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Chapter 55 : Tyrosine Recombinase Retrotransposons and Transposons

Authors: Russell T. M. Poulter1, Margi I. Butler2
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Affiliations: 1: Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand; 2: Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

Eukaryote retrotransposons have been organized into four major groups on the basis of their mechanistic features, open reading frame organization and reverse transcriptase (RT) phylogeny: long terminal repeat (LTR) retrotransposons, tyrosine recombinase (YR) encoding elements, Penelope-like elements (PLEs) and long interspersed nuclear elements (LINEs) ( ). The major feature distinguishing the tyrosine recombinase-encoding elements from other retrotransposons is that the YR elements encode a tyrosine recombinase ( ) that performs the role of integration. Other retroelements employ integrases (LTR retrotransposons) or endonucleases (LINEs and PLEs). Tyrosine recombinases (YRs) are widespread in prokaryotes, typically involved in site-specific recombination between similar or identical DNA sequences ( ). Representative examples include the Cre recombinase of bacteriophage P1, the FLP recombinase of yeast 2-micron circle plasmids, and the XerC and XerD recombinases of .

Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014
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Tyrosine Recombinase Retrotransposons and Transposons
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Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014
/content/10.1128/9781555819217.chap55.fig55-1
Figure 1
Structures of YR-encoding elements discussed in this chapter. These include: members of the DIRS-like group with ITRs and an ICR, a PAT-like element with ‘split’ direct repeats (SpPat1); Ngaro elements with ‘split’ direct repeats; a YR-encoding DNA transposon from (Crypton_Cn1). Repeat sequences are represented by boxed triangles. Shaded boxes represent ORFs. V-shaped lines represent introns. In the crypton, the stippled box represents the YR-encoding region, while the hatched box represents a putative DNA-binding domain.
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10.1128/9781555819217/fig55-1.gif
Image of Figure 1
Figure 1

Structures of YR-encoding elements discussed in this chapter. These include: members of the DIRS-like group with ITRs and an ICR, a PAT-like element with ‘split’ direct repeats (SpPat1); Ngaro elements with ‘split’ direct repeats; a YR-encoding DNA transposon from (Crypton_Cn1). Repeat sequences are represented by boxed triangles. Shaded boxes represent ORFs. V-shaped lines represent introns. In the crypton, the stippled box represents the YR-encoding region, while the hatched box represents a putative DNA-binding domain.

Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014
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Figure 2
Alignment of tyrosine recombinase conserved domains. A comparison of aligned tyrosine recombinase sequences from retrotransposons and DNA transposons with those from prokaryotes. Four regions of the recombinases are illustrated; the dashed lines common to all elements represent intervening regions of variable length. The conserved RHRY tetrad is denoted by *; the conserved CPV motif is overlined.
10.1128/9781555819217/fig55-2_thmb.gif
10.1128/9781555819217/fig55-2.gif
Image of Figure 2
Figure 2

Alignment of tyrosine recombinase conserved domains. A comparison of aligned tyrosine recombinase sequences from retrotransposons and DNA transposons with those from prokaryotes. Four regions of the recombinases are illustrated; the dashed lines common to all elements represent intervening regions of variable length. The conserved RHRY tetrad is denoted by *; the conserved CPV motif is overlined.

Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014
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Figure 3
Relationships among YR-encoding retroelements. This phylogenetic tree is based on an alignment of the conserved RT and RH protein sequences. Sequences from three LTR retrotransposons have been used as an outgroup: sushi (AF030881), Ty3 (M23367) and gypsy (AF033821). The tree was constructed by the Neighbour-joining method using MEGA5 ( ). Bootstrap support from 1050 replicates is indicated for branches with >50% support. Element descriptions can be found in Table 2 .
10.1128/9781555819217/fig55-3_thmb.gif
10.1128/9781555819217/fig55-3.gif
Image of Figure 3
Figure 3

Relationships among YR-encoding retroelements. This phylogenetic tree is based on an alignment of the conserved RT and RH protein sequences. Sequences from three LTR retrotransposons have been used as an outgroup: sushi (AF030881), Ty3 (M23367) and gypsy (AF033821). The tree was constructed by the Neighbour-joining method using MEGA5 ( ). Bootstrap support from 1050 replicates is indicated for branches with >50% support. Element descriptions can be found in Table 2 .

Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014
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Figure 4
Relationships among YR-encoding retrotransposons and DNA transposons. This phylogenetic tree is based on an alignment of the YR protein sequences. Sequences from prokaryote tyrosine recombinases have been used as an outgroup: Lambda recombinase (KDT52537), Tn916 from (U09422) and two tyrosine recombinases (XerC, CDL28161; XerD, CDL49882 ). The tree was constructed by the Neighbour-joining method using MEGA5 ( ). Bootstrap support from 1050 replicates is indicated for branches with >50% support. Element descriptions can be found in Table 2 .
10.1128/9781555819217/fig55-4_thmb.gif
10.1128/9781555819217/fig55-4.gif
Image of Figure 4
Figure 4

Relationships among YR-encoding retrotransposons and DNA transposons. This phylogenetic tree is based on an alignment of the YR protein sequences. Sequences from prokaryote tyrosine recombinases have been used as an outgroup: Lambda recombinase (KDT52537), Tn916 from (U09422) and two tyrosine recombinases (XerC, CDL28161; XerD, CDL49882 ). The tree was constructed by the Neighbour-joining method using MEGA5 ( ). Bootstrap support from 1050 replicates is indicated for branches with >50% support. Element descriptions can be found in Table 2 .

Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014
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Tables

Tyrosine Recombinase Retrotransposons and Transposons
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Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014
/content/10.1128/9781555819217.chap55.tab55-1
Table 1
DIRS-like elements in fish. All those in this table are from the Actinopterygii except (Sarcopterygii) and the little skate, (Chondrichthyes)
Generic image for table
Table 1

DIRS-like elements in fish. All those in this table are from the Actinopterygii except (Sarcopterygii) and the little skate, (Chondrichthyes)

Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014
/content/10.1128/9781555819217.chap55.tab55-2
TABLE 2
Tyrosine recombinase-encoding (YR) elements used for phylogenetic analyses in this study. The sources of the sequence data are held in the Genbank accessions, references or database sources shown. Element names are generated from the initial of the genus and either 2 or 3 initial letters from the species name of the organism in which the element is found
Generic image for table
TABLE 2

Tyrosine recombinase-encoding (YR) elements used for phylogenetic analyses in this study. The sources of the sequence data are held in the Genbank accessions, references or database sources shown. Element names are generated from the initial of the genus and either 2 or 3 initial letters from the species name of the organism in which the element is found

Citation: Poulter R, Butler M. 2015. Tyrosine Recombinase Retrotransposons and Transposons, p 1271-1291. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0036-2014

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