Retrons

Kunitoshi Yamanaka; Sumiko Inouye; Masayori Inoye; Tadashi Shimamoto

doi:10.1128/9781555817954.ch32

Chapter 32 : Retrons

Authors: Kunitoshi Yamanaka¹, Sumiko Inouye¹, Masayori Inoye¹, Tadashi Shimamoto²

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Affiliations: 1: Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 675 Hoes Ln., Piscataway, NJ 08854; 2: Faculty of Applied Biological Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Japan

Content Type: Monograph

Publication Year: 2002

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817954

Chapter DOI: 10.1128/9781555817954.ch32

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Abstract:

This chapter describes the genetic element called "retron," which is responsible for multicopy single-stranded DNA (msDNA) synthesis, and the mechanism of msDNA synthesis. It discusses the retron mobility and the relationship between retrons and pathogenicity. Retrons responsible for the synthesis of msDNA consist of three essential genes: msr for the RNA-coding region, msd for the DNA-coding region, and ret for reverse transcriptase (RT). A study of the codon usage for RTs revealed an interesting difference between retrons of Myxococcus xanthus and E. coli. The codon usage for RTs of M. xanthus is very typical for this species, further supporting the notion that retrons in myxobacteria are genetic elements that already existed in the genome of an ancestral bacterium before individual myxobacterial species evolved. In contrast, the codon usage for RTs of E. coli is significantly different from the general codon usage of E. coli. Emerging infectious diseases (EID) are a major public health issue of this millennium. It has been suggested that more virulent bacterial pathogens could emerge through recent acquisition of virulence factors. Retrons may be associated with bacterial pathogenicity, because all pathogenic Vibrio cholerae strains produce msDNA, whereas all nonpathogenic strains do not. Identification of the retron insertion site, biochemical and pathological characterization of retrons, effects of mutations in the retron on its pathogenicity, and characterization of open reading frames (ORFs) downstream of RT are expected to provide important insights into the function of retrons, their origins, and the pathogenicity of the persistent human disease.

Citation: Yamanaka K, Inouye S, Inoye M, Shimamoto T. 2002. Retrons, p 784-795. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch32

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Retrons

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Figure 1

Biosynthesis of msDNA. (A) Arrangement of msr, msd, and ret genes in a retron. Inverted repeats, a1/a2 and b1/ b2, are indicated by arrows. The G residue, which is used for priming cDNA synthesis, is circled. (B) The biosynthetic pathway of msDNA. The msr-msd region and ret can be expressed under separate promoters. The transcript from the msr-msd region is folded by forming stem structures between a1 and a2 inverted repeats as shown. The branching G residue is circled. The G residue opposite the branching G residue and an A:Upair immediately upstream of the G/G are highly conserved. The dotted line indicates the direction of cDNA synthesis from the branching G residue. Thick lines in the mRNA transcript correspond to the RNA molecule (msdRNA) in the msDNA. Gray lines in the msDNA correspond to the DNA molecule.

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Figure 1

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Figure 2

Structures of msDNAs from E. coli retrons: msDNA Ec48 from Mao et al. ( 36 ), msDNA Ec67 from Lampson et al. ( 25 ), msDNA Ec73 from Sun et al. ( 53 ), msDNA Ec78 from Lima and Lim ( 31 ), msDNA Ec83 from Lim ( 29 ), msDNA Ec86 from Lim and Maas ( 30 ), and msDNA Ec107 from Herzer et al. ( 7 ).

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Figure 2

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Figure 3

Alignment of all known E. coli RTs. Alignments were performed by visual examination of the sequences and adopted with some modifications from the previous report ( 19 ). Identical residues are shaded in black and functionally similar residues are shaded in gray. Residues shaded in black are biased toward Ec73, if other residues are also identical in the same row. Structural assignments for α and β structures are from the X-ray structure of HIV-RT ( 21 , 23 ). X and Y sequences are found in retron RTs and other non-LTR-RTs ( 19 ). The highly conserved VTGL sequence is marked by closed circles on the top, where the domain exchanges were performed between RT Ec73 and RT Ec86, as described in the text. The residues marked with stars are three Asp residues only known to be invariant among all known RTs and involved to form the catalytic triad essential for DNA polymerase activity ( 51 ).

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Figure 3

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Figure 4

Models for a retron RT forming a complex with a substrate. (A) A substrate-HIV-RT complex. The structure is cited from the report by Kohlstaedt et al. ( 23 ). However, P51 and the connection and RNase H domain of P66, which do not exist in the structure of retron RT, are shown by a dotted line. X and VTGL represent two unique domain existing only in retron RTs, and arrows indicate possible insertion sites of these domains. (B) The primer-template RNA molecule for msDNA is superimposed on A. (C) The recognition stem-loop structure interacts with the external part of the thumb as discussed in the text. In panels B and C, the recognition stem-loop structure is indicated by an arrow. The branching G residue is circled.

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Figure 4

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