Identification and Properties of Plateins,Major Proteins in the Cortical Alveolar Plates of Euplotes1

Morphogenesis of the ciliate cortex has been viewed as an attractive model system for studying the mechanisms behind the ordered assembly of subcellular structure. Based on the assumption that identifying protein components of the cortex would facilitate the study of cortical assembly, I have produced a number of monoclonal antibodies directed against components of the cortex of Euplotes aediculatus. Several of these antibodies react with the proteins comprising the alveolar plates. These thin polygonal scales, each enclosed within a flattened membranous sac (alveolus) just beneath the cell membrane, tightly abut in a confluent monolayer that appears to lend form and rigidity to the Euplotes cell cortex. Reactivity and specificity of these monoclonal antibodies for the alveolar plates was shown by immunofluorescence staining of whole-cell preparations and of cryosections, and by immuno-gold staining of thin sections by electron microscopy. On immunoblots of SDS-PAGE separated whole-cell extracts, the plate proteins are revealed as two to three closely spaced bands centered at an M_r of 97 kDa, and a larger relative at 125 kDa. Comparative peptide mapping reveals that the members of the 97-kDa protein cluster are closely related. However, the 125-kDa polypeptide varies significantly from the 97-kDa members, and hence is not likely a synthetic precursor. Because bands of these M_r values are prominent in Coomassie blue-stained gels of whole-cell extracts, and are greatly enriched in purified cortical preparations, they likely represent the major proteins comprising the alveolar plates of E. aediculatus. I have proposed the name platein for this family of proteins.     

Sequence and Properties of Cagein,a Coiled-Coil Scaffold Protein Linking Basal Bodies in the Polykinetids of the Ciliate Euplotes aediculatus

In the hypotrich ciliate Euplotes, many individual basal bodies are grouped together in tightly packed clusters, forming ventral polykinetids. These groups of basal bodies (which produce compound ciliary organelles such as cirri and oral membranelles) are cross-linked into ordered arrays by scaffold structures known as “basal-body cages.” The major protein comprising Euplotes cages has been previously identified and termed “cagein.” Screening a E. aediculatus cDNA expression library with anti-cagein antisera identified a DNA insert containing most of a putative cagein gene; standard PCR techniques were used to complete the sequence. Probes designed from this gene identified a macronuclear “nanochromosome” of ca. 1.5 kb in Southern blots against whole-cell DNA. The protein derived from this sequence (463 residues) is predicted to be hydrophilic and highly charged; however, the native cage structures are highly resistant to salt/detergent extraction. This insolubility could be explained by the coiled-coil regions predicted to extend over much of the length of the derived cagein polypeptide. One frameshift sequence is found within the gene, as well as a short intron. BLAST searches find many ciliates with evident homologues to cagein within their derived genomic sequences.     

Uronychia transfuga (O. F. Müller, 1786) Stein, 1859 (Ciliophora, Hypotrichia, Uronychiidae): Cortical Structure and Morphogenesis during Division

Morphogenesis of cell division was investigated in Uronychia transfuga utilizing both light microscopy of living and stained specimens and SEM of preserved specimens. The cortical morphogenetic pattern of Uronychia is similar in several respects to that of the members of the family Euplotidae. These features include: the de novo development of the opisthe oral primordium in a subcortical pouch; the development of frontoventral and transverse cirri for both the proter and opisthe from 5 cirral primordia that form de novo within a single latitudinal developmental zone; and the absence of right marginal cirri. The members of the genus Uronychia also show a number of unique characteristics: development of a proter oral primordium that causes partial replacement of the parental adoral zone of oral polykinetids during development of the proter; a large oral membrane that is divided into a right and left component; large caudal cirri that bend to the left; and dorsal kineties comprised of closely set paired-kinetosome kinetids. When compared to the other euplotid-like ciliates, these unique features support the placement of the genus Uronychia in a separate family, Uronychiidae.     

Characterization and taxonomic validity of the ciliate Oxytricha trifallax (Class Spirotrichea) based on multiple gene sequences: limitations in identifying genera solely by morphology

Oxytricha trifallax - an established model organism for studying genome rearrangements, chromosome structure, scrambled genes, RNA-mediated epigenetic inheritance, and other phenomena - has been the subject of a nomenclature controversy for several years. Originally isolated as a sibling species of O. fallax, O. trifallax was reclassified in 1999 as Sterkiella histriomuscorum, a previously identified species, based on morphological similarity. The proper identification of O. trifallax is crucial to resolve in order to prevent confusion in both the comparative genomics and the general scientific communities. We analyzed nine conserved nuclear gene sequences between the two given species and several related ciliates. Phylogenetic analyses suggest that O. trifallax and a bona fide S. histriomuscorum have accumulated significant evolutionary divergence from each other relative to other ciliates such that they should be unequivocally classified as separate species. We also describe the original isolation of O. trifallax, including its comparison to O. fallax, and we provide criteria to identify future isolates of O. trifallax.     

Conjugation in the Hypotrich Ciliate,Paraurostyla weissei (Stein): A Scanning Electron Microscope Study*

SYNOPSIS. Conjugation in Paraurostyla weissei has been investigated by scanning electron microscopy. In the course of conjugation, one member of each conjugating pair is resorbed. An organism that is being resorbed always lies to its partner's left and is always fused to its partner's oral region. A mechanism for the development of this asymmetry is proposed, based on the asymmetry of individual Paraurostyla. After resorption is complete, exconjugants enter a rounded, nonmotile stage which lasts several days. Exconjugants at this stage have been compared with cysts and have been found to be dissimilar.     

Phylogenetic position of Licnophora,Lechriopyla, and Schizocaryum,three unusual ciliates (phylum Ciliophora) endosymbiotic in echinoderms (phylum Echinodermata)

Various echinoderms are colonized by species from several classes of the Phylum Ciliophora, indicating that the echinoderm "habitat" has been invaded independently on numerous occasions throughout evolutionary history. Two "echinoderm" ciliates whose phylogenetic positions have been problematic are Licnophora macfarlandi Stevens, 1901 and Schizocaryum dogieli Poljansky and Golikova, 1957. Licnophora macfarlandi is an endosymbiont of the respiratory trees of holothuroids, and S. dogieli is found in the esophagus of echinoids. A third species, Lechriopyla mystax Lynch, 1930, is a plagiopylid ciliate found in the intestine of echinoids. Host echinoderms were collected near the Friday Harbor Laboratories, San Juan Island, WA. Specimens of S. dogieli and L. mystax were obtained from the esophagus and intestine, respectively, of the sea urchin Strongylocentrotus pallidus. Specimens of L. macfarlandi were collected from the fluid obtained from the respiratory trees of Parastichopus californicus. Using small subunit ribosomal RNA (SSrRNA) sequences of these three ciliates and a global alignment of SSrRNA sequences of other ciliates, we established the following. 1) Licnophora is a spirotrich ciliate, clearly related to the hypotrichs and stichotrichs; this is corroborated by its possession of macronuclear replication bands. 2) Lechriopyla is the sister genus to Plagiopyla and is a member of the Class Plagiopylea, which was predicted based on its cytology. 3) Schizocaryum clusters in the Class Oligohymenophorea and is most closely related to the scuticociliates; there are currently no morphological features known to relate Schizocaryum to the scuticociliates.     

Coding properties of macronuclear DNA molecules in Sterkiella nova (Oxytricha nova)

The DNA in the macronucleus of the stichotrichs like Sterkiella nova (formerly Oxytricha nova) occurs in short molecules ranging from approximately 200 bp to approximately 20,000 bp. It has been estimated that there are approximately 24,500 different sized DNA molecules in the macronucleus. Single genes have been assigned to approximately 130 different sized macronuclear molecules in various stichotrichs (12 in Sterkiella nova) and hypotrichs, suggesting that each of the -24,500 different sized molecules encodes a different gene. To test this proposition we sequenced 31 macronuclear molecules picked randomly from a plasmid library of macronuclear DNA and analyzed them for potential gene content. The open reading frames (ORFs) in three short molecules encode amino acid (aa) sequences that do not match sequences in GenBank. They may or may not encode genes. Twenty-eight of the 31 molecules contain ORFs encoding aa sequences with significant matches to sequences in GenBank. Six molecules contain more than one ORF with a significant match to GenBank. These results indicate that almost all, if not all of the -24,500 different molecules encode one or more genes, yielding an estimate of -26,800 genes in the macronucleus of S. nova.     

Evolution of programmed DNA rearrangements in a scrambled gene

Gene unscrambling in spirotrichous ciliates involves massive genome-wide DNA deletion and rearrangement events during development. During each sexual cycle, the somatic nucleus (macronucleus) regenerates from the germ line nucleus (micronucleus). Development of the polyploid somatic genome requires programmed DNA deletion of micronuclear-limited intragenic noncoding sequences and permutation and amplification of the protein-coding regions. Recent studies suggest that, despite novel insertions of endogenous transposon or foreign DNA into the germ line genome, ciliates possess a whole-genome surveillance system that guides the recapitulation of a functional somatic genome. This renders the germ line genome an extremely dynamic structure over evolutionary time. Here we describe the germ line and somatic architectures of the gene encoding alpha-telomere-binding protein in three early-diverging species (Holosticha sp., Uroleptus sp., and Paraurostyla weissei) and trace the natural history of DNA rearrangements in this gene in six species, including three previously studied oxytrichids. Comparisons of homologous coding regions between earlier and later diverging species provide evidence for fusion of scrambled germ line fragments as small as 24 bp during evolution, as well as simultaneous fragmentation and scrambling of the germ line locus and shifting of the boundaries between coding and noncoding DNA, leading to distinct gene architectures in each species. We infer an evolutionary recombination pathway that passes through identified intermediate species and gives rise to the observed patterns in all known species, capitalizing on their unique DNA rearrangement machinery and germ line flexibility.     

Complex germline architecture: two genes intertwined on two loci

The germline micronuclear genome of some ciliated protists can be scrambled, with coding segments disordered relative to the expressed macronuclear genome. Here, we report a surprisingly complex pair of genes that assemble from interwoven segments on two germline loci in the ciliate Uroleptus. This baroque organization requires two scrambled genes to be disentangled from each other from two clusters in the genome, one containing segments 1-2-4-5-6-8-11-13-15-16 and the other 7-9-3-10-12-14, with pieces 1-5 comprising the first gene and 6-16 the second gene. Both genes remain linked in the somatic genome on a 1.5-kb "nanochromosome." This study is the first to reveal that two genes can become scrambled during evolution with their coding segments intertwined. These twin scrambled genes underscore the beauty and exceptions of protist genome architecture, pointing to the critical need for evolutionary biologists to survey protist genomes broadly.