ISRf1, a transposable insertion sequence from Sinorhizobium fredii.

Sinorhizobium fredii strain HH103, a nitrogen-fixing bacterial symbiont of plants, contains an insertion sequence (IS) that can transpose into plasmid pMUS248 and activate a promoterless TcR gene that is normally not expressed. We have cloned and characterized this element, which we designate ISRf1. The IS is 1002 bp in length, contains a single 513-bp open reading frame (ORF), is flanked by imperfect 36-bp terminal inverted repeats, and creates 5-bp target duplications. Two copies of ISRf1 are present in the genome of HH103, but it is absent from 12 other Sinorhizobium and Rhizobium strains. The element transposes at a frequency of 2.7 x 10(-6) per generation per cell.

Different stop codon usage in two pseudohypotrich ciliates.

Based on rRNA phylogeny, morphologic and morphogenetic characters, two major groups of hypotrich ciliates can be distinguished: euhypotrichs and pseudohypotrichs. Through the sequencing of actin genes, we show here that, interestingly, the pseudohypotrichs Dyophrys sp. and Euplotes vannus have a different stop codon usage. In fact, the stop codon usage of the former species resembles that of euhypotrichs. This unexpected result is used to discuss the origin and acquisition of genetic code deviations in ciliates.

Glyceraldehyde-3-phosphate dehydrogenase from Tetrahymena pyriformis: enzyme purification and characterization of a gapC gene with primitive eukaryotic features.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC.1.2.1.12) was purified to electrophoretic homogeneity from an amicronucleated strain of the ciliate Tetrahymena pyriformis using a three-step procedure. The native enzyme is an homotetramer of 145 kDa exhibiting absolute specificity for NAD. In its catalytic properties it is similar to other glycolytic GAPDHs. Chromatofocusing analysis showed the presence of only one basic GAPDH isoform with an isoelectric point of 8.8. Western blots using a monospecific polyclonal antibody raised against the T. pyriformis GAPDH showed a single 36-kDa band corresponding to the enzyme subunit in the cytosolic protein fraction of this strain and the closely related species, both from the class Oligohymenophorea, Paramecium tetraurelia. No bands were immunodetected in the ciliate Colpoda inflata (class Colpodea) and in the diverse eukaryotes and eubacteria tested. A 0.5-kb DNA fragment which corresponds to an internal region of a gapC gene was generated by polymerase chain reaction using cDNA of T. pyriformis as template. This gene codes for a basic GAPDH protein with eukaryotic-diplomonad signatures and exhibits a codon usage biased in the manner typical for T. pyriformis genes. Southern blots performed both under homologous and heterologous conditions using this amplified cDNA fragment as a probe, indicated that it should be the only gapC gene present in the macronuclear genome of this ciliate, its expression being confirmed by Northern blot analysis. These results are discussed in connection with the peculiar genomic organization of ciliates and in the context of protist evolution.

PCR for detection of Shigella spp. in mayonnaise.

The use of PCR to amplify a specific virA gene fragment serves as a highly specific and sensitive method to detect virulent bacteria of the genus Shigella and enteroinvasive Escherichia coli. Amplification of a 215-bp DNA band was obtained by using isolated genomic DNA of Shigella, individual cells of Shigella dysenteriae, and mayonnaise contaminated with S. dysenteriae. Moreover, a multiplex PCR with specific (virA) and bacterium-restricted (16S ribosomal DNA) primers generated an amplification product of approximately 755 bp for all bacteria tested and an additional 215-bp product for Shigella and enteroinvasive E. coli.

Searching for excystment-regulated genes in Sterkiella histriomuscorum (Ciliophora, Oxytrichidae): a mRNA differential display analysis of gene expression in excysting cells.

In the absence of food, the oxytrichid Sterkiella histriomuscorum transforms like many ciliates into resting cysts. When transferred back into feeding medium, the cyst re-transforms into a vegetative cell. The entry into and exit from the dormant cyst stage are complex developmental processes still poorly investigated at the molecular level. Assuming that these changes in state could involve changes in gene expression, we have used the technique of mRNA differential display to detect differentially expressed genes in cysts and two different stages of excysting cell. Variation in the temporal expression pattern of transcripts could be detected and, in using an inverse-PCR strategy on circularized macronuclear DNA, we have sequenced the macronuclear genes of three of the isolated cDNAs. which correspond to 1) a nucleotide-binding domain-encoding gene, 2) a DHHC-domain-carrying gene, and 3) a phosphatase type 2C-encoding gene. For the first two genes, Northern blot analyses supported an excystment-associated regulated gene expression. We discuss their possible role during excystment and we show that the combination of differential display and inverse PCR constitutes a powerful approach to isolate excystment-regulated genes in hypotrichs.

Inhibition of the adenylylation of liver plasma membrane-bound proteins by plant and mammalian lectins.

Liver plasma membrane contains four major (130-kDa, 120-kDa, 110-kDa and 100-kDa) sialic acid-containing glycopolypeptides that are able to undergo adenylylation, as well as phosphorylation (San José et al. (1990) J. Biol. Chem. 265; 20653-20661). To gain insight into the regulation of these processes, lectins are employed to probe the extent of influence of their interaction with membrane fractions for these reactions. We demonstrate that the beta-galactoside-specific lectins from bovine heart and mistletoe at low concentrations inhibit the adenylylation of this set of plasma membrane glycopolypeptides. The extent of phosphorylation of these polypeptides is also reduced although to a lesser degree. Concanavalin A, too, inhibits the adenylylation of the plasma membrane glycopolypeptides, although higher concentrations of this lectin were required, whereas wheat germ lectin has only a very small inhibitory effect. The adenylylable polypeptides were isolated by concanavalin A-agarose chromatography upon elution with mannose. In agreement with this result, control experiments with a panel of neoglycoproteins indicate that mannose residues appear to be required for the concanavalin A-induced inhibition of the adenylylation. Neoglycoproteins containing mannose 6-phosphate, lactose, fucose, or sialic acid instead of mannose lack the ability to protect the adenylylation from the inhibitory action of concanavalin A. In contrast, none of the above-mentioned neoglycoproteins, nor asialofetuin, nor galactose-containing saccharides protect the adenylylation against the inhibitory effect of both the mistletoe and bovine heart lectins, emphasizing the importance of either high affinity carbohydrate ligands in the overall process, or other ligand sites for the lectins beside carbohydrates to affect the regulation of the adenylylation system.

Protein coding gene trees in ciliates: comparison with rRNA-based phylogenies.

We have reexamined the phylogeny of the ciliates using alpha-tubulin and phosphoglycerate kinase gene sequences. For alpha-tubulin, we have compared the amino acid and nucleotide sequences of 20 species representing seven of the nine classes of the phylum (Karyorelictea, Heterotrichea, Hypotrichea, Oligohymenophorea, Colpodea, Nassophorea, and Litostomatea). The phylogenetic tree resembles a bush from which three monophyletic lineages can be distinguished which correspond to the three classes Hypotrichea, Oligohymenophorea, and Litostomatea. For phosphoglycerate kinase, we have compared the amino acid sequences from 7 species representing three classes (Heterotrichea, Hypotrichea, and Oligohymenophorea). The branching pattern is resolved in three deeply separated branches with an early emergence of the heterotrich. Our comparative analysis shows that if alpha-tubulin phylogeny is not informative at the interclass level, the preliminary data from the phosphoglycerate kinase molecule appear more promising. Nevertheless, at low taxonomic level and at the class level, the resolved phylogenetic relationships inferred from both protein and rRNA sequence data are congruent.

Unusual characteristics of ciliate actins.

Actin is a cytoskeletal protein that is ubiquitous in eukaryotes, hence the corresponding genes and proteins have been isolated from numerous organisms as different as animals, plants, fungi and protozoa. Several atomic models are available for the monomeric as well as the filamentous form, and more than 70 proteins that bind actin and control filament dynamics have been isolated from diverse eukaryotes. Moreover, the function and dynamics of the actin cytoskeleton in several eukaryotic systems have been depicted in depth. Unlike other protozoa, such as amoeba, actin is not an abundant protein in ciliates, whose cytoskeleton is mainly composed of microtubular arrays. Ciliate actin has been studied in several species, and it was established early on that this ciliate protein is very different from that of other eukaryotes. Similarly, the actin-binding proteins studied in ciliates display great differences with those of other eukaryotes. Consequently, ciliate actin has been considered as "unconventional," and this review focuses on molecular data leading to this conclusion.

Paramecium tetraurelia encodes unconventional actin containing short introns.

The polymerase chain reaction was used to amplify and clone an actin gene fragment from Paramecium tetraurelia. This DNA fragment was 1,138 bp long, more than 96% of the actin coding sequence, and contained four in-frame UAA codons and two small introns located at positions unique in the actin intron catalogue. This is the first report for the phylum Ciliophora of an actin gene containing introns. The deduced amino acid sequence of this actin fragment shared 58-77% identity with other actins. When compared with rabbit alpha-muscle actin, similarities were observed mainly in subdomains 1 and 3, whereas subdomains 2 and 4 appeared to be more divergent.

Actin of Histriculus cavicola: characteristics of the highly divergent hypotrich ciliate actins.

A macronuclear gene-sized molecule carrying an actin gene from the hypotrich ciliate, Histriculus cavicola, was characterized. Southern blot analysis using a coding region probe suggested that actin in H. cavicola is encoded by a single gene. A comparison of the promoter regions indicated that the H. cavicola actin gene has a TATA box in the 5' flanking region in a position identical to those in other oxytrich ciliates. The coding sequence of this gene is not interrupted by any introns, and codes for a protein of 375 amino acid residues. This protein shares a high degree of similarity with other oxytrichid actins, and a relatively low similarity with actins from other eukaryotes. Comparative analyses of sequences indicated that most of the amino acid substitutions in hypotrich actins are found in surface loops, while the core structures are well-conserved. The sites that interact with DNase I and several regions involved in actin-actin contact have diverged considerably in hypotrich actins, while nucleotide-binding sites are the best-conserved interaction motif.

alpha-Tubulin of Histriculus cavicola (Ciliophora; Hypotrichea).

An alpha-tubulin gene fragment amplified by PCR from the hypotrichous ciliate Histriculus cavicola has been sequenced. This fragment, 1,182 bp long, contains an in-frame "stop" codon (UAA), which in other hypotrichous species codes for a glutamine residue. The comparison of the alpha-tubulin genes from several ciliates classes have revealed amino acid positions which could serve to distinguish these taxonomic groups.