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Wang T, Wang X, Zhao H, Huo L, Fu C. Uncovering a Subtype of Microviridins via the Biosynthesis Study of FR901451. ACS Chem Biol 2022; 17:3489-3498. [PMID: 36373602 DOI: 10.1021/acschembio.2c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Microviridins are a class of ribosomally synthesized and post-translationally modified peptides originally discovered from cyanobacteria, featured by intramolecular ω-ester and ω-amide bonds catalyzed by two ATP-grasp ligases. In this study, 104 biosynthetic gene clusters of microviridins from Bacteroidetes were bioinformatically analyzed, which unveiled unique features of precursor peptides. The analysis of core peptides revealed a microviridin-like biosynthetic gene cluster from Chitinophagia japonensis DSM13484 consisting of two potential precursors ChiA1 and ChiA2. Unexpectedly, the core peptide sequence of ChiA1 is consistent with the backbone of the elastase-inhibiting peptide FR901451, while ChiA2 is likely to be a precursor of an unknown product. However, an unusual C-terminal follower cleavage compared to the previously known microviridin pathways was observed and found to be dispensable for other modifications. To confirm the biosynthetic origin of FR901451, ATP-grasp ligases ChiC and ChiB were biochemically characterized to be responsible for the intramolecular ester and amide bond formation, respectively. In vitro reconstitution of the pathway showed the three-fold dehydrations of ChiA1 while unusual four-fold dehydrations were observed for ChiA2. Furthermore, in vivo gene coexpression facilitated the production of chitinoviridin A1 (FR901451) and two novel microviridin-class compounds chitinoviridin A2A and chitinoviridin A2B, with an extra macrolactone ring. All of these peptides showed potent inhibitory effects against elastase and chymotrypsin independently.
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Affiliation(s)
- Tingting Wang
- Workgroup Genome Mining for Secondary Metabolites, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Xiaotong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China.,Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Haowen Zhao
- Workgroup Genome Mining for Secondary Metabolites, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
| | - Liujie Huo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China.,Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Chengzhang Fu
- Workgroup Genome Mining for Secondary Metabolites, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Helmholtz Center for Infection Research, 38124 Braunschweig, Germany
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Brinkmann S, Spohn MS, Schäberle TF. Bioactive natural products from Bacteroidetes. Nat Prod Rep 2022; 39:1045-1065. [PMID: 35315462 DOI: 10.1039/d1np00072a] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Covering: up to end of January 2022Bacteria representing the phylum Bacteroidetes produce a diverse range of natural products, including polyketides, peptides and lactams. Here, we discuss unique aspects of the bioactive compounds discovered thus far, and the corresponding biosynthetic pathways if known, providing a comprehensive overview of the Bacteroidetes as a natural product reservoir.
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Affiliation(s)
- Stephan Brinkmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany.
| | - Marius S Spohn
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany.
| | - Till F Schäberle
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, 35392 Giessen, Germany. .,Institute for Insect Biotechnology, Justus Liebig University of Giessen, 35392 Giessen, Germany.,German Centre for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
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3
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Peptides and Peptidomimetics as Inhibitors of Enzymes Involved in Fibrillar Collagen Degradation. MATERIALS 2021; 14:ma14123217. [PMID: 34200889 PMCID: PMC8230458 DOI: 10.3390/ma14123217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022]
Abstract
Collagen fibres degradation is a complex process involving a variety of enzymes. Fibrillar collagens, namely type I, II, and III, are the most widely spread collagens in human body, e.g., they are responsible for tissue fibrillar structure and skin elasticity. Nevertheless, the hyperactivity of fibrotic process and collagen accumulation results with joints, bone, heart, lungs, kidneys or liver fibroses. Per contra, dysfunctional collagen turnover and its increased degradation leads to wound healing disruption, skin photoaging, and loss of firmness and elasticity. In this review we described the main enzymes participating in collagen degradation pathway, paying particular attention to enzymes degrading fibrillar collagen. Therefore, collagenases (MMP-1, -8, and -13), elastases, and cathepsins, together with their peptide and peptidomimetic inhibitors, are reviewed. This information, related to the design and synthesis of new inhibitors based on peptide structure, can be relevant for future research in the fields of chemistry, biology, medicine, and cosmeceuticals.
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Gavriilidou A, Gutleben J, Versluis D, Forgiarini F, van Passel MWJ, Ingham CJ, Smidt H, Sipkema D. Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. BMC Genomics 2020; 21:569. [PMID: 32819293 PMCID: PMC7440613 DOI: 10.1186/s12864-020-06971-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/05/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. RESULTS Comparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains. CONCLUSIONS Our study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.
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Affiliation(s)
- Asimenia Gavriilidou
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Johanna Gutleben
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dennis Versluis
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Francesca Forgiarini
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Mark W. J. van Passel
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Present address: Ministry of Health, Welfare and Sport, Parnassusplein 5, 2511 VX, The Hague, The Netherlands
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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Steinmetz H, Gerth K, Jansen R, Schläger N, Dehn R, Reinecke S, Kirschning A, Müller R. Elansolid A, a unique macrolide antibiotic from Chitinophaga sancti isolated as two stable atropisomers. Angew Chem Int Ed Engl 2011; 50:532-6. [PMID: 21154488 DOI: 10.1002/anie.201005226] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Heinrich Steinmetz
- Mikrobielle Wirkstoffe, Helmholtz Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig, Germany
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Steinmetz H, Gerth K, Jansen R, Schläger N, Dehn R, Reinecke S, Kirschning A, Müller R. Elansolid A, ein einzigartiges Antibiotikum aus Chitinophaga sancti: isoliert in Form von zwei stabilen Atropisomeren. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005226] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Brauer ABE, McBride JD, Kelly G, Matthews SJ, Leatherbarrow RJ. Resisting degradation by human elastase: commonality of design features shared by 'canonical' plant and bacterial macrocyclic protease inhibitor scaffolds. Bioorg Med Chem 2007; 15:4618-28. [PMID: 17470393 DOI: 10.1016/j.bmc.2007.03.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 03/26/2007] [Accepted: 03/30/2007] [Indexed: 10/23/2022]
Abstract
A previously unexplained difference in the resistance to enzymatic hydrolysis of 11-mer Bowman-Birk-type inhibitors of human leukocyte elastase that differ in P1 is found to correlate with the strength of a particular intramolecular hydrogen bond within the inhibitor. This transannular hydrogen bond stabilizes the side chain of the conserved P2 Thr in a 'canonical' +60 degrees -rotamer chi(1) conformation and thereby directs it for a close interaction with the enzyme's catalytic His. As the implications of this NMR analysis are neither limited to this macrocyclic scaffold derived from plant proteins nor to a particular serine protease, we present a unified analysis with inhibitory bacterial depsipeptides of 7-12 residues in length that share key design features for which we propose communal functional explanations.
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Affiliation(s)
- Arnd B E Brauer
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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Kinoshita T, Kitatani T, Warizaya M, Tada T. Structure of the complex of porcine pancreatic elastase with a trimacrocyclic peptide inhibitor FR901451. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:808-11. [PMID: 16511165 PMCID: PMC1978120 DOI: 10.1107/s1744309105026047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 08/16/2005] [Indexed: 11/10/2022]
Abstract
Porcine pancreatic elastase (PPE) resembles the attractive drug target leukocyte elastase, which has the ability to degrade connective tissue in the body. The crystal structure of PPE complexed with a novel trimacrocyclic peptide inhibitor, FR901451, was solved at 1.9 A resolution. The inhibitor occupied the subsites S3 through S3' of PPE and induced conformational changes in the side chains of Arg64 and Arg226, which are located at the edges of the substrate-binding cleft. Structural comparison of five PPE-inhibitor complexes, including the FR901451 complex and non-ligated PPE, reveals that the residues forming the S2, S1, S1' and S2' subsites in the cleft are rigid, but the two arginine residues playing a part in the S3 and S3' subsites are flexible. Structural comparison of PPE with human leukocyte elastase (HLE) implies that the inhibitor binds to HLE in a similar manner to the FR901451-PPE complex. This structural insight may help in the design of potent elastase inhibitors.
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Affiliation(s)
- Takayoshi Kinoshita
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Gakuen-cho 1-1, Sakai, Osaka 599-8531, Japan
| | - Tomoya Kitatani
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Gakuen-cho 1-1, Sakai, Osaka 599-8531, Japan
| | - Masaichi Warizaya
- Lead Generation Research Laboratory, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
| | - Toshiji Tada
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Gakuen-cho 1-1, Sakai, Osaka 599-8531, Japan
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Hill DC, Wrigley SK, Nisbet LJ. Novel screen methodologies for identification of new microbial metabolites with pharmacological activity. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 1998; 59:73-121. [PMID: 9435461 DOI: 10.1007/bfb0102297] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Micro-organisms continue to provide an important source of chemical diversity for the discovery of compounds with new biological activities. Microbial metabolites discovered recently using assays to detect compounds with potential pharmacological utility are surveyed and found to represent an extensive range of structural types produced by a wide variety of organisms. Assays used for screening samples produced by microbial processes must be robust, sensitive and specific and able to operate above a background of potential interferences from a number of sources. Discovery assays currently in use fall into three main categories cell-based, receptor-ligand interaction and enzyme inhibition assays. Trends in the use of these assays and new developments in assay technology applicable to the screening of microbial samples are examined with particular reference to the high throughput screening environment. For microbial screening to be a competitive route to new drug leads, the disciplines involved must be engineered into a seamlessly integrated process to deliver novel compounds with the required biological properties rapidly.
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McBride MJ, Baker SA. Development of techniques to genetically manipulate members of the genera Cytophaga, Flavobacterium, Flexibacter, and Sporocytophaga. Appl Environ Microbiol 1996; 62:3017-22. [PMID: 8702294 PMCID: PMC168088 DOI: 10.1128/aem.62.8.3017-3022.1996] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Bacteroides-Cytophaga-Flavobacterium branch of the eubacterial phylogenetic tree contains a diverse group of bacterial species. Techniques for the genetic manipulation of Bacteroides spp. are well developed (A. A. Salyers, N. B. Shoemaker, and E. P. Guthrie, Crit. Rev. Microbiol. 14:49-71, 1987). Recently we developed techniques to genetically manipulate the gliding bacterium Cytophaga johnsonae (M. J. McBride and M. J. Kempf, J. Bacteriol. 178:583-590, 1996). We now demonstrate that some of these techniques allow genetic manipulation of a number of environmentally or medically significant bacteria in this group. The Bacteroides transposon Tn4351 was introduced into Cytophaga hutchinsonii, Cytophaga succinicans, Flavobacterium meningosepticum, Flexibacter canadensis, Flexibacter sp. strain FS1, and Sporocytophaga myxococcoides by conjugation. Tn4351 integrated itself into the host chromosomes and conferred erythromycin resistance. We isolated several auxotrophic mutants of Flavobacterium meningosepticum following Tn4351 mutagenesis. The C. johnsonae-Escherichia coli shuttle vector pCP11 functioned in C. succinicans but not in the other bacteria. pLYL03 did not replicate in any of these bacteria and should function as a convenient suicide vector. The identification of a system of gene transfer, a selectable marker, a suicide vector, and a transposon that functions in these diverse bacteria allows genetic manipulations to be performed.
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Affiliation(s)
- M J McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee 53201, USA.
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