Reconsidering plasmid maintenance factors for computational plasmid design

Hirokazu Yano, Masaki Shintani, Masaru Tomita, Haruo Suzuki, Taku Oshima

Research output: Contribution to journalReview article

1 Citation (Scopus)

Abstract

Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.

Original languageEnglish
Pages (from-to)70-81
Number of pages12
JournalComputational and Structural Biotechnology Journal
Volume17
DOIs
Publication statusPublished - 2019 Jan 1

Fingerprint

Plasmids
Genes
Maintenance
Genome
Bioinformatics
Microorganisms
Bacteria
Cells
Genetic Selection
Computational Biology
Gram-Negative Bacteria
Parasites
Population

Keywords

  • Bioinformatics
  • Genome design
  • Host-parasite coevolution
  • Plasmid persistence
  • Synthetic biology
  • Vector design

ASJC Scopus subject areas

  • Biotechnology
  • Biophysics
  • Structural Biology
  • Biochemistry
  • Genetics
  • Computer Science Applications

Cite this

Reconsidering plasmid maintenance factors for computational plasmid design. / Yano, Hirokazu; Shintani, Masaki; Tomita, Masaru; Suzuki, Haruo; Oshima, Taku.

In: Computational and Structural Biotechnology Journal, Vol. 17, 01.01.2019, p. 70-81.

Research output: Contribution to journalReview article

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