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Kuznetsova AI, Ivanova EA, Samylina OS, Kurbanova FG, Gruzdev DS, Kanapatskiy TA, Pimenov NV. Prokaryotic Communities in Saline Soils of the Lake Elton Area in a Soil Catena along the Khara River. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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2
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Ortseifen V, Kalinowski J, Pühler A, Rückert C. The complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) carrying gene clusters for the biosynthesis of tetracenomycin C, 5`-hydroxy streptomycin, and acarbose. J Biotechnol 2017; 262:84-88. [PMID: 28917933 DOI: 10.1016/j.jbiotec.2017.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 11/30/2022]
Abstract
The secondary metabolite acarbose is used worldwide in the clinical treatment of diabetes mellitus type 2 patients. Acarbose is a - glucosidase inhibitor and supports patients to control their blood glucose as well as their serum insulin levels. The secondary metabolite is produced by strains of the class Actinobacteria, in particular from Actinoplanes sp. SE50/110, which is a progenitor of today`s production strains. Moreover, secondary metabolite clusters could also be identified in Streptomyces coelicoflavus ZG0656 as well as Streptomyces glaucescens GLA.O. In this study, the genome S. glaucescens GLA.O with focus on the acarbose biosynthesis cluster (gac-cluster) was analyzed. First, the tetracenomycin C and the 5`-hydroxy streptomycin gene clusters could be described completely. Then the gac gene region in S. glaucescens GLA.O is compared to the other known biosynthesis gene cluster. In comparison to Actinoplanes sp. SE50/110 the gac-cluster showed structural variances, like the missing homolog of the glycosyltransferase AcbD in the whole genome of S. glaucescens GLA.O. Due to the lack of the glycosyltransferase, it was of particular interest whether additional acarviose metabolites other than acarbose could be formed. For detection of acarviose metabolites biosynthesis the supernatant of S. glaucescens GLA.O grown in starch supplemented complex media was harvested at 72 and 96 hours. Although a homolog of the known glycosyltransferase is absent, the LC-MS-supported analysis revealed that a spectrum of acarviose metabolites was formed.
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Affiliation(s)
- Vera Ortseifen
- Senior Research Group Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; CLIB-Graduate Cluster Industrial Biotechnology, CLIB2021, Völklinger Strasse 4, 40219 Düsseldorf, Germany; Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany; Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Senior Research Group Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, Center for Biotechnology, Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany.
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Wolf T, Schneiker-Bekel S, Neshat A, Ortseifen V, Wibberg D, Zemke T, Pühler A, Kalinowski J. Genome improvement of the acarbose producer Actinoplanes sp. SE50/110 and annotation refinement based on RNA-seq analysis. J Biotechnol 2017; 251:112-123. [PMID: 28427920 DOI: 10.1016/j.jbiotec.2017.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/11/2017] [Accepted: 04/14/2017] [Indexed: 12/16/2022]
Abstract
Actinoplanes sp. SE50/110 is the natural producer of acarbose, which is used in the treatment of diabetes mellitus type II. However, until now the transcriptional organization and regulation of the acarbose biosynthesis are only understood rudimentarily. The genome sequence of Actinoplanes sp. SE50/110 was known before, but was resequenced in this study to remove assembly artifacts and incorrect base callings. The annotation of the genome was refined in a multi-step approach, including modern bioinformatic pipelines, transcriptome and proteome data. A whole transcriptome RNA-seq library as well as an RNA-seq library enriched for primary 5'-ends were used for the detection of transcription start sites, to correct tRNA predictions, to identify novel transcripts like small RNAs and to improve the annotation through the correction of falsely annotated translation start sites. The transcriptome data sets were also applied to identify 31 cis-regulatory RNA structures, such as riboswitches or RNA thermometers as well as three leaderless transcribed short peptides found in putative attenuators upstream of genes for amino acid biosynthesis. The transcriptional organization of the acarbose biosynthetic gene cluster was elucidated in detail and fourteen novel biosynthetic gene clusters were suggested. The accurate genome sequence and precise annotation of the Actinoplanes sp. SE50/110 genome will be the foundation for future genetic engineering and systems biology studies.
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Affiliation(s)
- Timo Wolf
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Susanne Schneiker-Bekel
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Armin Neshat
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Vera Ortseifen
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Till Zemke
- Product Supply, Bayer Pharma AG, Friedrich Ebert Str. 217-475, 42117 Wuppertal, Germany
| | - Alfred Pühler
- Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
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Lu C, Zhang X, Jiang M, Bai L. Enhanced salinomycin production by adjusting the supply of polyketide extender units in Streptomyces albus. Metab Eng 2016; 35:129-137. [PMID: 26969249 DOI: 10.1016/j.ymben.2016.02.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 01/28/2016] [Accepted: 02/23/2016] [Indexed: 11/19/2022]
Abstract
The anticoccidial salinomycin is a polyketide produced by Streptomyces albus and requires malonyl-CoAs, methylmalonyl-CoAs, and ethylmalonyl-CoAs for the backbone assembly. Genome sequencing of S. albus DSM 41398 revealed a high percentage of genes involved in lipid metabolism, supporting the high salinomycin yield in oil-rich media. Seven PKS/PKS-NRPS gene clusters in the genome were found to be actively transcribed and had been individually deleted, which resulted in significantly improved salinomycin production. However, a combined deletion of PKS-NRPS-2 and PKS-6 showed no further improvement. Whereas the concentrations of malonyl-CoA and methylmalonyl-CoA were increased, the concentration of ethylmalonyl-CoA remained low in the mutants. An endogenous crotonyl-CoA reductase gene (ccr) was overexpressed in the ΔPKS-NRPS-2/ΔPKS-6 mutant, resulting in improved production. Combination of cluster deletions and over-expression of ccr gene led to an overall titer improvement of salinomycin from 0.60 to 6.60g/L. This engineering strategy can be implemented for various natural polyketides production.
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Affiliation(s)
- Chenyang Lu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaojie Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.
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Belda-Ferre P, Williamson J, Simón-Soro Á, Artacho A, Jensen ON, Mira A. The human oral metaproteome reveals potential biomarkers for caries disease. Proteomics 2015; 15:3497-507. [PMID: 26272225 DOI: 10.1002/pmic.201400600] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 07/27/2015] [Accepted: 08/10/2015] [Indexed: 12/30/2022]
Abstract
Tooth decay is considered the most prevalent human disease worldwide. We present the first metaproteomic study of the oral biofilm, using different mass spectrometry approaches that have allowed us to quantify individual peptides in healthy and caries-bearing individuals. A total of 7771 bacterial and 853 human proteins were identified in 17 individuals, which provide the first available protein repertoire of human dental plaque. Actinomyces and Coryneybacterium represent a large proportion of the protein activity followed by Rothia and Streptococcus. Those four genera account for 60-90% of total diversity. Healthy individuals appeared to have significantly higher amounts of L-lactate dehydrogenase and the arginine deiminase system, both implicated in pH buffering. Other proteins found to be at significantly higher levels in healthy individuals were involved in exopolysaccharide synthesis, iron metabolism and immune response. We applied multivariate analysis in order to find the minimum set of proteins that better allows discrimination of healthy and caries-affected dental plaque samples, detecting seven bacterial and five human protein functions that allow determining the health status of the studied individuals with an estimated specificity and sensitivity over 96%. We propose that future validation of these potential biomarkers in larger sample size studies may serve to develop diagnostic tests of caries risk that could be used in tooth decay prevention.
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Affiliation(s)
- Pedro Belda-Ferre
- FISABIO Foundation, Center for Advanced Research in Public Health, Valencia, Spain
| | - James Williamson
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Áurea Simón-Soro
- FISABIO Foundation, Center for Advanced Research in Public Health, Valencia, Spain
| | - Alejandro Artacho
- FISABIO Foundation, Center for Advanced Research in Public Health, Valencia, Spain
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Alex Mira
- FISABIO Foundation, Center for Advanced Research in Public Health, Valencia, Spain
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Complete genome sequence of Streptomyces sp. CNQ-509, a prolific producer of meroterpenoid chemistry. J Biotechnol 2015; 216:140-1. [PMID: 26319318 DOI: 10.1016/j.jbiotec.2015.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 11/24/2022]
Abstract
Streptomyces sp. CNQ-509 is a marine actinomycete belonging to the MAR4 streptomycete lineage. MAR4 strains have been linked to the production of diverse and otherwise rare meroterpenoid compounds. The genome sequence of Streptomyces sp. CNQ-509 was found to contain 29 putative gene clusters for the biosynthesis of secondary metabolites, some of them potentially involved in the formation of meroterpenoid molecules.
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Wendler S, Otto A, Ortseifen V, Bonn F, Neshat A, Schneiker-Bekel S, Walter F, Wolf T, Zemke T, Wehmeier UF, Hecker M, Kalinowski J, Becher D, Pühler A. Comprehensive proteome analysis of Actinoplanes sp. SE50/110 highlighting the location of proteins encoded by the acarbose and the pyochelin biosynthesis gene cluster. J Proteomics 2015; 125:1-16. [DOI: 10.1016/j.jprot.2015.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/02/2015] [Accepted: 04/12/2015] [Indexed: 01/05/2023]
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8
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Vinardell JM, Acosta-Jurado S, Zehner S, Göttfert M, Becker A, Baena I, Blom J, Crespo-Rivas JC, Goesmann A, Jaenicke S, Krol E, McIntosh M, Margaret I, Pérez-Montaño F, Schneiker-Bekel S, Serranía J, Szczepanowski R, Buendía AM, Lloret J, Bonilla I, Pühler A, Ruiz-Sainz JE, Weidner S. The Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:811-24. [PMID: 25675256 DOI: 10.1094/mpmi-12-14-0397-fi] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Sinorhizobium fredii HH103 is a fast-growing rhizobial strain infecting a broad range of legumes including both American and Asiatic soybeans. In this work, we present the sequencing and annotation of the HH103 genome (7.25 Mb), consisting of one chromosome and six plasmids and representing the structurally most complex sinorhizobial genome sequenced so far. Comparative genomic analyses of S. fredii HH103 with strains USDA257 and NGR234 showed that the core genome of these three strains contains 4,212 genes (61.7% of the HH103 genes). Synteny plot analysis revealed that the much larger chromosome of USDA257 (6.48 Mb) is colinear to the HH103 (4.3 Mb) and NGR324 chromosomes (3.9 Mb). An additional region of the USDA257 chromosome of about 2 Mb displays similarity to plasmid pSfHH103e. Remarkable differences exist between HH103 and NGR234 concerning nod genes, flavonoid effect on surface polysaccharide production, and quorum-sensing systems. Furthermore a number of protein secretion systems have been found. Two genes coding for putative type III-secreted effectors not previously described in S. fredii, nopI and gunA, have been located on the HH103 genome. These differences could be important to understand the different symbiotic behavior of S. fredii strains HH103, USDA257, and NGR234 with soybean.
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Affiliation(s)
- José-María Vinardell
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Sebastián Acosta-Jurado
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Susanne Zehner
- 2 Technische Universität Dresden, Institut für Genetik, Helmholtzstrasse 10, 01062 Dresden, Germany
| | - Michael Göttfert
- 2 Technische Universität Dresden, Institut für Genetik, Helmholtzstrasse 10, 01062 Dresden, Germany
| | - Anke Becker
- 3 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Faculty of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Irene Baena
- 4 Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049-Madrid, Spain
| | - Jochem Blom
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Juan Carlos Crespo-Rivas
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Alexander Goesmann
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Elizaveta Krol
- 3 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Faculty of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Matthew McIntosh
- 3 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Faculty of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Isabel Margaret
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Francisco Pérez-Montaño
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Susanne Schneiker-Bekel
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Javier Serranía
- 3 LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Faculty of Biology, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35043 Marburg, Germany
| | - Rafael Szczepanowski
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - Ana-María Buendía
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Javier Lloret
- 4 Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049-Madrid, Spain
| | - Ildefonso Bonilla
- 4 Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049-Madrid, Spain
| | - Alfred Pühler
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
| | - José-Enrique Ruiz-Sainz
- 1 Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla. Avda. Reina Mercedes 6, C.P. 41012 Sevilla, Spain
| | - Stefan Weidner
- 5 Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitaetsstr. 27, 33615 Bielefeld, Germany
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Rückert C, Albersmeier A, Busche T, Jaenicke S, Winkler A, Friðjónsson ÓH, Hreggviðsson GÓ, Lambert C, Badcock D, Bernaerts K, Anne J, Economou A, Kalinowski J. Complete genome sequence of Streptomyces lividans TK24. J Biotechnol 2015; 199:21-2. [PMID: 25680930 DOI: 10.1016/j.jbiotec.2015.02.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
Abstract
Streptomyces lividans TK24 is the standard host for the heterologous expression of a number of different proteins and antibiotic-synthesizing enzymes. As such, it is often used as an experimental microbial cell factory for the production of secreted heterologous proteins including human cytokines and industrial enzymes, and of several antibiotics. It accepts methylated DNA and is an ideal Streptomyces cloning system. Here, we report the complete genome sequence of S. lividans TK24 that includes a plasmid-less genome of 8.345Mbp (72.24% G+C content).
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Affiliation(s)
- Christian Rückert
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Sebastian Jaenicke
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | | | | | | | - Daniel Badcock
- GlaxoSmithKline, 315 Cambridge Science Park, Cambridge CB4 0WG, UK
| | - Kristel Bernaerts
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Belgium
| | - Jozef Anne
- Laboratory of Molecular Bacteriology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium; Institute of Molecular Biology and Biotechnology-FoRTH and Department of Biology-University of Crete, Iraklio, Crete, Greece.
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany.
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Complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) consisting of a linear chromosome and one linear plasmid. J Biotechnol 2015; 194:81-3. [PMID: 25499805 DOI: 10.1016/j.jbiotec.2014.11.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 11/22/2022]
Abstract
Here we report the complete and finished genome sequence of Streptomyces glaucescens GLA.O (DSM 40922), a natural producer of the alpha-glucosidase inhibitor acarbose, which is used in the treatment of type-2 diabetes mellitus. The genome of S. glaucescens GLA.O consists of two replicons, the chromosome with a size of 7,453,200bp and a G+C content of 73.0% as well as a plasmid named pSglau1 with a size of 170,574bp and a G+C content of 69.06%.
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Carbon source dependent biosynthesis of acarviose metabolites in Actinoplanes sp. SE50/110. J Biotechnol 2014; 191:113-20. [DOI: 10.1016/j.jbiotec.2014.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 07/30/2014] [Accepted: 08/14/2014] [Indexed: 11/21/2022]
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Complete genome sequence of Corynebacterium casei LMG S-19264T (=DSM 44701T), isolated from a smear-ripened cheese. J Biotechnol 2014; 189:76-7. [PMID: 25193709 DOI: 10.1016/j.jbiotec.2014.08.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 08/25/2014] [Indexed: 11/21/2022]
Abstract
We report the complete genome sequence of Corynebacterium casei LMG S-19264(T) (=DSM 44701(T)) which was isolated from the surface of an Irish farmhouse smear-ripened cheese. The genome of C. casei LMG S-19264(T) consists of three replicons: the chromosome (3,113,488 bp, 55.69% G+C content), the plasmid pCASE1 (2461 bp, 56.77% G+C content) and the plasmid pCASE2 (16,264 bp, 55.08% G+C content), encoding a total of 2908 protein coding genes. Analysis of the sequence data revealed a large region of ∼ 98 kb with an average G+C content of ∼ 65% that was acquired by horizontal gene transfer.
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Stegmann E, Albersmeier A, Spohn M, Gert H, Weber T, Wohlleben W, Kalinowski J, Rückert C. Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17T (=DSM 44213T) producing (S,S)-N,N′-ethylenediaminedisuccinic acid. J Biotechnol 2014; 189:46-7. [DOI: 10.1016/j.jbiotec.2014.08.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
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14
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Rebets Y, Tokovenko B, Lushchyk I, Rückert C, Zaburannyi N, Bechthold A, Kalinowski J, Luzhetskyy A. Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae. BMC Genomics 2014; 15:885. [PMID: 25301375 PMCID: PMC4210621 DOI: 10.1186/1471-2164-15-885] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/03/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Kutzneria is a representative of a rarely observed genus of the family Pseudonocardiaceae. Kutzneria species were initially placed in the Streptosporangiaceae genus and later reconsidered to be an independent genus of the Pseudonocardiaceae. Kutzneria albida is one of the eight known members of the genus. This strain is a unique producer of the glycosylated polyole macrolide aculeximycin which is active against both bacteria and fungi. Kutzneria albida genome sequencing and analysis allow a deeper understanding of evolution of this genus of Pseudonocardiaceae, provide new insight in the phylogeny of the genus, as well as decipher the hidden secondary metabolic potential of these rare actinobacteria. RESULTS To explore the biosynthetic potential of Kutzneria albida to its full extent, the complete genome was sequenced. With a size of 9,874,926 bp, coding for 8,822 genes, it stands alongside other Pseudonocardiaceae with large circular genomes. Genome analysis revealed 46 gene clusters potentially encoding secondary metabolite biosynthesis pathways. Two large genomic islands were identified, containing regions most enriched with secondary metabolism gene clusters. Large parts of this secondary metabolism "clustome" are dedicated to siderophores production. CONCLUSIONS Kutzneria albida is the first species of the genus Kutzneria with a completely sequenced genome. Genome sequencing allowed identifying the gene cluster responsible for the biosynthesis of aculeximycin, one of the largest known oligosaccharide-macrolide antibiotics. Moreover, the genome revealed 45 additional putative secondary metabolite gene clusters, suggesting a huge biosynthetic potential, which makes Kutzneria albida a very rich source of natural products. Comparison of the Kutzneria albida genome to genomes of other actinobacteria clearly shows its close relations with Pseudonocardiaceae in line with the taxonomic position of the genus.
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Affiliation(s)
- Yuriy Rebets
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Bogdan Tokovenko
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Igor Lushchyk
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Christian Rückert
- />Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Nestor Zaburannyi
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
| | - Andreas Bechthold
- />Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Stefan-Meier-Strasse 19, 79104 Freiburg, Germany
| | - Jörn Kalinowski
- />Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andriy Luzhetskyy
- />Helmholtz-Institute for Pharmaceutical Research Saarland, Saarland University Campus, Building C2.3, 66123 Saarbrücken, Germany
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Al-Dilaimi A, Albersmeier A, Kalinowski J, Rückert C. Complete genome sequence of Corynebacterium vitaeruminis DSM 20294T, isolated from the cow rumen as a vitamin B producer. J Biotechnol 2014; 189:70-1. [PMID: 25193714 DOI: 10.1016/j.jbiotec.2014.08.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
We report the complete genome sequence of Corynebacterium vitaeruminis DSM 20294(T) which was identified as the producer of B vitamins in the rumen of cows. The genome of C. vitaeruminis DSM 20294(T) consists of a single replicon, the chromosome with a size of 2,931,780 bp and a G+C content of 65.53%. The genome encodes for 2,580 protein coding genes, among them those for a complete pathway to synthesize biotin.
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Affiliation(s)
- Arwa Al-Dilaimi
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany; Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, Germany.
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Rückert C, Szczepanowski R, Albersmeier A, Goesmann A, Fischer N, Steinkämper A, Pühler A, Biener R, Schwartz D, Kalinowski J. Complete genome sequence of the actinobacterium Actinoplanes friuliensis HAG 010964, producer of the lipopeptide antibiotic friulimycin. J Biotechnol 2014; 178:41-2. [PMID: 24637369 DOI: 10.1016/j.jbiotec.2014.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
Abstract
Actinoplanes friuliensis HAG 010964 (DSM 7358) was isolated from a soil sample from the Friuli region in Italy and characterized as a producer of the antibiotic friulimycin. The complete genome sequence includes genomic information of secondary metabolite biosynthesis and of its lifestyle. Genbank/EMBL/DDBJ Accession Nr: CP006272 (chromosome).
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Affiliation(s)
- Christian Rückert
- Technology Platform Genomics, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Rafael Szczepanowski
- Technology Platform Genomics, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics Resource Facility, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Nicole Fischer
- University of Applied Sciences Esslingen, Department of Natural Sciences, Kanalstrasse 33, 73728 Esslingen, Germany
| | - Anne Steinkämper
- University of Applied Sciences Esslingen, Department of Natural Sciences, Kanalstrasse 33, 73728 Esslingen, Germany
| | - Alfred Pühler
- Senior Research Group, Genome Research of Industrial Microorganisms, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Richard Biener
- University of Applied Sciences Esslingen, Department of Natural Sciences, Kanalstrasse 33, 73728 Esslingen, Germany
| | - Dirk Schwartz
- University of Applied Sciences Esslingen, Department of Natural Sciences, Kanalstrasse 33, 73728 Esslingen, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany.
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Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A. Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts. J Biotechnol 2014; 190:85-95. [PMID: 24642337 DOI: 10.1016/j.jbiotec.2014.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/25/2014] [Accepted: 03/01/2014] [Indexed: 11/16/2022]
Abstract
Actinoplanes sp. SE50/110 is the producer of the alpha-glucosidase inhibitor acarbose, which is an economically relevant and potent drug in the treatment of type-2 diabetes mellitus. In this study, we present the detection of transcription start sites on this genome by sequencing enriched 5'-ends of primary transcripts. Altogether, 1427 putative transcription start sites were initially identified. With help of the annotated genome sequence, 661 transcription start sites were found to belong to the leader region of protein-coding genes with the surprising result that roughly 20% of these genes rank among the class of leaderless transcripts. Next, conserved promoter motifs were identified for protein-coding genes with and without leader sequences. The mapped transcription start sites were finally used to improve the annotation of the Actinoplanes sp. SE50/110 genome sequence. Concerning protein-coding genes, 41 translation start sites were corrected and 9 novel protein-coding genes could be identified. In addition to this, 122 previously undetermined non-coding RNA (ncRNA) genes of Actinoplanes sp. SE50/110 were defined. Focusing on antisense transcription start sites located within coding genes or their leader sequences, it was discovered that 96 of those ncRNA genes belong to the class of antisense RNA (asRNA) genes. The remaining 26 ncRNA genes were found outside of known protein-coding genes. Four chosen examples of prominent ncRNA genes, namely the transfer messenger RNA gene ssrA, the ribonuclease P class A RNA gene rnpB, the cobalamin riboswitch RNA gene cobRS, and the selenocysteine-specific tRNA gene selC, are presented in more detail. This study demonstrates that sequencing of enriched 5'-ends of primary transcripts and the identification of transcription start sites are valuable tools for advanced genome annotation of Actinoplanes sp. SE50/110 and most probably also for other bacteria.
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Affiliation(s)
- Patrick Schwientek
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Armin Neshat
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Andreas Klein
- Bayer HealthCare AG, Friedrich-Ebert-Str. 475, 42117 Wuppertal, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Susanne Schneiker-Bekel
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Sergej Wendler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jens Stoye
- Genome Informatics Research Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
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18
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Duncan K, Haltli B, Gill KA, Kerr RG. Bioprospecting from marine sediments of New Brunswick, Canada: exploring the relationship between total bacterial diversity and actinobacteria diversity. Mar Drugs 2014; 12:899-925. [PMID: 24531187 PMCID: PMC3944522 DOI: 10.3390/md12020899] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/07/2014] [Accepted: 01/21/2014] [Indexed: 12/16/2022] Open
Abstract
Actinomycetes are an important resource for the discovery of natural products with therapeutic properties. Bioprospecting for actinomycetes typically proceeds without a priori knowledge of the bacterial diversity present in sampled habitats. In this study, we endeavored to determine if overall bacterial diversity in marine sediments, as determined by 16S rDNA amplicon pyrosequencing, could be correlated with culturable actinomycete diversity, and thus serve as a powerful tool in guiding future bioprospecting efforts. Overall bacterial diversity was investigated in eight marine sediments from four sites in New Brunswick, Canada, resulting in over 44,000 high quality sequences (x = 5610 per sample). Analysis revealed all sites exhibited significant diversity (H' = 5.4 to 6.7). Furthermore, statistical analysis of species level bacterial communities (D = 0.03) indicated community composition varied according to site and was strongly influenced by sediment physiochemical composition. In contrast, cultured actinomycetes (n = 466, 98.3% Streptomyces) were ubiquitously distributed among all sites and distribution was not influenced by sediment composition, suggesting that the biogeography of culturable actinomycetes does not correlate with overall bacterial diversity in the samples examined. These actinomycetes provide a resource for future secondary metabolite discovery, as exemplified by the antimicrobial activity observed from preliminary investigation.
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Affiliation(s)
- Katherine Duncan
- Department of Biomedical Sciences, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada.
| | - Bradley Haltli
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada.
| | - Krista A Gill
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada.
| | - Russell G Kerr
- Department of Biomedical Sciences, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada.
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Draft Genome Sequence of Streptomyces niveus NCIMB 11891, Producer of the Aminocoumarin Antibiotic Novobiocin. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01146-13. [PMID: 24407644 PMCID: PMC3886957 DOI: 10.1128/genomea.01146-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptomyces niveus NCIMB 11891 is the producer of the gyrase inhibitor novobiocin, which belongs to the aminocoumarin class of antibiotics. The genome sequence of this strain was found to contain, besides the gene cluster for novobiocin, a putative gene cluster for the macrolactam antibiotic BE-14106 and further secondary metabolite gene clusters.
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20
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Draft Genome Sequence of Streptomyces roseochromogenes subsp. oscitans DS 12.976, Producer of the Aminocoumarin Antibiotic Clorobiocin. GENOME ANNOUNCEMENTS 2014; 2:2/1/e01147-13. [PMID: 24407645 PMCID: PMC3886958 DOI: 10.1128/genomea.01147-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Streptomyces roseochromogenes subsp. oscitans DS 12.976 is the producer of the gyrase-inhibiting aminocoumarin antibiotic clorobiocin. Here, we present a draft genome sequence of this strain, in which we identified the clorobiocin gene cluster as well as an unusually high number (43) of further putative secondary metabolite clusters.
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21
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Rückert C, Szczepanowski R, Albersmeier A, Goesmann A, Iftime D, Musiol EM, Blin K, Wohlleben W, Pühler A, Kalinowski J, Weber T. Complete genome sequence of the kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids. J Biotechnol 2013; 168:739-40. [PMID: 24140291 DOI: 10.1016/j.jbiotec.2013.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/04/2013] [Indexed: 11/29/2022]
Abstract
Streptomyces collinus Tü 365 (DSMZ 40733), isolated from Kouroussa (Guinea), is the producer of the elfamycin family antibiotic kirromycin, which inhibits bacterial protein biosynthesis by interfering with elongation factor EF-Tu. Here, we report on the Streptomyces collinus Tü 365 complete genome sequence of the 8.27 MB chromosome and the two plasmids SCO1 and SCO2.
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Affiliation(s)
- Christian Rückert
- Technologieplattform Genomik, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 27, 33615 Bielefeld, Germany
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22
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The cytosolic and extracellular proteomes of Actinoplanes sp. SE50/110 led to the identification of gene products involved in acarbose metabolism. J Biotechnol 2013; 167:178-89. [DOI: 10.1016/j.jbiotec.2012.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 08/01/2012] [Accepted: 08/10/2012] [Indexed: 02/06/2023]
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23
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Comparative RNA-sequencing of the acarbose producer Actinoplanes sp. SE50/110 cultivated in different growth media. J Biotechnol 2013; 167:166-77. [DOI: 10.1016/j.jbiotec.2012.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 09/18/2012] [Accepted: 10/28/2012] [Indexed: 12/14/2022]
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Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, Hallam S, Konstantinidis K, Tyson G, Wincker P, Sullivan MB. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics 2013; 14:320. [PMID: 23663384 PMCID: PMC3655917 DOI: 10.1186/1471-2164-14-320] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/02/2013] [Indexed: 11/15/2022] Open
Abstract
Background Microbes drive the biogeochemistry that fuels the planet. Microbial viruses modulate their hosts directly through mortality and horizontal gene transfer, and indirectly by re-programming host metabolisms during infection. However, our ability to study these virus-host interactions is limited by methods that are low-throughput and heavily reliant upon the subset of organisms that are in culture. One way forward are culture-independent metagenomic approaches, but these novel methods are rarely rigorously tested, especially for studies of environmental viruses, air microbiomes, extreme environment microbiology and other areas with constrained sample amounts. Here we perform replicated experiments to evaluate Roche 454, Illumina HiSeq, and Ion Torrent PGM sequencing and library preparation protocols on virus metagenomes generated from as little as 10pg of DNA. Results Using %G + C content to compare metagenomes, we find that (i) metagenomes are highly replicable, (ii) some treatment effects are minimal, e.g., sequencing technology choice has 6-fold less impact than varying input DNA amount, and (iii) when restricted to a limited DNA concentration (<1μg), changing the amount of amplification produces little variation. These trends were also observed when examining the metagenomes for gene function and assembly performance, although the latter more closely aligned to sequencing effort and read length than preparation steps tested. Among Illumina library preparation options, transposon-based libraries diverged from all others and adaptor ligation was a critical step for optimizing sequencing yields. Conclusions These data guide researchers in generating systematic, comparative datasets to understand complex ecosystems, and suggest that neither varied amplification nor sequencing platforms will deter such efforts.
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Affiliation(s)
- Sergei A Solonenko
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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Solonenko SA, Sullivan MB. Preparation of metagenomic libraries from naturally occurring marine viruses. Methods Enzymol 2013; 531:143-65. [PMID: 24060120 DOI: 10.1016/b978-0-12-407863-5.00008-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microbes are now well recognized as major drivers of the biogeochemical cycling that fuels the Earth, and their viruses (phages) are known to be abundant and important in microbial mortality, horizontal gene transfer, and modulating microbial metabolic output. Investigation of environmental phages has been frustrated by an inability to culture the vast majority of naturally occurring diversity coupled with the lack of robust, quantitative, culture-independent methods for studying this uncultured majority. However, for double-stranded DNA phages, a quantitative viral metagenomic sample-to-sequence workflow now exists. Here, we review these advances with special emphasis on the technical details of preparing DNA sequencing libraries for metagenomic sequencing from environmentally relevant low-input DNA samples. Library preparation steps broadly involve manipulating the sample DNA by fragmentation, end repair and adaptor ligation, size fractionation, and amplification. One critical area of future research and development is parallel advances for alternate nucleic acid types such as single-stranded DNA and RNA viruses that are also abundant in nature. Combinations of recent advances in fragmentation (e.g., acoustic shearing and tagmentation), ligation reactions (adaptor-to-template ratio reference table availability), size fractionation (non-gel-sizing), and amplification (linear amplification for deep sequencing and linker amplification protocols) enhance our ability to generate quantitatively representative metagenomic datasets from low-input DNA samples. Such datasets are already providing new insights into the role of viruses in marine systems and will continue to do so as new environments are explored and synergies and paradigms emerge from large-scale comparative analyses.
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Affiliation(s)
- Sergei A Solonenko
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes. Nat Biotechnol 2012; 30:1225-31. [PMID: 23159880 DOI: 10.1038/nbt.2427] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 10/19/2012] [Indexed: 11/08/2022]
Abstract
Lysosomal storage diseases are treated with human lysosomal enzymes produced in mammalian cells. Such enzyme therapeutics contain relatively low levels of mannose-6-phosphate, which is required to target them to the lysosomes of patient cells. Here we describe a method for increasing mannose-6-phosphate modification of lysosomal enzymes produced in yeast. We identified a glycosidase from C. cellulans that 'uncaps' N-glycans modified by yeast-type mannose-Pi-6-mannose to generate mammalian-type N-glycans with a mannose-6-phosphate substitution. Determination of the crystal structure of this glycosidase provided insight into its substrate specificity. We used this uncapping enzyme together with α-mannosidase to produce in yeast a form of the Pompe disease enzyme α-glucosidase rich in mannose-6-phosphate. Compared with the currently used therapeutic version, this form of α-glucosidase was more efficiently taken up by fibroblasts from Pompe disease patients, and it more effectively reduced cardiac muscular glycogen storage in a mouse model of the disease.
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Draft genome sequence of Corynebacterium bovis DSM 20582, which causes clinical mastitis in dairy cows. J Bacteriol 2012; 194:4437. [PMID: 22843578 DOI: 10.1128/jb.00839-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine mastitis represents the most economically important disease in dairy cows and can be caused by Corynebacterium bovis, a commensal in the bovine udder. The draft genome sequence provides insights into the adaptation of this bacterium to the bovine habitat and its lipolytic capabilities to utilize components of cow's milk.
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Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. J Bacteriol 2012; 194:6818-27. [PMID: 23043000 DOI: 10.1128/jb.01592-12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Streptomyces davawensis JCM 4913 synthesizes the antibiotic roseoflavin, a structural riboflavin (vitamin B(2)) analog. Here, we report the 9,466,619-bp linear chromosome of S. davawensis JCM 4913 and a 89,331-bp linear plasmid. The sequence has an average G+C content of 70.58% and contains six rRNA operons (16S-23S-5S) and 69 tRNA genes. The 8,616 predicted protein-coding sequences include 32 clusters coding for secondary metabolites, several of which are unique to S. davawensis. The chromosome contains long terminal inverted repeats of 33,255 bp each and atypical telomeres. Sequence analysis with regard to riboflavin biosynthesis revealed three different patterns of gene organization in Streptomyces species. Heterologous expression of a set of genes present on a subgenomic fragment of S. davawensis resulted in the production of roseoflavin by the host Streptomyces coelicolor M1152. Phylogenetic analysis revealed that S. davawensis is a close relative of Streptomyces cinnabarinus, and much to our surprise, we found that the latter bacterium is a roseoflavin producer as well.
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Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A. The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. BMC Genomics 2012; 13:112. [PMID: 22443545 PMCID: PMC3364876 DOI: 10.1186/1471-2164-13-112] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 03/23/2012] [Indexed: 11/16/2022] Open
Abstract
Background Actinoplanes sp. SE50/110 is known as the wild type producer of the alpha-glucosidase inhibitor acarbose, a potent drug used worldwide in the treatment of type-2 diabetes mellitus. As the incidence of diabetes is rapidly rising worldwide, an ever increasing demand for diabetes drugs, such as acarbose, needs to be anticipated. Consequently, derived Actinoplanes strains with increased acarbose yields are being used in large scale industrial batch fermentation since 1990 and were continuously optimized by conventional mutagenesis and screening experiments. This strategy reached its limits and is generally superseded by modern genetic engineering approaches. As a prerequisite for targeted genetic modifications, the complete genome sequence of the organism has to be known. Results Here, we present the complete genome sequence of Actinoplanes sp. SE50/110 [GenBank:CP003170], the first publicly available genome of the genus Actinoplanes, comprising various producers of pharmaceutically and economically important secondary metabolites. The genome features a high mean G + C content of 71.32% and consists of one circular chromosome with a size of 9,239,851 bp hosting 8,270 predicted protein coding sequences. Phylogenetic analysis of the core genome revealed a rather distant relation to other sequenced species of the family Micromonosporaceae whereas Actinoplanes utahensis was found to be the closest species based on 16S rRNA gene sequence comparison. Besides the already published acarbose biosynthetic gene cluster sequence, several new non-ribosomal peptide synthetase-, polyketide synthase- and hybrid-clusters were identified on the Actinoplanes genome. Another key feature of the genome represents the discovery of a functional actinomycete integrative and conjugative element. Conclusions The complete genome sequence of Actinoplanes sp. SE50/110 marks an important step towards the rational genetic optimization of the acarbose production. In this regard, the identified actinomycete integrative and conjugative element could play a central role by providing the basis for the development of a genetic transformation system for Actinoplanes sp. SE50/110 and other Actinoplanes spp. Furthermore, the identified non-ribosomal peptide synthetase- and polyketide synthase-clusters potentially encode new antibiotics and/or other bioactive compounds, which might be of pharmacologic interest.
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Affiliation(s)
- Patrick Schwientek
- Senior research group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Germany
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