STUDIES ON THE IMMOBILIZATION ANTIGENS OF PARAMECIUM. IV. PROPERTIES OF THE DIFFERENT ANTIGENS

Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNA interference-mediated silencing in Paramecium tetraurelia

Antigenic or phenotypic variation is a widespread phenomenon of expression of variable surface protein coats on eukaryotic microbes. To clarify the mechanism behind mutually exclusive gene expression, we characterized the genetic properties of the surface antigen multigene family in the ciliate Paramecium tetraurelia and the epigenetic factors controlling expression and silencing. Genome analysis indicated that the multigene family consists of intrachromosomal and subtelomeric genes; both classes apparently derive from different gene duplication events: whole-genome and intrachromosomal duplication. Expression analysis provides evidence for telomere position effects, because only subtelomeric genes follow mutually exclusive transcription. Microarray analysis of cultures deficient in Rdr3, an RNA-dependent RNA polymerase, in comparison to serotype-pure wild-type cultures, shows cotranscription of a subset of subtelomeric genes, indicating that the telomere position effect is due to a selective occurrence of Rdr3-mediated silencing in subtelomeric regions. We present a model of surface antigen evolution by intrachromosomal gene duplication involving the maintenance of positive selection of structurally relevant regions. Further analysis of chromosome heterogeneity shows that alternative telomere addition regions clearly affect transcription of closely related genes. Consequently, chromosome fragmentation appears to be of crucial importance for surface antigen expression and evolution. Our data suggest that RNAi-mediated control of this genetic network by trans-acting RNAs allows rapid epigenetic adaptation by phenotypic variation in combination with long-term genetic adaptation by Darwinian evolution of antigen genes.

IMPORTANCE

Alternating surface protein structures have been described for almost all eukaryotic microbes, and a broad variety of functions have been described, such as virulence factors, adhesion molecules, and molecular camouflage. Mechanisms controlling gene expression of variable surface proteins therefore represent a powerful tool for rapid phenotypic variation across kingdoms in pathogenic as well as free-living eukaryotic microbes. However, the epigenetic mechanisms controlling synchronous expression and silencing of individual genes are hardly understood. Using the ciliate Paramecium tetraurelia as a (epi)genetic model, we showed that a subtelomeric gene position effect is associated with the selective occurrence of RNAi-mediated silencing of silent surface protein genes, suggesting small interfering RNA (siRNA)-mediated epigenetic cross talks between silent and active surface antigen genes. Our integrated genomic and molecular approach discloses the correlation between gene position effects and siRNA-mediated trans-silencing, thus providing two new parameters for regulation of mutually exclusive gene expression and the genomic organization of variant gene families.

Immunogenetic analysis of proteins of Paramecium VI. Additional evidence for the expression of several loci in animals of a single antigenic type

A paramecium generally bears on its surface but one immobilization antigen from among the many it may have the potentiality for expressing. By assaying soluble extracts of whole cells, it had been demonstrated previously that animals of the E serotype may possess the cross-reacting G antigen. Now the existence of these secondary antigens—immobilization antigens undetected by in vivo tests—has been extended to include unrelated antigens, e.g. G antigen in animals of C serotype.

The amount of these cryptic immobilization antigens varies from stock to stock; also within a stock cultures harvested at different times may have quite different quantities.

The secondary and primary G antigens appear to be indistinguishable by the criteria of antigenic specificities, immunoelectrophoretic mobilities sedimentation rates and ammonium sulfate solubilities. As to their distribution within the cell, both secondary and primary antigens are located primarily on or within the cilia.

Immunogenetic analysis of proteins of Paramecium V. Detection of specific determinants in strains lacking a surface antigen

Several stocks of Paramecium aurelia that had never expressed an E serotype were examined for E-reacting material. The regular presence of the cross-reacting antigen G in these stocks ruled out the use of hapten inhibition and other standard immunological techniques. Consequently, a genetic approach was attempted in which hybrids of the E-deficient strains and non-E stocks were bred, and antigen isolated and tested for the existence of molecules with a specificity differing from that of the E-containing parent.

Gel diffusion analysis suggested that E antigen from a hybrid indeed could differ from the ‘normal’ E. One of these hybrid clones which behaved as though its E antigen may have possessed a determinant contributed by the E-deficient strain was used as an immunizing antigen. The antibodies elicited possessed specificity unique for the hybrid. Thus the possession of E-like determinants by E-deficient stocks was confirmed.

Immunological studies of isolated particulates of Paramecium aurella. I. Antigenic relationships between cytoplasmic organelles and evidence for mitochondrial variations as demonstrated by gel diffusion

Mitochondria and other particulates—cilia, trichocysts, and "small granules"—have been isolated from several stocks of Paramecium aurelia, syngen 2. Antisera against these particles and against breis have been used to characterize the fractions by diffusion in gel. Evidence is presented for the relationship of particles, as demonstrated by immunologic cross-reactivity of the soluble antigens extracted from them. Although some antigens are unique for a fraction, cross-reacting antigens in two or more fractions, as determined by "spur" formation in agar, suggest a relationship between morphologically diverse particles. A procedure for studying cross-reactions in gels is described using the specific immobilization antigens as a model. The localization of these antigens within cilia, and perhaps trichocysts, has been confirmed. Other organelles, specifically mitochondria and "small granules," appear to alter their specificity spontaneously and reversibly during cell reproduction, a pattern reminiscent of the immobilization serotypes which can transform to one another during clonal growth.

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

When paramecium primaurelia expresses the D serotype, a major high molecular weight mRNA species is detected in the cytoplasm. Using the cDNA derived from this mRNA as a probe, three very similar genes, D alpha, D beta and D gamma, were cloned. Of these three genes, we show that only the D alpha mRNA is present in the cytoplasm of cells expressing the D serotype and corresponds to the major mRNA species. The nucleotide sequence of the entire coding region of the D alpha gene, as well as the upstream and downstream sequences, has been determined. The 7632-nucleotide open reading frame encodes a putative protein that displays the characteristic cysteine residue periodicity of Paramecium surface antigens but does not contain central tandemly repeated sequences. Partial sequences of the two nonexpressed genes D beta and D gamma indicate a high percentage of identity (90%-95%) with the D alpha gene, suggesting that D beta and D gamma genes are either very similar surface protein genes whose transcription is repressed trough mutual exclusion, or perhaps are pseudogenes. A region of variable DNA rearrangement was identified 1 kb upstream of the D gamma gene. This macronuclear region arises from the same micronuclear locus by alternative excision of internal eliminated sequences during macronuclear development.

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.

Molecular and genetic analyses of the B type surface protein gene from Paramecium tetraurelia

The gene encoding the B type variable surface protein from Paramecium tetraurelia stock 51 has been cloned and sequenced. The 7,182 nucleotide open reading frame contains no introns and encodes a cysteine-rich protein that has a periodic structure including three nearly perfect tandem repeats in the central region. Interestingly, the B gene is located near a macronuclear telomere as was shown previously for two other paramecium surface protein genes. In this paper, we characterize four independent mutants with complete macronuclear deletions of the B gene. Previous analysis of different macronuclear deletion mutants of the A surface protein gene demonstrated two types of inheritance: typical Mendelian segregation (as illustrated by d12) and cytoplasmic inheritance (shown by d48). F1 analysis of four B- mutants crossed with wild-type cells reveals heterozygous F1 cell lines derived from both parental cytoplasms contain approximately the same copy number of the B gene, as expected for a recessive Mendelian mutation. Analysis of F2 progeny from three of these four B- mutant crosses indicates that one of the three exhibits a Mendelian 1:1 segregation ratio of B+ and B- cell lines. The other two show a preponderance of B+ cells, but this is not correlated with the parental cytoplasmic type. In addition to having a large number of B+ individuals, the d12.144, A-, B- mutant produced some F2 progeny that stably maintain less than normal macronuclear amounts of the A gene and/or the B gene.

Cysteine residue periodicity is a conserved structural feature of variable surface proteins from Paramecium tetraurelia

The DNA sequences of the entire coding regions of the A and C type variable surface protein genes from Paramecium tetraurelia, stock 51 have been determined. The 8151 nucleotide open reading frame of the A gene contains several tandem repeats of 210 nucleotides within the central portion of the molecule as well as a periodic structure defined by cysteine residues. The 6699 nucleotide open reading frame of the C gene does not contain any identifiable tandem repeats or internal similarity but maintains a periodicity based on the cysteine residue spacing. The deduced amino acid sequences encoded by the two genes are most similar within the 600 amino-terminal and 600 carboxyl-terminal amino acid residues, the central portions show only limited sequence similarity. We conclude that internal repeats are not a conserved feature of variable surface proteins in Paramecium and discuss the possible importance of the regular pattern of cysteine residues.

Conserved sequences flank variable tandem repeats in two alleles of the G surface protein of Paramecium primaurelia

We describe the cloning and the sequencing of a macronuclear DNA fragment of Paramecium primaurelia, strain 168, encompassing the entire coding region of the 168G surface protein gene. Comparison of its nucleotide and its deduced amino acid sequences to those of the allelic surface protein 156G, previously described, reveals the rigorous conservation of a highly periodic structure. This structure is based on the presence of 37 periods of about 75 residues, each period containing eight cysteine residues. The differences between the two proteins are clustered in the central part of the sequence, which is itself made of quasi-identical tandem repeats. We propose that these repeats constitute the domain exposed on the surface of the cells and present the characteristics of concerted evolution.

Molecular biology of the genes for immobilization antigens in Paramecium

Several genes for surface antigens of the Paramecium aurelia complex of species have been isolated. In addition to known deletions of the 51A gene, we have obtained deletions involving the 51B gene and have developed a procedure for obtaining deletions of additional genes. Both Mendelian and non-Mendelian deletions of both the A and B genes have been found. In the non-Mendelian deletions the genes are present in the micronuclei and absent in the macronuclei. Processing of micronuclear DNA into new macronuclear DNA at conjugation and autogamy is under the control of the old macronucleus, and newly forming macronuclei become exactly like the old. Thus in the non-Mendelian mutants, macronuclei have a specific antigen gene deleted and also are impaired in their ability to direct normal DNA processing at the next conjugation or autogamy. These cases, along with others, show that this system of macronuclear control is a fundamental feature of ciliate genetics. The sequence of the 51A and 51C genes is described and compared with the 156G and 51H genes obtained by others. The 51A and 156G genes are remarkably similar while 51C and 51H are rather different. No introns or pseudogenes have been observed. Some, possibly all, of the genes are on the ends of chromosomes. Characteristic upstream and downstream sequences adjacent to the coding portions of the genes are given. The sequences UAA and UAG are preferred over CAA and CAG for glutamine while UGA is the true stop codon.

Biochemical studies of the excitable membrane of paramecium tetraurelia. IX. Antibodies against ciliary membrane proteins

The excitable ciliary membrane of Paramecium regulates the direction of the ciliary beat, and thereby the swimming behavior of this organism. One approach to the problem of identifying the molecular components of the excitable membrane is to use antibodies as probes of function. We produced rabbit antisera against isolated ciliary membranes and against partially purified immobilization antigens derived from three serotypes (A, B, and H), and used these antisera as reagents to explore the role of specific membrane proteins in the immobilization reaction and in behavior. The immobilization characteristics and serotype cross-reactivities of the antisera were examined. We identified the antigens recognized by these sera using immunodiffusion and immunoprecipitation with 35S-labeled ciliary membranes. The major antigen recognized in homologous combinations of antigen-antiserum is the immobilization antigen (i-antigen), approximately 250,000 mol wt. Several secondary antigens, including a family of polypeptides of 42,000-45,000 mol wt, are common to the membranes of serotypes A, B, and H, and antibodies against these secondary antigens can apparently immobilize cells. This characterization of antiserum specificity has provided the basis for our studies on the effects of the antibodies on electrophysiological properties of cells and electron microscopic localization studies, which are reported in the accompanying paper. We have also used these antibodies to study the mechanism of cell immobilization by antibodies against the i-antigen. Monovalent fragments (Fab) against purified i-antigens bound to, but did not immobilize, living cells. Subsequent addition of goat anti-Fab antibodies caused immediate immobilization, presumably by cross-linking Fab fragments already bound to the surface. We conclude that antigen-antibody interaction per se is not sufficient for immobilization, and that antibody bivalency, which allows antigen cross-linking, is essential.

Structure and expression of genes for surface proteins in Paramecium

Surface proteins from 11 antigenic types of Paramecium tetraurelia vary in molecular weight from 251,000 to 308,000. The size of a series of polyadenylated RNAs obtained from these types were correlated with the sizes of the proteins and judged to be the mRNAs for the proteins. The mRNAs were used to identify genomic DNA clones containing complementary sequences. The gene for antigen A was present in one copy per genome, and the data suggest that extensive introns were absent. When restriction enzyme digests of DNA from cultures of paramecia with active and inactive genes were probed with portions of the cloned genes, no evidence for rearrangements or changes in gene dosage was found.

Immunological crossreactivity of Paramecium surface antigens: conformational differences account for cell surface specificity

Surface antigens (i-Ags) G and D of Paramecium primaurelia, reported earlier to be completely unrelated on the basis of peptide mapping and immunological tests, were compared and found to be similar in molecular weight (Mr 235,000), isoelectric point (ca. 4.5), and amino acid composition. They are tightly folded proteins with more than 100 intramolecular disulfide bonds. Native i-Ags and their CNBr fragments were blotted onto nitrocellulose and labeled with a battery of homologous and heterologous antibodies fractionated on native and reduced i-Ag immunoadsorbents. It was found the i-Ags retained part of their antigenic structure upon cleavage and reduction. Analysis of labeling revealed that the two proteins share many of their antigenic sites, though they are completely distinct in their native conformation. Immunofluorescence and immunoadsorption on fixed cells confirmed these results. Antigenic crossreactivity also was found with surface antigens of a ciliate outside the Paramecium species complex. It is concluded that surface specificity of paramecia is due, in this case, to the expression of related proteins in different conformations.

Radioimmunoassay of Paramoecium surface antigens

A radioimmunoassay for the quantitative determination of the immobilization antigens of Paramoecium is described. The use of this technique in the identification of closely related antigens is discussed in terms of antigen `profiles', derived from precipitin tests with several antisera.