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MBE Advance Access first published online on November 1, 2007
This version published online on November 13, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm238
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© 2007 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Research Article

Patterns of Evolution in the Unique tRNA Gene Arrays of the Genus Entamoeba

Blessing Tawari1,4,#, Ibne Karim M. Ali1,5,#, Claire Scott1,6, Michael A. Quail2, Matthew Berriman2, Neil Hall2,3,7 and C. Graham Clark1,*

1 Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, GB
2 The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, GB
3 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, USA

* Corresponding Author. Tel +44-20-7927-2351, FAX +44-20-7636-8739, e-mail address: graham.clark{at}lshtm.ac.uk

Received for publication July 26, 2007. Revision received October 2, 2007. Accepted for publication October 27, 2007.

Genome sequencing of the protistan parasite Entamoeba histolytica HM-1:IMSS revealed that almost all the tRNA genes are organized into tandem arrays that make up over 10% of the genome. The 25 distinct array units contain up to 5 tRNA genes each and some also encode the 5S RNA. Between adjacent genes in array units are complex short tandem repeats resembling microsatellites. To investigate the origins and evolution of this unique gene organization, we have undertaken a genome survey to determine the array unit organization in four other species of Entamoeba - E. dispar, E. moshkovskii, E. terrapinae and E. invadens - and have explored the short tandem repeat structure in other isolates of E. histolytica

The genome surveys revealed that E. dispar has the same array unit organization as E. histolytica, including the presence and numerical variation of short tandem repeats between adjacent genes. However, the individual repeat sequences are completely different to those in E. histolytica. All other species of Entamoeba studied also have tandem arrays of clustered tRNA genes, but the gene composition of the array units often differs from that in E. histolytica/E. dispar. None of the other species’ arrays exhibit the complex short tandem repeats between adjacent genes although simple tandem duplications are occasionally seen. The degree of similarity in organization reflects the phylogenetic relationships among the species studied.

Within individual isolates of E. histolytica most copies of the array unit are uniform in sequence with only minor variation in the number and organization of the short tandem repeats. Between isolates, however, substantial differences in short tandem repeat number and organization can exist although the individual repeat sequences tend to be conserved.

The origin of this unique gene organization in the genus Entamoeba clearly predates the common ancestor of the species investigated to date and their function remains unclear.

Key Words: Entamoeba • tRNA genes • Repeated DNA • Recombination

# Equal contribution to this work.

4 Schering Health Care Ltd., Burgess Hill, West Sussex , GB

5 Division of Infectious Diseases and International Health, University of Virginia Health System, MR4 Building Room 2115, Lane Road, Charlottesville, VA, USA

6 Queen Mary's School of Medicine and Dentistry, Institute of Cell and Molecular Science, Centre for Cutaneous Research, 4 Newark Street, Whitechapel, London E1 2AT, GB

7 School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, GB


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