Genome-scale metabolic representation of Amycolatopsis balhimycina
Journal article, 2012

Infection caused by methicillin-resistant Staphylococcus aureus (MRSA) is an increasing societal problem. Typically, glycopeptide antibiotics are used in the treatment of these infections. The most comprehensively studied glycopeptide antibiotic biosynthetic pathway is that of balhimycin biosynthesis in Amycolatopsis balhimycina. The balhimycin yield obtained by A. balhimycina is, however, low and there is therefore a need to improve balhimycin production. In this study, we performed genome sequencing, assembly and annotation analysis of A. balhimycina and further used these annotated data to reconstruct a genome-scale metabolic model for the organism. Here we generated an almost complete A. balhimycina genome sequence comprising 10,562,587 base pairs assembled into 2,153 contigs. The high GC-genome (similar to 69%) includes 8,585 open reading frames (ORFs). We used our integrative toolbox called SEQTOR for functional annotation and then integrated annotated data with biochemical and physiological information available for this organism to reconstruct a genome-scale metabolic model of A. balhimycina. The resulting metabolic model contains 583 ORFs as protein encoding genes (7% of the predicted 8,585 ORFs), 407 EC numbers, 647 metabolites and 1,363 metabolic reactions. During the analysis of the metabolic model, linear, quadratic and evolutionary programming algorithms using flux balance analysis (FBA), minimization of metabolic adjustment (MOMA), and OptGene, respectively were applied as well as phenotypic behavior and improved balhimycin production were simulated. The A. balhimycina model shows a good agreement between in silico data and experimental data and also identifies key reactions associated with increased balhimycin production. The reconstruction of the genome-scale metabolic model of A. balhimycina serves as a basis for physiological characterization. The model allows a rational design of engineering strategies for increasing balhimycin production in A. balhimycina and glycopeptide production in general.

glycopeptide

staphylococcus-aureus

secondary metabolites

families

metabolic reconstruction

antibiotics

amino-acid

genome annotation

protein

streptomyces-coelicolor a3(2)

Amycolatopsis balhimycina

mycobacterium-tuberculosis

sequence

biosynthesis

database

balhimycin

modeling

Author

Wanwipa Vongsangnak

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

L. F. Figueiredo

Technical University of Denmark (DTU)

Fluxome A/S

Friedrich Schiller University Jena

J. Forster

Fluxome A/S

T. Weber

University of Tübingen

J. Thykaer

Technical University of Denmark (DTU)

E. Stegmann

University of Tübingen

W. Wohlleben

University of Tübingen

Jens B Nielsen

Chalmers, Chemical and Biological Engineering, Life Sciences, System Biology

Biotechnology and Bioengineering

0006-3592 (ISSN) 1097-0290 (eISSN)

Vol. 109 7 1798-1807

Subject Categories

Industrial Biotechnology

Areas of Advance

Life Science Engineering (2010-2018)

DOI

10.1002/bit.24436

More information

Latest update

3/29/2018