Sequence, codon usage and cysteine periodicity of the SerH1 gene and in the encoded surface protein of Tetrahymena thermophila

Analysis of amino acid and codon usage in Paramecium bursaria

The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis.

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

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.

Antigenic Variation in Ciliates: Antigen Structure, Function, Expression

In the past decades, the major focus of antigen variation research has been on parasitic protists. However, antigenic variation occurs also in free-living protists. The antigenic systems of the ciliates Paramecium and Tetrahymena have been studied for more than 100 yr. In spite of different life strategies and distant phylogenetic relationships of free-living ciliates and parasitic protists, their antigenic systems have features in common, such as the presence of repeated protein motifs and multigene families. The function of variable surface antigens in free-living ciliates is still unknown. Up to now no detailed monitoring of antigen expression in free-living ciliates in natural habitats has been performed. Unlike stochastic switching in parasites, antigen expression in ciliates can be directed, e.g. by temperature, which holds great advantages for research on the expression mechanism. Regulated expression of surface antigens occurs in an exclusive way and the responsible mechanism is complex, involving both transcriptional and post-transcriptional features. The involvement of homology-dependent effects has been proposed several times but has not been proved yet.

Polymorphism and selection at the SerH immobilization antigen locus in natural populations of Tetrahymena thermophila

The SerH locus of Tetrahymena thermophila is one of several paralogous loci with genes encoding variants of the major cell surface protein known as the immobilization antigen (i-ag). The locus is highly polymorphic, raising questions concerning functional equivalency and selective forces acting on its multiple alleles. Here, we compare the sequences and expression of SerH1, SerH3, SerH4, SerH5, and SerH6. The precursor i-ags are highly similar. They are rich in alanine, serine, threonine, and cysteine and they share nearly identical ER translocation and GPI addition signals. The locations of the 39 cysteines are highly conserved, particularly in the 3.5 central, imperfect tandem repeats in which 8 periodic cysteines punctuate alternating short and long stretches of amino acids. Hydrophobicity patterns are also conserved. Nevertheless, amino acid sequence identity is low, ranging from 60.7 to 82.9%. At the nucleotide level, from 9.7 to 26.7% of nucleotide sites are polymorphic in pairwise comparisons. Expression of each allele is regulated by temperature-sensitive mRNA stability. H mRNAs are stable at <36 degrees but are unstable at >36 degrees. The H5 mRNA, which is less affected by temperature, has a different arrangement of the putative mRNA destabilization motif AUUUA. Statistical analysis of SerH genes indicates that the multiple alleles are neutral. Significantly low ratios of the rates of nonsynonymous to synonymous amino acid substitutions suggest that the multiple alleles are subject to purifying (negative) selection enforcing constraints on structure.

Molecular characterization of the SerL paralogs of Tetrahymena thermophila

In the pond ciliate Tetrahymena thermophila, expression of genes encoding variant forms of the cell surface immobilization antigen (i-ag) is regulated by environmental conditions. Multiple isoforms of the L i-ags are found on the surface of cells grown at <20 degrees C as well as on the surface of rseC mutants which express SerL genes constitutively. Five cDNAs encoding variant L i-ags of rseC were sequenced and their expression studied. Two additional SerL genes from natural isolates were sequenced. Members of the SerL family encode polypeptides with 148, 316, or 371 amino acids, and the i-ags have two, five, or six imperfect repeats, respectively, flanked by putative ER translocation and GPI addition signals. Each repeat contains six periodic cysteines, in contrast to eight or ten in other i-ags of T. thermophila. At least three of the five genes constitutively expressed in rseC mutants are differentially expressed in cells expressing other i-ags. Northern analysis and RT-PCR indicate that expression of some members of the SerL family is regulated by both transcription and mRNA stability while another member is regulated primarily by mRNA stability.

Sequence and expression of the SerJ immobilization antigen gene of Tetrahymena thermophila regulated by dominant epistasis

In ciliates, variable surface protein genes encoding the immobilization antigen (-ag) are expressed under different environmental conditions, including temperature and salt stress. These i-ags are GPI-linked and coat the entire external surface of the cell, including the cilia. In Tetrahymena thermophila-ag in natural isolates is the result of dominant epistasis masking the expression of the H i-ag ordinarily expressed at 20-36 degrees C. This report describes the expression and sequence of the Ser-ag. J is present on the cell surface up to 38 degrees C; above 38 degrees C SerSeranked by an A-rich 5' UTR and a 3' UTR containing putative mRNA destabilization motifs. The encoded J polypeptide consists of 438 amino acids and is rich in alanine, cysteine, serine and threonine. The N- and resemble signal peptide and GPI-anchor addition sites, respectively. The majority of the molecule consists of four imperfect repeats with 10 periodic cysteines per repeat in the pattern CX(6)CX(2)CX(21)CX(4)CX(13-15)CX(2)CX(18)CX(3)CX(11)CX(9-10). Although H i-ags encoded by paralogous SerH genes have 3.5 imperfect repeats with eight periodic cysteines per repeat, J nevertheless resembles H with respect to amino acid composition, codon usage, N- and C-termini, the arrangement of the cysteine periods, and regulation by mRNA stability. However, despite these similarities and epistasis, the evolutionary relationship between SerH and SerJ is unclear.

The gene for an abundant parasite coat protein predicts tandemly repetitive metal binding domains

Immobilization antigens are highly abundant surface membrane proteins that coat the surface of hymenostomatid ciliates. While their function is unknown, recent studies with the common fish parasite, Ichthyophthirius multifiliis, suggest their involvement in a novel mechanism of humoral immunity involving an effect of antibody on parasite behavior. To gain further insight into the nature of these proteins, we have cloned a gene encoding the 48kDa i-antigen of I. multifiliis. Analysis of the gene (designated IAG48[G1]) reveals a single, uninterrupted reading frame that predicts a protein of 442 amino acids. Based on its deduced amino acid sequence, the protein contains hydrophobic amino acid domains at its N- and C-terminus that are characteristic of signal peptide and GPI-anchor addition sites, respectively. The most striking feature of the predicted protein, however, is a series of tandem repeats that spans most of its length. The repeats themselves are characterized by periodic cysteine residues that fall into register when the homologous segments are aligned. Interestingly, the spacing of cysteines (C-X2,3-C) within a framework of larger (C-X2-C-X20-C-X3-C-X20-C-X2-C) motifs is entirely consistent with the structure of known zinc-binding proteins. Finally, comparison of the coding sequence of the 48kDa i-antigen gene with a partial cDNA previously thought to encode this protein reveals nearly complete identity except at their 3' ends, suggesting that alternative forms of the antigen exist.

High frequency intragenic recombination during macronuclear development in Tetrahymena thermophila restores the wild-type SerH1 gene

Macronuclear development in ciliates is characterized by extensive rearrangement of genetic material, including sequence elimination, chromosome fragmentation and telomere addition. Intragenic recombination is a relatively rare, but evolutionarily important phenomenon occurring in mitosis and meiosis in a wide variety of organisms. Here, we show that high frequency intragenic recombination, on the order of 30%, occurs in the developing amitotic macronucleus of the ciliate Tetrahymena thermophila. Such recombination, occurring between two nonsense transition mutations separated by 726 nucleotides, reproducibly restores wild-type expression of the SerH1 surface protein gene, thus mimicking complementation in trans heterozygotes. Recombination must be considered a potentially important aspect of macronuclear development, producing gene combinations not present in the germinal micronucleus.

Molecular characterization of the D surface protein gene subfamily in Paramecium tetraurelia

When Paramecium tetraurelia expresses the D serotype, detectable by serum tests, high molecular mRNA could be isolated, which corresponds to the molecular mass of the D surface protein. Using this D specific mRNA as a probe for screenings in different genomic libraries a subfamily of five very similar genes was found, named alpha-51D, gamma 1-51D, gamma 2-51D, delta-51D, and epsilon-51D. Each of them is about 8-kb long, they show regions of identity to each other, and there is no evidence that any are defective genes or pseudogenes. Up to now serotype D is the only known serotype showing this phenomenon. Another novel feature is that two of the D isogenes are closely linked. The sequence for the entire coding region of the alpha-51D gene has been determined, as well as the upstream and downstream noncoding regions. Its deduced amino acid sequence shows the same characteristic cysteine periodicity displayed by all other immobilization antigen (i-ag) genes from Paramecium. However, in contrast to most other such genes, tandem repeats are missing from the 7599-bp long coding region of the alpha-51D gene. When the sequences of the type 51D genes are compared to each other, the similarity is very high and extends to coding as well as to noncoding regions. Similarity within noncoding regions is usually only observed for allelic i-ag genes. We conclude that the type D genes constitute a family of isogenes that are nonallelic. They contain slightly different consensus sequences with possible functions as regulatory regions.