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Blifernez-Klassen O, Klassen V, Wibberg D, Cebeci E, Henke C, Rückert C, Chaudhari S, Rupp O, Blom J, Winkler A, Al-Dilaimi A, Goesmann A, Sczyrba A, Kalinowski J, Bräutigam A, Kruse O. Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia. Sci Rep 2021; 11:1726. [PMID: 33462312 PMCID: PMC7813871 DOI: 10.1038/s41598-021-81082-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023] Open
Abstract
Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.
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Affiliation(s)
- Olga Blifernez-Klassen
- grid.7491.b0000 0001 0944 9128Algae Biotechnology and Bioenergy, Faculty of Biology, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany ,grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Viktor Klassen
- grid.7491.b0000 0001 0944 9128Algae Biotechnology and Bioenergy, Faculty of Biology, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany ,grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Daniel Wibberg
- grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Enis Cebeci
- grid.7491.b0000 0001 0944 9128Algae Biotechnology and Bioenergy, Faculty of Biology, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Christian Henke
- grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany ,grid.7491.b0000 0001 0944 9128Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Christian Rückert
- grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Swapnil Chaudhari
- grid.7491.b0000 0001 0944 9128Algae Biotechnology and Bioenergy, Faculty of Biology, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany ,grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Oliver Rupp
- grid.8664.c0000 0001 2165 8627Bioinformatics and Systems Biology, Justus-Liebig-University, Heinrich-Buff-Ring 58, 35392 Gießen, Germany
| | - Jochen Blom
- grid.8664.c0000 0001 2165 8627Bioinformatics and Systems Biology, Justus-Liebig-University, Heinrich-Buff-Ring 58, 35392 Gießen, Germany
| | - Anika Winkler
- grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Arwa Al-Dilaimi
- grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Alexander Goesmann
- grid.8664.c0000 0001 2165 8627Bioinformatics and Systems Biology, Justus-Liebig-University, Heinrich-Buff-Ring 58, 35392 Gießen, Germany
| | - Alexander Sczyrba
- grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany ,grid.7491.b0000 0001 0944 9128Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andrea Bräutigam
- grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany ,grid.7491.b0000 0001 0944 9128Computational Biology, Faculty of Biology, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Olaf Kruse
- grid.7491.b0000 0001 0944 9128Algae Biotechnology and Bioenergy, Faculty of Biology, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany ,grid.7491.b0000 0001 0944 9128Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
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Abstract
The German Network for Bioinformatics Infrastructure (de.NBI) is a national initiative funded by the German Federal Ministry of Education and Research (BMBF). The mission of de.NBI is (i) to provide high-quality bioinformatics services to users in basic and applied life sciences research from academia, industry and biomedicine; (ii) to offer bioinformatics training to users in Germany and Europe through a wide range of workshops and courses; and (iii) to foster the cooperation of the German bioinformatics community with international network structures such as the European life-sciences Infrastructure for biological Information (ELIXIR). The network was launched by the BMBF in March 2015 and now includes 40 service projects operated by 30 project partners that are organized in eight service centers. The de.NBI staff develops further and maintains almost 100 bioinformatics services for the human, plant and microbial research fields and provides comprehensive training courses to support users with different expertise levels in bioinformatics. In the future, de.NBI will expand its activities to the European level, as the de.NBI consortium was assigned by the BMBF to establish and run the German node of ELIXIR.
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Affiliation(s)
- Andreas Tauch
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße, Bielefeld, Germany
| | - Arwa Al-Dilaimi
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße, Bielefeld, Germany
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Farr M, Ferreira S, Al-Dilaimi A, Bögeholz S, Goesmann A, Kalinowski J, Knabbe C, Faber L, Oliveira JP, Rudolph V. Fabry disease: Detection of Alu-mediated exon duplication by NGS. Mol Cell Probes 2019; 45:79-83. [PMID: 30936019 DOI: 10.1016/j.mcp.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 11/25/2022]
Abstract
Monogenetic diseases can be analyzed routinely by targeted DNA sequencing. If causative variants are not found, complementary methods like RNA sequencing or analysis of copy number variations by multiplex ligation-dependent probe amplification have to be considered. In the latter, especially exonic duplications or deletions can be detected, but the precise sites of mutations remain unclear. As we demonstrate in this casuistic report of Fabry disease, next-generation sequencing (NGS) of a long-range PCR product can identify the recombination site directly and illuminate the underlying molecular mechanism.
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Affiliation(s)
- Martin Farr
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany.
| | - Susana Ferreira
- Unidade de Genética, Departamento de Patologia, Faculdade de Medicina, Universidade do Porto, Alameda Hernâni Monteiro, 4200-319, Porto, Portugal; i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Arwa Al-Dilaimi
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Sonja Bögeholz
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Cornelius Knabbe
- Institute for Laboratory and Transfusion Medicine, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - Lothar Faber
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
| | - João Paulo Oliveira
- Unidade de Genética, Departamento de Patologia, Faculdade de Medicina, Universidade do Porto, Alameda Hernâni Monteiro, 4200-319, Porto, Portugal; i3S -Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal; Serviço de Genética Médica, Centro Hospitalar Universitário de São João, Alameda Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Volker Rudolph
- Clinic for General and Interventional Cardiology/Angiology, Herz- und Diabeteszentrum NRW, Ruhr-Universität Bochum, Bad Oeynhausen, Germany
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Baulig A, Helmle I, Bader M, Wolf F, Kulik A, Al-Dilaimi A, Wibberg D, Kalinowski J, Gross H, Kaysser L. Biosynthetic reconstitution of deoxysugar phosphoramidate metalloprotease inhibitors using an N-P-bond-forming kinase. Chem Sci 2019; 10:4486-4490. [PMID: 31057776 PMCID: PMC6482885 DOI: 10.1039/c9sc00641a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/11/2019] [Indexed: 12/24/2022] Open
Abstract
Phosphoramidon is a potent metalloprotease inhibitor and a widespread tool in cell biology research. It contains a dipeptide backbone that is uniquely linked to a 6-deoxysugar via a phosphoramidate bridge. Herein, we report the identification of a gene cluster for the formation of phosphoramidon and its detailed characterization. In vitro reconstitution of the biosynthesis established TalE as a phosphoramidate-forming kinase and TalC as the glycosyltransferase which installs the l-rhamnose moiety by phosphoester linkage.
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Affiliation(s)
- Alexandra Baulig
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Irina Helmle
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany .
| | - Marius Bader
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Felix Wolf
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Andreas Kulik
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT) , Microbiology/Biotechnology , University of Tübingen , 72076 Tübingen , Germany
| | - Arwa Al-Dilaimi
- Center for Biotechnology (CeBiTec) , Bielefeld University , 33615 Bielefeld , Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec) , Bielefeld University , 33615 Bielefeld , Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec) , Bielefeld University , 33615 Bielefeld , Germany
| | - Harald Gross
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
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Al-Dilaimi A, Bednarz H, Lömker A, Niehaus K, Kalinowski J, Rückert C. Revisiting Corynebacterium glyciniphilum (ex Kubota et al., 1972) sp. nov., nom. rev., isolated from putrefied banana. Int J Syst Evol Microbiol 2014; 65:177-182. [PMID: 25323597 DOI: 10.1099/ijs.0.065102-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain of a species of the genus Corynebacterium, designated AJ 3170(T), was isolated during the 1980s from putrefied bananas. Since then, there have been no further updates on the description of the strain or its phylogenetic classification. However, phylogenetic analysis of this strain using 16S rRNA and in silico DNA-DNA hybridization has confirmed that it is a member of the genus Corynebacterium and that strain AJ 3170(T) clusters with Corynebacterium variabile DSM 44702(T), Corynebacterium terpenotabidum Y-11(T) and Corynebacterium nuruki S6-4(T) in one subgroup. Furthermore, a combination of enzymatic, chemical, and morphological characterization techniques was applied in order to describe strain AJ 3170(T) further. The strain grew well at pH values of 6-10 and at temperatures of 30-41 °C. The major fatty acids were C16 : 0 (42.15 %), C18 : 1ω9c (41.6 %) and C18 : 0 10-methyl (TBSA) (8.56 %). The whole-cell sugars were determined to comprise galactose, arabinose and ribose. On the basis of this phenotypic, chemotaxonomic and phylogenetic characterization, it is proposed that strain AJ 3170(T) represents a novel species, for which the name Corynebacterium glyciniphilum sp. nov. is proposed; the type strain is AJ 3170(T) ( = DSM 45795(T) = ATCC 21341(T)).
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Affiliation(s)
- Arwa Al-Dilaimi
- Microbial Genomics and Biotechnology, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, D-33615 Bielefeld, Germany
| | - Alexander Lömker
- Microbial Genomics and Biotechnology, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, D-33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany.,Microbial Genomics and Biotechnology, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany
| | - Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, D-33615 Bielefeld, Germany.,Microbial Genomics and Biotechnology, CeBiTec, Bielefeld University, D-33615 Bielefeld, 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] [What about the content of this article? (0)] [Affiliation(s)] [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, Albersmeier A, Al-Dilaimi A, Bednarz H, Niehaus K, Szczepanowski R, Kalinowski J. Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11(T) (= DSM 44721(T)). Stand Genomic Sci 2014; 9:505-13. [PMID: 25197436 PMCID: PMC4149027 DOI: 10.4056/sigs.4588337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Corynebacterium terpenotabidum Takeuchi et. al 1999 is a member of the genus Corynebacterium, which contains Gram-positive and non-spore forming bacteria with a high G+C content. C. terpenotabidum was isolated from soil based on its ability to degrade squalene and belongs to the aerobic and non-hemolytic Corynebacteria. It displays tolerance to salts (up to 8%) and is related to Corynebacterium variabile involved in cheese ripening. As this is a type strain of Corynebacterium, this project describing the 2.75 Mbp long chromosome with its 2,369 protein-coding and 72 RNA genes will aid the G enomic E ncyclopedia of Bacteria and Archaea project.
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Affiliation(s)
- Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Andreas Albersmeier
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Arwa Al-Dilaimi
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Hanna Bednarz
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany
| | | | - Jörn Kalinowski
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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Bogen C, Al-Dilaimi A, Albersmeier A, Wichmann J, Grundmann M, Rupp O, Lauersen KJ, Blifernez-Klassen O, Kalinowski J, Goesmann A, Mussgnug JH, Kruse O. Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production. BMC Genomics 2013; 14:926. [PMID: 24373495 PMCID: PMC3890519 DOI: 10.1186/1471-2164-14-926] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 12/19/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Microalgae are gaining importance as sustainable production hosts in the fields of biotechnology and bioenergy. A robust biomass accumulating strain of the genus Monoraphidium (SAG 48.87) was investigated in this work as a potential feedstock for biofuel production. The genome was sequenced, annotated, and key enzymes for triacylglycerol formation were elucidated. RESULTS Monoraphidium neglectum was identified as an oleaginous species with favourable growth characteristics as well as a high potential for crude oil production, based on neutral lipid contents of approximately 21% (dry weight) under nitrogen starvation, composed of predominantly C18:1 and C16:0 fatty acids. Further characterization revealed growth in a relatively wide pH range and salt concentrations of up to 1.0% NaCl, in which the cells exhibited larger structures. This first full genome sequencing of a member of the Selenastraceae revealed a diploid, approximately 68 Mbp genome with a G + C content of 64.7%. The circular chloroplast genome was assembled to a 135,362 bp single contig, containing 67 protein-coding genes. The assembly of the mitochondrial genome resulted in two contigs with an approximate total size of 94 kb, the largest known mitochondrial genome within algae. 16,761 protein-coding genes were assigned to the nuclear genome. Comparison of gene sets with respect to functional categories revealed a higher gene number assigned to the category "carbohydrate metabolic process" and in "fatty acid biosynthetic process" in M. neglectum when compared to Chlamydomonas reinhardtii and Nannochloropsis gaditana, indicating a higher metabolic diversity for applications in carbohydrate conversions of biotechnological relevance. CONCLUSIONS The genome of M. neglectum, as well as the metabolic reconstruction of crucial lipid pathways, provides new insights into the diversity of the lipid metabolism in microalgae. The results of this work provide a platform to encourage the development of this strain for biotechnological applications and production concepts.
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Affiliation(s)
- Christian Bogen
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Arwa Al-Dilaimi
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Andreas Albersmeier
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Julian Wichmann
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Michael Grundmann
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Oliver Rupp
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Kyle J Lauersen
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Olga Blifernez-Klassen
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | | | - Alexander Goesmann
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Jan H Mussgnug
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
| | - Olaf Kruse
- Department of Biology/Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, Bielefeld 33615, Germany
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Rückert C, Albersmeier A, Al-Dilaimi A, Niehaus K, Szczepanowski R, Kalinowski J. Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093(T) (= DSM 44683(T)). Stand Genomic Sci 2012; 7:284-93. [PMID: 23408721 PMCID: PMC3569386 DOI: 10.4056/sigs.3236691] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corynebacterium halotolerans Chen et al. 2004 is a member of the genus Corynebacterium which contains Gram-positive bacteria with a high G+C content. C. halotolerans, isolated from a saline soil, belongs to the non-lipophilic, non-pathogenic corynebacteria. It displays a high tolerance to salts (up to 25%) and is related to the pathogenic corynebacteria C. freneyi and C. xerosis. As this is a type strain in a subgroup of Corynebacterium without complete genome sequences, this project describing the 3.14 Mbp long chromosome and the 86.2 kbp plasmid pCha1 with their 2,865 protein-coding and 65 RNA genes will aid the Genomic Encyclopedia ofBacteria andArchaea project.
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Affiliation(s)
- Christian Rückert
- Technology Platform Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany
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Strobel T, Al-Dilaimi A, Blom J, Gessner A, Kalinowski J, Luzhetska M, Pühler A, Szczepanowski R, Bechthold A, Rückert C. Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae. BMC Genomics 2012; 13:465. [PMID: 22958348 PMCID: PMC3469384 DOI: 10.1186/1471-2164-13-465] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/30/2012] [Indexed: 12/04/2022] Open
Abstract
Background The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast. Results To better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified. Conclusion S. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain’s potential for natural product synthesis.
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Affiliation(s)
- Tina Strobel
- Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Freiburg 79104, Germany
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Pérez Chaparro PJ, McCulloch JA, Cerdeira LT, Al-Dilaimi A, Canto de Sá LL, de Oliveira R, Tauch A, de Carvalho Azevedo VA, Cruz Schneider MP, da Silva ALDC. Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads. J Microbiol Methods 2011; 87:208-12. [PMID: 21871929 DOI: 10.1016/j.mimet.2011.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 08/04/2011] [Accepted: 08/08/2011] [Indexed: 10/17/2022]
Abstract
Multiple Displacement Amplification (MDA) of DNA using φ29 (phi29) DNA polymerase amplifies DNA several billion-fold, which has proved to be potentially very useful for evaluating genome information in a culture-independent manner. Whole genome sequencing using DNA from a single prokaryotic genome copy amplified by MDA has not yet been achieved due to the formation of chimeras and skewed amplification of genomic regions during the MDA step, which then precludes genome assembly. We have hereby addressed the issue by using 10 ng of genomic Vibrio cholerae DNA extracted within an agarose plug to ensure circularity as a starting point for MDA and then sequencing the amplified yield using the SOLiD platform. We successfully managed to assemble the entire genome of V. cholerae strain LMA3984-4 (environmental O1 strain isolated in urban Amazonia) using a hybrid de novo assembly strategy. Using our method, only 178 out of 16,713 (1%) of contigs were not able to be inserted into either chromosome scaffold, and out of these 178, only 3 appeared to be chimeras. The other contigs seem to be the result of template-independent non-specific amplification during MDA, yielding spurious reads. Extraction of genomic DNA within an agarose plug in order to ensure circularity of the extracted genome might be key to minimizing amplification bias by MDA for WGS.
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Affiliation(s)
- Paula Juliana Pérez Chaparro
- Laboratório de Polimorfismo do DNA, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
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