Operon structure optimization by random self-assembly

Yusuke Nakagawa, Katsuyuki Yugi, Kenji Tsuge, Mitsuhiro Itaya, Hiroshi Yanagawa, Yasubumi Sakakibara

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Synthetic biology is an emerging research area that aims to investigate natural biological phenomena and reconstruct complex artificial biological systems. Recent development of genetic engineering such as multiple gene assembly method accelerates the synthetic biology study. Ordered gene assembly in Bacillus subtilis (OGAB method) is to assemble multiple genes in one step using an intrinsic B. subtilis plasmid transformation system and enables to reconstitute sets of relevant genes. The OGAB method assembles multiple DNA fragments with a fixed order and orientation and constructs an operon structure in a resultant plasmid. However, the optimal order and orientation to reconstitute a set of genes are generally not trivial and depends on several factors in host bacteria, where the "optimal" means the efficiency of biosynthesis induced by transferred genes in a metabolic pathway. We propose a method to apply self-assembly technique to optimization problem of operon structure. Self-assembly of multiple genes generates all possible orders of genes on operon structure. The number of generated orders on operon structure becomes the factorial of the number of multiple genes. All generated orders of multiple genes are then introduced into E. coli cells and most prominent colony for biosynthesis is extracted. We show some preliminary experiment to construct more efficient orders for five genes in the carotenoid biosynthetic pathway, and found a new order that is more efficient than previous studies for gene order.

Original languageEnglish
Pages (from-to)173-181
Number of pages9
JournalNatural Computing
Volume9
Issue number1
DOIs
Publication statusPublished - 2010

Fingerprint

Self assembly
Genes
Biosynthesis
Genetic engineering
Bacilli
Biological systems
Escherichia coli
Bacteria
DNA

Keywords

  • Biosynthetic pathway
  • Carotenoid
  • Operon structure
  • Ordered gene assembly
  • Self-assembly
  • Synthetic biology

ASJC Scopus subject areas

  • Computer Science Applications

Cite this

Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H., & Sakakibara, Y. (2010). Operon structure optimization by random self-assembly. Natural Computing, 9(1), 173-181. https://doi.org/10.1007/s11047-009-9141-0

Operon structure optimization by random self-assembly. / Nakagawa, Yusuke; Yugi, Katsuyuki; Tsuge, Kenji; Itaya, Mitsuhiro; Yanagawa, Hiroshi; Sakakibara, Yasubumi.

In: Natural Computing, Vol. 9, No. 1, 2010, p. 173-181.

Research output: Contribution to journalArticle

Nakagawa, Y, Yugi, K, Tsuge, K, Itaya, M, Yanagawa, H & Sakakibara, Y 2010, 'Operon structure optimization by random self-assembly', Natural Computing, vol. 9, no. 1, pp. 173-181. https://doi.org/10.1007/s11047-009-9141-0
Nakagawa, Yusuke ; Yugi, Katsuyuki ; Tsuge, Kenji ; Itaya, Mitsuhiro ; Yanagawa, Hiroshi ; Sakakibara, Yasubumi. / Operon structure optimization by random self-assembly. In: Natural Computing. 2010 ; Vol. 9, No. 1. pp. 173-181.
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