TY - JOUR
T1 - Reconsidering plasmid maintenance factors for computational plasmid design
AU - Yano, Hirokazu
AU - Shintani, Masaki
AU - Tomita, Masaru
AU - Suzuki, Haruo
AU - Oshima, Taku
N1 - Funding Information:
We thank members of the Institute for Advanced Biosciences at Keio University for useful discussions. We also thank three anonymous reviewers for suggestions for improving this review. This work was supported in part by research funding from Keio University , Yamagata Prefecture, and Tsuruoka City to H.S. and M.T. and by Japan Society for the Promotion of Science (JSPS) KAKENHI (grant numbers 26106001 and 26450090 to T.O., 15H05618 to M.S., and 18K06357 to H.Y.). Computational resources were provided by the Data Integration and Analysis Facility, National Institute for Basic Biology. We would like to thank Editage ( www.editage.jp ) for English language editing.
Publisher Copyright:
© 2018 The Authors
PY - 2019/1/1
Y1 - 2019/1/1
N2 - 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.
AB - 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.
KW - Bioinformatics
KW - Genome design
KW - Host-parasite coevolution
KW - Plasmid persistence
KW - Synthetic biology
KW - Vector design
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U2 - 10.1016/j.csbj.2018.12.001
DO - 10.1016/j.csbj.2018.12.001
M3 - Review article
AN - SCOPUS:85059190743
SN - 2001-0370
VL - 17
SP - 70
EP - 81
JO - Computational and Structural Biotechnology Journal
JF - Computational and Structural Biotechnology Journal
ER -