de Chastonay Y et al. (1991) Worm Breeder's Gazette "PAT element sequence suggesting a retroid transposition mode"

Link CD, Maller F, Felder H, de Chastonay Y

[Worm Breeder's Gazette, 1991]

The PAT elements of Panagrellus redivivus, described earlier (de Chastonay et al., WBG 11,4), code for a major transcript (about 900nt long) which maps to the preferentially deleted portion of PAT entities. Sequence analysis of this region has revealed the presence of a single, COOH terminal cysteine motif, thought to be exclusively characteristic of retroid GAG proteins. Longer exposition of Northern blots lights up further PAT specific signals, the most noteworthy of which is an approx. 1800nt band mapping slightly downstream of the putative GAG gene. A 587 amino acid ORF, as deduced from nucleic acid studies, is found in the corresponding region. ORF2, as we refer to it here, contains a YXDD box and neighboring motifs typical for reverse transcriptase (RT). The RT region is COOH terminally followed by a tether and an RNaseH motif. Analysis of sequences further downstream suggests the presence of an endonuclease, albeit lacking a metal binding domain. No protease like motif was found in either of these ORFs. PAT ORFs 1 and 2 are on the same reading frame, but they have no overlap and the transcripts detected on Northern blot are discrete. Hence, ratio of GAG to Pol is not regulated by a translational frame- shifting mechanism but, rather, seems to be regulated at the transcriptional level. The strong transcription rate of ORF1 is paralleled by the presence of a TATA and a CAAT box, while the latter regulatory signal is not found preceding the weakly transcribed, putative Pol gene (ORF2). Two further ORFs (i.e., 3 and 4) are located further downstream, but neither one has an apparent trans- membrane domain, as one would expect from a putative Env gene of infectious retroids. These structural features put together incite us to classify PAT elements as retrotransposons, and optimal alignments with published RT sequences, as well as the order of functional domains in ORF2, seem to assign PAT to the Gypsy group of retroid elements. As described (WBG, op. Cit.), however, PAT has a split DR structure, the only precedent of this being the Toc-1 element of Chlamydomonas reinhardtii (Day et al. EMBO J. 7,1917-1927,1988). We therefore propose to dub these elements 'Para-retrotransposons', 'para' reflecting the positions of DRs if a transposition intermediate of these elements was circular. [See Figure 1]

de Chastonay Y et al. (1990) Worm Breeder's Gazette "Genome complexity of Panagrellus redivivus shrunk by the presence of abundant satellite DNA."

Mueller F, de Chastonay Y, Tobler H

[Worm Breeder's Gazette, 1990]

The genome of Panagrellus redivivus contains two distinct satellites, dubbed E155 and E167. They have a reiteration frequency of nearly 30, 000 copies per haploid genome for the former and of about 40,000 for E167. There is no homology between the two satellites and neither of them cross-hybridizes to C. elegans or A. Lumbricoides DNA. As deduced from genomic Southern blots, the repeats are arranged in long tandem arrays and the two repeat classes are not intermingled. Northern blot analysis turned out to be negative for both satellites at the pg level using 10 g total Panagrellus redivivus RNA per slot, corresponding to the majority of transcription studies done on satellite DNAs. P. redivivus and C. elegans have nearly identical genome sizes. However, whereas the latter nematode has very little satellite DNA, such sequences represent at least 17% of the P. redivivus genome. This proportion is quite high considering the C-value of merely 70 Mb in P. redivivus, thought to be the lower limit for metazoans. Consequently, maximal genome complexity is of 58 Mb which is approximately equivalent to the genome size of the slime mold Dictyostelium discoideum. Although the P. redivivus genome remains complex enough to englobe the predicted 35,000 kb coding sequences of the closely related nematode C. elegans, the low complexity does set a milestone in terms of the C-value paradox. Moreover, the genome of C. elegans contains 17% of moderately repeated sequences, as found by reassociation kinetics. Some of these sequences are genes which must be equally represented in P. redivivus. Another fraction is made up of transposable elements, an example of which is the PAT element, recently isolated from P. redivivus and present in about 10 to 50 copies per haploid genome. The majority of middle repetitive elements, however, have been poorly studied, but a possible function for these remains the control of gene expression. Such regulatory elements would surely also be required in P. redivivus and if so, would yet decrease the genome complexity to a further extent, perhaps implying the necessity to re-evaluate minimal gene numbers required in simple nematodes.

de Chastonay Y et al. (1990) Worm Breeder's Gazette "PAT elements, candidates for an adequate transposon tagging system in C. elegans."

Mueller F, Tobler H, de Chastonay Y, Link CD

[Worm Breeder's Gazette, 1990]

PAT, a transposable element of Panagrellus redivivus, was identified after its insertion and thus the creation of a spontaneous mutation in the Unc-22 gene of the nematode. Copy numbers per haploid genome range from 10 to 50, depending on Panagrellus strains, and the distribution of PAT elements is rather scattered. The predominant and presumably autonomous form is about 5.6 kb long, but several internally deleted elements are also detected in the genomes. The deletions analyzed are all confined to one and the same half of the element and do not comprise repeated element sequences. Direct repeat (DR) arrangement is not as in typical retroids. Rather, an integral DR is found inside, while opposed DR halves are found to flank the elements. Organization with respect to half DRs (A and B) is alternate (A...BA..B), implying that PAT elements were not created by the insertion of separate elements into or next to one another. This DR arrangement seems to be conserved in most PAT elements. Moreover, internal PAT domains are always associated with DR sequences while the latter seem to also pre-exist as solo DRs in the genome. No exact target site duplication was found flanking the elements for which the borders were sequenced, however, a possible insertion site specificity can be deduced (i.e., A..AC). Northern blot hybridization does not indicate the presence of full length transcripts, rather excluding a retroid mode of transposition. Merely one transcript of about 900nt length is detected on blots having 10 g total RNA per track. Furthermore, the transcript maps to the preferentially deleted region of PAT elements. Within reasonable limits of speculation, this transcript could code for a transposase- like protein, unless the factors necessary for transposition were to be provided in trans. The deleted forms might therefore well depend on full length elements for transposition. Cross-hybridization to C. elegans as well as to A. Iumbricoides genomic DNA turned out to be negative under high stringency conditions. Hence, deleterious elements in combination with putatively autonomous full length elements, merely lacking border sequences, could be interesting candidates for a 'jump-starter/mutator' transposon tagging system, to be injected in the closely related nematode C. elegans.

Zarkower D et al. (1994) Worm Breeder's Gazette "mab-3 YAC Rescue"

De Bono M, Hodgkin JA, Zarkower D

[Worm Breeder's Gazette, 1994]

mab-3 YAC rescue David Zarkower, Mario de Bono, and Jonathan Hodgkin MRC Laboratory of Molecular Biology, Cambridge, England

De Stasio E et al. (1994) Worm Breeder's Gazette "Mutagenesis of C. elegans Using N-ethyl-N-nitrosourea."

De Stasio E, Stanislaus D, Lephoto C

[Worm Breeder's Gazette, 1994]

Mutagenesis of C. elegans using N-ethyl-N-nitrosourea Elizabeth De Stasio, Dinesh Stanislaus and Catherine Lephoto. Department of Biology, Lawrence University, Appleton, Wl 54911

Huang Y-J et al. (1994) Worm Breeder's Gazette "From Ascaris to C. elegans: A Way to Study Gene Structure and Function"

Tobler H, Huang Y-J, Mueller F

[Worm Breeder's Gazette, 1994]

FROM ASCARIS TO C. ELEGANS: A WAY TO STUDY GENE STRUCTURE AND FUNCTION Huang Y-J., Tobler H. and Muller F., Institute of Zoology, University of Pribourg, Perolles, CH-1700 Fribourg, Switzerland

Imadzu H et al. (1994) Worm Breeder's Gazette "Two Tropomyosins Expressed in Body Wall and the Third Did In Pharynx of Caenorhabditis elegans"

Kagawa H, Sakube Y, Imadzu H

[Worm Breeder's Gazette, 1994]

TWO TROPOMYOSINS EXPRBSSBD IN BODY WALL AND THE THIRD DID IN PHARYNX OF CAENORHABDDITIS ELEGANS. H. Imadzu, Y. Sakube and H. gagawa. Department of Biology, Faculty of Science, Okayama University, Okayama, 700 Japan.

Plasterk RHA et al. (1994) Worm Breeder's Gazette "Reverse Genetics Using Transposon Tc1: A Progress Report"

Plasterk RHA, de Vroomen M

[Worm Breeder's Gazette, 1994]

Reverse genetics using transposon Tcl: A progress report Ronald H.A. Plasterk, Marianne de Vroomen, the Netherlands Cancer Institute, Division of Molecular Biology, Plesmanlaan 121,1066 CX Amsterdam, the Netherlands, fax + 31 20 6172625, phone +31 20 5122081, E-mail RPLAS@NKI.NL

Sakube Y et al. (1994) Worm Breeder's Gazette "The Genome Structure and Expression of Promoter/lacZ Fusion Genes of C. elegans Ryanodine Receptor"

Imadzu H, Sakube Y, Kagawa H

[Worm Breeder's Gazette, 1994]

The Genome Structure and Expression of Promoter/lacZ Fusion Genes of the C. elegans Ryanodine Receptor Y. Sakube, H. Imadzu and H. Kagawa, Laboratory of Molecular Biology, Faculty of Science, Okayama University, Okayama, 700 Japan C51918@JPNKUDPC

Kitamura S et al. (1994) Worm Breeder's Gazette "The Troponin C Gene, tnc-1, of Caenorhabditis elegans: Genome Structure and Mutation Sites of pat-10"

Williams BD, Kitamura S, Kagawa H, Sakube Y, Matsumoto S

[Worm Breeder's Gazette, 1994]

The troponin C gene, tnc-1 of Caenorhabditis elegans: Genome structure and mutation sites of pat-10 S. KITAMURA, B. WILLIAMS*, Y. SAKUBE, S. MATSUMOTO and H. KAGAWA, Dept. of Biol., Fac. of Sci., Okayama University, Japan, 700. *;Dept. of Gen., Washington Univ. School of Med., St. Louis