Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli

Authors

  • Mitsuoki Kawano,

    Corresponding author
    1. Research and Education Center for Genetic Information, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.
    • *For correspondence. E-mail hmori@gtc.aist-nara.ac.jp; Tel. (+81) 743 72 5660; Fax (+81) 743 72 5669.

      Present address: Cell Biology and Metabolism Branch, National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-5430, USA.

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  • Taku Oshima,

    1. CREST, JST (Japan Science and Technology).
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  • Hiroaki Kasai,

    1. Marine Biotechnology Institute, Kamaishi Laboratories, Iwate 026-0001, Japan.
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  • Hirotada Mori

    Corresponding author
    1. Research and Education Center for Genetic Information, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.
    • *For correspondence. E-mail hmori@gtc.aist-nara.ac.jp; Tel. (+81) 743 72 5660; Fax (+81) 743 72 5669.

      Present address: Cell Biology and Metabolism Branch, National Institutes of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-5430, USA.

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Summary

Genome sequence analyses of Escherichia coli K-12 revealed four copies of long repetitive elements. These sequences are designated as long direct repeat (LDR) sequences. Three of the repeats (LDR-A, -B, -C), each approximately 500 bp in length, are located as tandem repeats at 27.4 min on the genetic map. Another copy (LDR-D), 450 bp in length and nearly identical to LDR-A, -B and -C, is located at 79.7 min, a position that is directly opposite the position of LDR-A, -B and -C. In this study, we demonstrate that LDR-D encodes a 35-amino-acid peptide, LdrD, the overexpression of which causes rapid cell killing and nucleoid condensation of the host cell. Northern blot and primer extension analysis showed constitutive transcription of a stable mRNA ( 370 nucleotides) encoding LdrD and an unstable cis-encoded antisense RNA ( 60 nucleotides), which functions as a trans-acting regulator of ldrD translation. We propose that LDR encodes a toxin–antitoxin module. LDR-homologous sequences are not present on any known plasmids but are conserved in Salmonella and other enterobacterial species.

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