Universität zu Köln

Unthan, Simon, Baumgart, Meike ORCID: 0000-0002-9874-1151, Radek, Andreas, Herbst, Marius, Siebert, Daniel, Bruehl, Natalie, Bartsch, Anna, Bott, Michael ORCID: 0000-0002-4701-8254, Wiechert, Wolfgang ORCID: 0000-0001-8501-0694, Marin, Kay, Hans, Stephan, Kraemer, Reinhard, Seibold, Gerd ORCID: 0000-0002-9823-8134, Frunzke, Julia ORCID: 0000-0001-6209-7950, Kalinowski, Joern, Rueckert, Christian, Wendisch, Volker F. ORCID: 0000-0003-3473-0012 and Noack, Stephan ORCID: 0000-0001-9784-3626 (2015). Chassis organism from Corynebacterium glutamicum - a top-down approach to identify and delete irrelevant gene clusters. Biotechnol. J., 10 (2). S. 290 - 302. WEINHEIM: WILEY-V C H VERLAG GMBH. ISSN 1860-7314

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Abstract

For synthetic biology applications, a robust structural basis is required, which can be constructed either from scratch or in a top-down approach starting from any existing organism. In this study, we initiated the top-down construction of a chassis organism from Corynebacterium glutamicum ATCC 13032, aiming for the relevant gene set to maintain its fast growth on defined medium. We evaluated each native gene for its essentiality considering expression levels, phylogenetic conservation, and knockout data. Based on this classification, we determined 41 gene clusters ranging from 3.7 to 49.7 kbp as target sites for deletion. 36 deletions were successful and 10 genome-reduced strains showed impaired growth rates, indicating that genes were hit, which are relevant to maintain biological fitness at wild-type level. In contrast, 26 deleted clusters were found to include exclusively irrelevant genes for growth on defined medium. A combinatory deletion of all irrelevant gene clusters would, in a prophage-free strain, decrease the size of the native genome by about 722 kbp (22%) to 2561 kbp. Finally, five combinatory deletions of irrelevant gene clusters were investigated. The study introduces the novel concept of relevant genes and demonstrates general strategies to construct a chassis suitable for biotechnological application.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Unthan, Simon UNSPECIFIED UNSPECIFIED UNSPECIFIED Baumgart, Meike UNSPECIFIED orcid.org/0000-0002-9874-1151 UNSPECIFIED Radek, Andreas UNSPECIFIED UNSPECIFIED UNSPECIFIED Herbst, Marius UNSPECIFIED UNSPECIFIED UNSPECIFIED Siebert, Daniel UNSPECIFIED UNSPECIFIED UNSPECIFIED Bruehl, Natalie UNSPECIFIED UNSPECIFIED UNSPECIFIED Bartsch, Anna UNSPECIFIED UNSPECIFIED UNSPECIFIED Bott, Michael UNSPECIFIED orcid.org/0000-0002-4701-8254 UNSPECIFIED Wiechert, Wolfgang UNSPECIFIED orcid.org/0000-0001-8501-0694 UNSPECIFIED Marin, Kay UNSPECIFIED UNSPECIFIED UNSPECIFIED Hans, Stephan UNSPECIFIED UNSPECIFIED UNSPECIFIED Kraemer, Reinhard UNSPECIFIED UNSPECIFIED UNSPECIFIED Seibold, Gerd UNSPECIFIED orcid.org/0000-0002-9823-8134 UNSPECIFIED Frunzke, Julia UNSPECIFIED orcid.org/0000-0001-6209-7950 UNSPECIFIED Kalinowski, Joern UNSPECIFIED UNSPECIFIED UNSPECIFIED Rueckert, Christian UNSPECIFIED UNSPECIFIED UNSPECIFIED Wendisch, Volker F. UNSPECIFIED orcid.org/0000-0003-3473-0012 UNSPECIFIED Noack, Stephan UNSPECIFIED orcid.org/0000-0001-9784-3626 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-413812
DOI:	10.1002/biot.201400041
Journal or Publication Title:	Biotechnol. J.
Volume:	10
Number:	2
Page Range:	S. 290 - 302
Date:	2015
Publisher:	WILEY-V C H VERLAG GMBH
Place of Publication:	WEINHEIM
ISSN:	1860-7314
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language COMPLETE GENOME SEQUENCE; MOLECULAR ANALYSIS; SYNTHETIC BIOLOGY; STRAIN; BACTERIUM; SYSTEMS; OVERPRODUCTION; CONSTRUCTION; LEADS; CELL Multiple languages Biochemical Research Methods; Biotechnology & Applied Microbiology Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/41381