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Chapter 32 : Retrons

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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: for the RNA-coding region, for the DNA-coding region, and for reverse transcriptase (RT). A study of the codon usage for RTs revealed an interesting difference between retrons of and . The codon usage for RTs of 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 is significantly different from the general codon usage of . 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 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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DNA Synthesis
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Genetic Elements
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Single-Stranded Satellite DNA
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Nucleotide Excision Repair
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Figures

Image of Figure 1
Figure 1

Biosynthesis of msDNA. (A) Arrangement of and 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 region and can be expressed under separate promoters. The transcript from the 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.

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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Image of Figure 2
Figure 2

Structures of msDNAs from retrons: msDNA Ec48 from Mao et al. ( ), msDNA Ec67 from Lampson et al. ( ), msDNA Ec73 from Sun et al. ( ), msDNA Ec78 from Lima and Lim ( ), msDNA Ec83 from Lim ( ), msDNA Ec86 from Lim and Maas ( ), and msDNA Ec107 from Herzer et al. ( ).

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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Image of Figure 3
Figure 3

Alignment of all known RTs. Alignments were performed by visual examination of the sequences and adopted with some modifications from the previous report ( ). 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 ( ). X and Y sequences are found in retron RTs and other non-LTR-RTs ( ). 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 ( ).

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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Image of Figure 4
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. ( ). 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.

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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