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Chapter 31 : Mobile Introns: Pathways and Proteins

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Abstract:

While the role of group I and group II intron-encoded proteins in homing has been well defined, the function of these proteins in intron dissemination to new sites remains the subject of intense study. These mobile introns, their intron-encoded proteins, and the mechanisms by which mobility occurs are the subject of this chapter. Although transition metals are not required for colicin DNase activity, it is likely that they play a stabilizing role related to the membrane translocation that must occur for colicin’s biological function. These data lend credence to the idea that the HNH domain, like the GIY-YIG domain, is an endonu clease cassette that can become associated with other protein domains to form multifunctional proteins. The open reading frames (ORFs) specifying group II intron-encoded proteins, when present, are located in the loop region of the structural domain IV, with most of the coding sequence outside the intron catalytic core. Of the three activities of the group II intron-encoded proteins, the maturase domain is present in all known cases. Endonuclease activity of an intron-encoded protein was first shown for the yeast mtDNA introns aI1 and aI2. Group I and group II introns are self-splicing elements with wide genomic distribution, reflecting their dispersal through active mobility mechanisms. These two types of introns represent different ways in which selfish elements exploit functions that promote their invasiveness. Basic research into the structure and function of intron-encoded proteins and of the dynamics of mobility pathways is yielding a refined view of their modus operandi.

Citation: Belfort M, Derbyshire V, Parker M, Cousineau B, Lambowitz A. 2002. Mobile Introns: Pathways and Proteins, p 761-783. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch31

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DNA Synthesis
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Group II Introns
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Genetic Elements
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Group I Introns
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Human immunodeficiency virus 1
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Figures

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Figure 1

Intron splicing pathways and structures. Introns are grouped according to splicing pathway. The intron structures shown correspond to the intron type that appears on a grey background.

Citation: Belfort M, Derbyshire V, Parker M, Cousineau B, Lambowitz A. 2002. Mobile Introns: Pathways and Proteins, p 761-783. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch31
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Image of Figure 3
Figure 3

Group II intron RNP. (A) Domains of intron-encoded proteins. Abbreviations: M, maturase; E, endonuclease; Z, conserved domain adjacent to RT. (B) The RNPbound to DNA. Abbreviations, IS, intron insertion site; CS, protein cleavage site. The intron and exon binding site interactions (IBS-EBS and δ-δ′) are defined in the text. (C) Critical target residues. The intron insertion site is marked by a downward-directed arrow, and the protein cleavage site is marked by an upward-directed arrow. Critical residues for protein recognition are shown as white letters on a black background, and important but noncritical residues are boxed.

Citation: Belfort M, Derbyshire V, Parker M, Cousineau B, Lambowitz A. 2002. Mobile Introns: Pathways and Proteins, p 761-783. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch31
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Image of Figure 2
Figure 2

Group I intron homing pathways. After cleavage of the recipient and exonucleolytic degradation (step 1), 3′ends of the cleaved recipient invade the intron donor allele (step 2). Thereafter, either the DSBRor synthesis-dependent strand annealing (SDSA) pathways can be followed (steps 3 to 6) as shown and described in the text. The dumbbell represents intron endonuclease, I-I. The intron is shown in black; grey horizontal arrows indicate exonucleolytic degradation.

Citation: Belfort M, Derbyshire V, Parker M, Cousineau B, Lambowitz A. 2002. Mobile Introns: Pathways and Proteins, p 761-783. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch31
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Tables

Generic image for table
Table 1

Intron distribution

Citation: Belfort M, Derbyshire V, Parker M, Cousineau B, Lambowitz A. 2002. Mobile Introns: Pathways and Proteins, p 761-783. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch31
Generic image for table
Table 2

Characteristics of homing endonucleases

Citation: Belfort M, Derbyshire V, Parker M, Cousineau B, Lambowitz A. 2002. Mobile Introns: Pathways and Proteins, p 761-783. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch31

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