Operon structure optimization by random self-assembly

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 transfered 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
Title of host publicationDNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers
Pages33-40
Number of pages8
DOIs
Publication statusPublished - 2009 Nov 27
Event14th International Meeting on DNA Computing, DNA14 - Prague, Czech Republic
Duration: 2008 Jun 22008 Jun 9

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5347 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other14th International Meeting on DNA Computing, DNA14
CountryCzech Republic
CityPrague
Period08/6/208/6/9

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H., & Sakakibara, Y. (2009). Operon structure optimization by random self-assembly. In DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers (pp. 33-40). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5347 LNCS). https://doi.org/10.1007/978-3-642-03076-5_4