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Yuri Pinheiro Alves de Souza, Fábio Faria da Mota, Alexandre Soares Rosado
We report here the 3,586,065-bp draft genome of Geobacillus sp. LEMMY01, which was isolated (axenic culture) from a thermophilic chemolitoautotrophic consortium obtained from the site of a burning grass pile. The genome contains biosynthetic gene clusters coding for secondary metabolites, such as terpene and lantipeptide, confirming the biotechnological potential of this strain.
May 11, 2017: Genome Announcements
Kirill S Mironov, Maria A Sinetova, Kenzhegul Bolatkhan, Bolatkhan K Zayadan, Vera V Ustinova, Elena V Kupriyanova, Alexandra N Skrypnik, Natalya E Gogoleva, Yuriy V Gogolev, Dmitry A Los
Here, we report the draft genome of the filamentous cyanobacterium Desertifilum sp. strain IPPAS B-1220, isolated from Lake Shar-Nuur, Mongolia. The genome of 6.1 Mb codes for 5,113 genes. Genome mining revealed 10 clusters for the synthesis of bioactive compounds (nonribosomal peptides, polyketides, bacteriocins, and lantipeptides) with potential biotechnological or medical importance.
November 17, 2016: Genome Announcements
Muhd Danish-Daniel, Gan Han Ming, Mohd Ezhar Mohd Noor, Yeong Yik Sung, Gires Usup
Bacillus sp. strain UMTAT18 was isolated from the harmful dinoflagellate Alexandrium tamiyavanichii Its genome consists of 5,479,367 bp with 5,546 open reading frames, 102 tRNAs, and 29 rRNAs. Gene clusters for biosynthesis of nonribosomal peptides, bacteriocin, and lantipeptide were identified. It also contains siderophore and genes related to stress tolerance.
October 6, 2016: Genome Announcements
Hisayuki Komaki, Akira Hosoyama, Shuhei Yabe, Akira Yokota, Yoshihito Uchino, Hideaki Takano
Here, we report the draft genome sequence of Thermogemmatispora onikobensis NBRC 111776(T), an aerial mycelium- and spore-forming thermophilic bacterium belonging to the class Ktedonobacteria The genome contains five biosynthetic gene clusters coding for secondary metabolites, such as terpene, thiopeptide, lantipeptide, nonribosomal peptide, and lassopeptide, suggesting the potential to produce secondary metabolites.
October 13, 2016: Genome Announcements
Hideaki Takano, Yuhei Matsui, Junpei Nomura, Masahiro Fujimoto, Naoto Katsumata, Takafumi Koyama, Isamu Mizuno, Shoichi Amano, Hatsumi Shiratori-Takano, Mamoru Komatsu, Haruo Ikeda, Kenji Ueda
AmfS, a class III lantipeptide serves as a morphogen in Streptomyces griseus. Here, we constructed a high production system of AmfS in S. griseus. We isolated S. griseus Grd1 strain defective in glucose repression of aerial mycelium formation and found it suitable for the overproduction of AmfS. Two expression vectors carrying the strong and constitutive ermE2 promoter were constructed using a multicopy number plasmid, pIJ702. The use of the Grd1 strain combined with the expression vectors enabled high production of AmfS by S...
January 2017: Bioscience, Biotechnology, and Biochemistry
Auke J van Heel, Tomas G Kloosterman, Manuel Montalban-Lopez, Jingjing Deng, Annechien Plat, Baptiste Baudu, Djoke Hendriks, Gert N Moll, Oscar P Kuipers
To find the right conditions to isolate natively expressed antimicrobial peptides from a wide range of different microorganisms can be a challenge. Here, we exploited a heterologous expression system to produce and characterize several novel lantibiotics. We identified 54 novel putative class I and class II lantibiotics after inspecting all publicly available prokaryotic genomes using the in-house developed mining tool BAGEL3. The genes encoding these new lantibiotics fused to the nisin leader peptide gene sequence were synthesized, and the constructs were plugged into the nisin expression and modification system...
October 21, 2016: ACS Synthetic Biology
Kai Blin, Marnix H Medema, Daniyal Kazempour, Michael A Fischbach, Rainer Breitling, Eriko Takano, Tilmann Weber
Microbial secondary metabolites are a potent source of antibiotics and other pharmaceuticals. Genome mining of their biosynthetic gene clusters has become a key method to accelerate their identification and characterization. In 2011, we developed antiSMASH, a web-based analysis platform that automates this process. Here, we present the highly improved antiSMASH 2.0 release, available at For the new version, antiSMASH was entirely re-designed using a plug-and-play concept that allows easy integration of novel predictor or output modules...
July 2013: Nucleic Acids Research
Gabrielle N Thibodeaux, Wilfred A van der Donk
Phosphorylation is an abundant post-translational modification involved in a myriad of cell signaling pathways. Herein, we have engineered the class II lantipeptide synthetase ProcM to generate a variety of peptides containing O-phosphoserine (pSer) and O-phosphothreonine (pThr) residues, either in vitro or in vivo.
November 7, 2012: Chemical Communications: Chem Comm
Huan Wang, Wilfred A van der Donk
Lantipeptides are ribosomally synthesized and posttranslationally modified peptides containing lanthionine and/or labionin structures. In this study, a novel class III lantipeptide termed catenulipeptin was discovered from Catenulispora acidiphila DSM 44928, and its biosynthesis was reconstituted in vitro. The multifunctional enzyme AciKC catalyzes both dehydration and cyclization of its peptide substrate AciA and installs two labionin structures in catenulipeptin. AciKC shows promiscuity with respect to cosubstrate and accepts all four NTPs...
September 21, 2012: ACS Chemical Biology
Weixin Tang, Wilfred A van der Donk
Prochlorosins make up a class of secondary metabolites produced by strains of Prochlorococcus, single-cell, planktonic marine cyanobacteria. These polycyclic peptides contain lanthionine and methyllanthionine residues that result in thioether cross-links. In Prochlorococcus MIT9313, a single enzyme, ProcM, catalyzes the posttranslational modification of 29 linear peptide substrates to generate a library of highly diverse cyclic peptides. To investigate the catalytic promiscuity of ProcM, we chose four prochlorosins previously demonstrated to be produced by the organism for detailed structural characterization...
May 29, 2012: Biochemistry
Frank T Hofmann, Jack W Szostak, Florian P Seebeck
In this report we present a method to identify functional artificial lantipeptides. In vitro translation coupled with an enzyme-free protocol for posttranslational modification allows preparation of more than 10(11) different lanthionine containing peptides. This diversity can be searched for functional molecules using mRNA-lantipeptide display. We validated this approach by isolating binders toward Sortase A, a transamidase which is required for virulence of Staphylococcus aureus. The interaction of selected lantipeptides with Sortase A is highly dependent on the presence of a (2S,6R)-lanthionine in the peptide and an active conformation of the protein...
May 16, 2012: Journal of the American Chemical Society
Patrick J Knerr, Wilfred A van der Donk
Aided by genome-mining strategies, knowledge of the prevalence and diversity of ribosomally synthesized natural products (RNPs) is rapidly increasing. Among these are the lantipeptides, posttranslationally modified peptides containing characteristic thioether cross-links imperative for bioactivity and stability. Though this family was once thought to be a limited class of antimicrobial compounds produced by gram-positive bacteria, new insights have revealed a much larger diversity of activity, structure, biosynthetic machinery, and producing organisms than previously appreciated...
2012: Annual Review of Biochemistry
Roland D Kersten, Yu-Liang Yang, Yuquan Xu, Peter Cimermancic, Sang-Jip Nam, William Fenical, Michael A Fischbach, Bradley S Moore, Pieter C Dorrestein
Peptide natural products show broad biological properties and are commonly produced by orthogonal ribosomal and nonribosomal pathways in prokaryotes and eukaryotes. To harvest this large and diverse resource of bioactive molecules, we introduce here natural product peptidogenomics (NPP), a new MS-guided genome-mining method that connects the chemotypes of peptide natural products to their biosynthetic gene clusters by iteratively matching de novo tandem MS (MS(n)) structures to genomics-based structures following biosynthetic logic...
October 9, 2011: Nature Chemical Biology
Florian P Seebeck, Alonso Ricardo, Jack W Szostak
We have devised a protocol for enzyme-free insertion of dehydroalanine, dehydrobutyrine and thioether crosslinks into translated peptides. In vitro translation using 4-selenalysine and 4-selenoisoleucine as substitutes for lysine and isoleucine yields peptides that can be converted to polycyclic structures using mild chemistry in water. This methodology presents a gateway for exploring the potential of artificial lantipeptides as scaffolds for drug development.
June 7, 2011: Chemical Communications: Chem Comm
Yanxiang Shi, Xiao Yang, Neha Garg, Wilfred A van der Donk
Lantipeptides are ribosomally synthesized and posttranslationally modified peptides containing thioether cross-links. We describe the preparation of seven different lantipeptides in Escherichia coli and demonstrate that this methodology can be used to incorporate nonproteinogenic amino acids.
March 2, 2011: Journal of the American Chemical Society
Juan E Velásquez, Wilfred A van der Donk
In recent years, the number of known peptide natural products that are synthesized via the ribosomal pathway has rapidly grown. Taking advantage of sequence homology among genes encoding precursor peptides or biosynthetic proteins, in silico mining of genomes combined with molecular biology approaches has guided the discovery of a large number of new ribosomal natural products, including lantipeptides, cyanobactins, linear thiazole/oxazole-containing peptides, microviridins, lasso peptides, amatoxins, cyclotides, and conopeptides...
February 2011: Current Opinion in Chemical Biology
Bo Li, Daniel Sher, Libusha Kelly, Yanxiang Shi, Katherine Huang, Patrick J Knerr, Ike Joewono, Doug Rusch, Sallie W Chisholm, Wilfred A van der Donk
Our understanding of secondary metabolite production in bacteria has been shaped primarily by studies of attached varieties such as symbionts, pathogens, and soil bacteria. Here we show that a strain of the single-celled, planktonic marine cyanobacterium Prochlorococcus-which conducts a sizable fraction of photosynthesis in the oceans-produces many cyclic, lanthionine-containing peptides (lantipeptides). Remarkably, in Prochlorococcus MIT9313 a single promiscuous enzyme transforms up to 29 different linear ribosomally synthesized peptides into a library of polycyclic, conformationally constrained products with highly diverse ring topologies...
June 8, 2010: Proceedings of the National Academy of Sciences of the United States of America
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