Biology Faculty Articles
Document Type
Article
Publication Date
10-31-2012
Publication Title
PLOS ONE
Keywords
Retrotransposons, Rice, Oryza, Plant genomics, Protein structure prediction, Maize, Electrostatics, Phylogenetic analysis
ISSN
1932-6203
Volume
7
Issue/No.
10
First Page
e48595
Abstract
Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and in silico approaches were used to determine the origin of Retrosat2 and putative function of ORF0. Our data show that not only is Retrosat2 highly abundant in the Oryza genus, it may yet be active in rice. Homologs of Retrosat2 were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the Retrosat2 family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of Retrosat2. Unlike the ORF1, the ORF0 sequences from Retrosat2 and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, Retrosat2 and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of Retrosat2 homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species.
Additional Comments
Funding: The National Science Foundation 0424833, Division of Biological Infrastructure (DBI) 0603927, Integrated and Organismal Biology (IOS) 0701382 and Molecular and Cellular Biosciences (MCB) 1026200 provided funding. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
NSUWorks Citation
Gao, Dongying; Jose Jimenez-Lopez; Aiko Iwata; Navdeep Gill; and Scott Jackson. 2012. "Functional and Structural Divergence of an Unusual LTR Retrotransposon Family in Plants." PLOS ONE 7, (10): e48595. doi:https://doi.org/10.1371/journal.pone.0048595.
ORCID ID
http://orcid.org/0000-0003-3746-1866
DOI
https://doi.org/10.1371/journal.pone.0048595
Comments
Copyright: 2012 Gao et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.