Universität zu Köln

Spaller, Thomas, Kling, Eva, Gloeckner, Gernot, Hillmann, Falk ORCID: 0000-0002-5493-930X and Winckler, Thomas (2016). Convergent evolution of tRNA gene targeting preferences in compact genomes. Mob. DNA, 7. LONDON: BIOMED CENTRAL LTD. ISSN 1759-8753

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Abstract

Background: In gene-dense genomes, mobile elements are confronted with highly selective pressure to amplify without causing excessive damage to the host. The targeting of tRNA genes as potentially safe integration sites has been developed by retrotransposons in various organisms such as the social amoeba Dictyostelium discoideum and the yeast Saccharomyces cerevisiae. In D. discoideum, tRNA gene-targeting retrotransposons have expanded to approximately 3 % of the genome. Recently obtained genome sequences of species representing the evolutionary history of social amoebae enabled us to determine whether the targeting of tRNA genes is a generally successful strategy for mobile elements to colonize compact genomes. Results: During the evolution of dictyostelids, different retrotransposon types independently developed the targeting of tRNA genes at least six times. DGLT-A elements are long terminal repeat (LTR) retrotransposons that display integration preferences similar to 15 bp upstream of tRNA gene-coding regions reminiscent of the yeast Ty3 element. Skipper elements are chromoviruses that have developed two subgroups: one has canonical chromo domains that may favor integration in centromeric regions, whereas the other has diverged chromo domains and is found similar to 100 bp downstream of tRNA genes. The integration of D. discoideum non-LTR retrotransposons similar to 50 bp upstream (TRE5 elements) and similar to 100 bp downstream (TRE3 elements) of tRNA genes, respectively, likely emerged at the root of dictyostelid evolution. We identified two novel non-LTR retrotransposons unrelated to TREs: one with a TRE5-like integration behavior and the other with preference similar to 4 bp upstream of tRNA genes. Conclusions: Dictyostelid retrotransposons demonstrate convergent evolution of tRNA gene targeting as a probable means to colonize the compact genomes of their hosts without being excessively mutagenic. However, high copy numbers of tRNA gene-associated retrotransposons, such as those observed in D. discoideum, are an exception, suggesting that the targeting of tRNA genes does not necessarily favor the amplification of position-specific integrating elements to high copy numbers under the repressive conditions that prevail in most host cells.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Spaller, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED Kling, Eva UNSPECIFIED UNSPECIFIED UNSPECIFIED Gloeckner, Gernot UNSPECIFIED UNSPECIFIED UNSPECIFIED Hillmann, Falk UNSPECIFIED orcid.org/0000-0002-5493-930X UNSPECIFIED Winckler, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-266149
DOI:	10.1186/s13100-016-0073-9
Journal or Publication Title:	Mob. DNA
Volume:	7
Date:	2016
Publisher:	BIOMED CENTRAL LTD
Place of Publication:	LONDON
ISSN:	1759-8753
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language LTR RETROTRANSPOSABLE ELEMENTS; DICTYOSTELIUM-DISCOIDEUM; SACCHAROMYCES-CEREVISIAE; REVERSE TRANSCRIPTION; TRANSPOSABLE ELEMENTS; REPETITIVE ELEMENTS; MOBILE ELEMENTS; INTEGRATION; PROTEIN; INITIATION Multiple languages Genetics & Heredity Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/26614