Mobile Introns: Pathways and Proteins

Marlene Belfort; Victoria Derbyshire; Monica M. Parker; Benoit Cousineau; Alan M. Lambowitz

doi:10.1128/9781555817954.ch31

Chapter 31 : Mobile Introns: Pathways and Proteins

Authors: Marlene Belfort¹, Victoria Derbyshire¹, Monica M. Parker¹, Benoit Cousineau², Alan M. Lambowitz³

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Affiliations: 1: Molecular Genetics Program, Wadsworth Center, New York State Department of Health and School of Public Health, State University of New York at Albany, Albany, NY 12201-2002; 2: Department of Microbiology and Immunology, McGill University, Montreal, Québec H3A 2B4, Canada; 3: Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX 78712

Content Type: Monograph

Publication Year: 2002

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817954

Chapter DOI: 10.1128/9781555817954.ch31

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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: 0.50235236
Group II Introns: 0.49311265
Genetic Elements: 0.47791463
Group I Introns: 0.47176298
Human immunodeficiency virus 1: 0.4659338

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Mobile Introns: Pathways and Proteins

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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.

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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.

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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.

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Figure 3

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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-TevI. The intron is shown in black; grey horizontal arrows indicate exonucleolytic degradation.

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Figure 2

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Tables

Mobile Introns: Pathways and Proteins

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Table 1

Intron distribution a

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Table 1

Intron distribution a

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Table 2

Characteristics of homing endonucleases

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Table 2

Characteristics of homing endonucleases