, Volz C, Herrmann J, Abou Fayad A, Adam S, Köhnke J, Trauner D, Müller R. Structure and Biosynthesis of Crocagins: Polycyclic Posttranslationally Modified Ribosomal Peptides fromChondromyces crocatus. Angew Chem Int Ed Engl 2017; 56:7407-7410. [DOI: 10.1002/anie.201612640] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/08/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Konrad Viehrig
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Frank Surup
- Helmholtz Center for Infection Research (HZI); Department Microbial Drugs; Inhoffenstraße 7 38124 Braunschweig Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig; Germany
| | - Carsten Volz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Antoine Abou Fayad
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Sebastian Adam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Jesko Köhnke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
| | - Dirk Trauner
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Helmholtz Center for Infection Research and Pharmaceutical Biotechnology; Saarland University; Campus, Building E8.1 66123 Saarbrücken Germany
- Helmholtz Center for Infection Research (HZI); Department Microbial Drugs; Inhoffenstraße 7 38124 Braunschweig Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig; Germany
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28
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Affiliation(s)
- Silke C. Wenzel
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
| | - Rolf Müller
- Saarland University; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology; Saarland University Campus, Building E8.1 66123 Saarbrücken Germany
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