Genome-wide prediction of the polymorphic Ser gene family in Tetrahymena thermophila based on motif analysis.

Patrath Ponsuwanna,Krittikorn Kümpornsin,Thanat Chookajorn,Kelly A Brayton

doi:10.1371/journal.pone.0105201

Patrath Ponsuwanna, Krittikorn Kümpornsin + Show 2 more

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https://doi.org/10.1371/journal.pone.0105201

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Abstract

Even though antigenic variation is employed among parasitic protozoa for host immune evasion, Tetrahymena thermophila, a free-living ciliate, can also change its surface protein antigens. These cysteine-rich glycosylphosphatidylinositol (GPI)-linked surface proteins are encoded by a family of polymorphic Ser genes. Despite the availability of T. thermophila genome, a comprehensive analysis of the Ser family is limited by its high degree of polymorphism. In order to overcome this problem, a new approach was adopted by searching for Ser candidates with common motif sequences, namely length-specific repetitive cysteine pattern and GPI anchor site. The candidate genes were phylogenetically compared with the previously identified Ser genes and classified into subtypes. Ser candidates were often found to be located as tandem arrays of the same subtypes on several chromosomal scaffolds. Certain Ser candidates located in the same chromosomal arrays were transcriptionally expressed at specific T. thermophila developmental stages. These Ser candidates selected by the motif analysis approach can form the foundation for a systematic identification of the entire Ser gene family, which will contribute to the understanding of their function and the basis of T. thermophila antigenic variation.

Highlights

Tetrahymena thermophila is a single-celled ciliate found in temperate freshwater [1,2]
In order to systematically search for Ser candidates, two criteria were applied based on the common features found in existing i-ag proteins namely, the presence of Cys residue pattern block CXlongCXshortC and the GPI-anchor signal located at the Cterminus
T. thermophila i-ag was originally identified as variant surface antigen

Summary

Introduction

Tetrahymena thermophila is a single-celled ciliate found in temperate freshwater [1,2]. T. thermophila naturally feeds on bacteria, but it can grow in media under laboratory conditions [3]. It has two nuclei, a micronucleus (MIC) as a germ line and a macronucleus (MAC) as a source specific for gene expression [4]. During the development of the new MAC, the parental MAC becomes degraded [4,5]. This unique biology of T. thermophila makes it an important model organism leading to seminal discoveries in the field of molecular biology [2]

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