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

Link CD, Felder H, Maller F, 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 "PAT elements, candidates for an adequate transposon tagging system in C. elegans."

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

[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.

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

de Chastonay Y, Mueller F, 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.

Perreault J et al. (2007) Mol Biol Evol "Ro-associated Y RNAs in metazoans: evolution and diversification."

Perreault JP, Boire G, Perreault J

[Mol Biol Evol, 2007]

The Y genes encode small non-coding RNAs whose functions remain elusive, whose numbers vary between species, and whose major property is to be bound by the Ro60 protein (or its ortholog in other species). To better understand the evolution of the Y gene family, we performed a homology search in 27 different genomes along with a structural search using Y RNA specific motifs. These searches confirmed that Y RNAs are well conserved in the animal kingdom and resulted in the detection of several new Y RNA genes, including the first Y RNAs in insects and a second Y RNA detected in Caenorhabditis elegans. Unexpectedly, Y5 genes were retrieved almost as frequently as Y1 and Y3 genes, and, consequently are not the result of a relatively recent apparition as is generally believed. Investigation of the organization of the Y genes demonstrated that the synteny was conserved among species. Interestingly, it revealed the presence of six putative "fossil" Y genes, all of which were Y4 and Y5 related. Sequence analysis led to inference of the ancestral sequences for all Y RNAs. In addition, the evolution of existing Y RNAs was deduced for many families, orders and classes. Moreover, a consensus sequence and secondary structure for each Y species was determined. Further evolutionary insight was obtained from the analysis of several thousand Y retropseudogenes among various species. Taken together, these results confirm the rich and diversified evolution history of Y RNAs.

Yamaguchi M et al. (2016) Biochim Biophys Acta "NF-Y in invertebrates."

Ali MS, Ly LL, Yoshida H, Yamaguchi M, Yoshioka Y

[Biochim Biophys Acta, 2016]

BothDrosophila melanogaster and Caenorhabditis elegans (C. elegans) are useful model organisms to study in vivo roles of NF-Y during development. Drosophila NF-Y (dNF-Y) consists of three subunits dNF-YA, dNF-YB and dNF-YC. In some tissues, dNF-YC-related protein Mes4 may replace dNF-YC in dNF-Y complex. Studies with eye imaginal disc-specific dNF-Y-knockdown flies revealed that dNF-Y positively regulates the sevenless gene encoding a receptor tyrosine kinase, a component of the ERK pathway and negatively regulates the Sensless gene encoding a transcription factor to ensure proper development of R7 photoreceptor cells together with proper R7 axon targeting. dNF-Y also controls the Drosophila Bcl-2 (debcl) to regulate apoptosis. In thorax development, dNF-Y is necessary for both proper Drosophila JNK (basket) expression and JNK signaling activity that is responsible for thorax development. Drosophila p53 gene was also identified as one of the dNF-Y target genes in this system. C. elegans contains two forms of NF-YA subunit, CeNF-YA1 and CeNF-YA2. C. elegans NF-Y (CeNF-Y) therefore consists of CeNF-YB, CeNF-YC and either CeNF-YA1 or CeNF-YA2. CeNF-Y negatively regulates expression of the Hox gene egl-5 (ortholog of Drosophila Abdominal-B) that is involved in tail patterning. CeNF-Y also negatively regulates expression of the tbx-2 gene that is essential for development of the pharyngeal muscles, specification of neural cell fate and adaptation in olfactory neurons. Negative regulation of the expression of egl-5 and tbx-2 by CeNF-Y provides new insight into the physiological meaning of negative regulation of gene expression by NF-Y during development. In addition, studies on NF-Y in platyhelminths are also summarized.

Burns RG (1996) Trends in Cell Biology "Reply: Defining the gamma-, delta- and epsilon-tubulins."

Burns RG

[Trends in Cell Biology, 1996]

Keeling and Logsdon propose that the y-like sequences from Caenorhabditis elegans and Saccharomyces cerevisiae are bona fide y-tubulins that have undergone rapid evolutionary divergence. Indeed, genetic and localization studies with the yeast epsilon-tubulin (encoded by the TUB4 gene) reveal striking similarities to the bona fide y-tubulins, whereas there is no apparent human analogue to the C. elegans delta-tubulin among the 60 available human y-tubulin expressed-sequence tags. (ESTs).

Gardiner TJ et al. (2009) RNA "A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication."

Langley AR, Krude T, Christov CP, Gardiner TJ

[RNA, 2009]

Noncoding Y RNAs are required for the reconstitution of chromosomal DNA replication in late G1 phase template nuclei in a human cell-free system. Y RNA genes are present in all vertebrates and in some isolated nonvertebrates, but the conservation of Y RNA function and key determinants for its function are unknown. Here, we identify a determinant of Y RNA function in DNA replication, which is conserved throughout vertebrate evolution. Vertebrate Y RNAs are able to reconstitute chromosomal DNA replication in the human cell-free DNA replication system, but nonvertebrate Y RNAs are not. A conserved nucleotide sequence motif in the double-stranded stem of vertebrate Y RNAs correlates with Y RNA function. A functional screen of human Y1 RNA mutants identified this conserved motif as an essential determinant for reconstituting DNA replication in vitro. Double-stranded RNA oligonucleotides comprising this RNA motif are sufficient to reconstitute DNA replication, but corresponding DNA or random sequence RNA oligonucleotides are not. In intact cells, wild-type hY1 or the conserved RNA duplex can rescue an inhibition of DNA replication after RNA interference against hY3 RNA. Therefore, we have identified a new RNA motif that is conserved in vertebrate Y RNA evolution, and essential and sufficient for Y RNA function in human chromosomal DNA replication.

Erickson DL et al. (2006) J Bacteriol "Serotype differences and lack of biofilm formation characterize Yersinia pseudotuberculosis infection of the Xenopsylla cheopis flea vector of Yersinia pestis."

Jarrett CO, Erickson DL, Wren BW, Hinnebusch BJ

[J Bacteriol, 2006]

Yersinia pestis, the agent of plague, is usually transmitted by fleas. To produce a transmissible infection, Y. pestis colonizes the flea midgut and forms a biofilm in the proventricular valve, which blocks normal blood feeding. The enteropathogen Yersinia pseudotuberculosis, from which Y. pestis recently evolved, is not transmitted by fleas. However, both Y. pestis and Y. pseudotuberculosis form biofilms that adhere to the external mouthparts and block feeding of Caenorhabditis elegans nematodes, which has been proposed as a model of Y. pestis-flea interactions. We compared the ability of Y. pestis and Y. pseudotuberculosis to infect the rat flea Xenopsylla cheopis and to produce biofilms in the flea and in vitro. Five of 18 Y. pseudotuberculosis strains, encompassing seven serotypes, including all three serotype O3 strains tested, were unable to stably colonize the flea midgut. The other strains persisted in the flea midgut for 4 weeks but did not increase in numbers, and none of the 18 strains colonized the proventriculus or produced a biofilm in the flea. Y. pseudotuberculosis strains also varied greatly in their ability to produce biofilms in vitro, but there was no correlation between biofilm phenotype in vitro or on the surface of C. elegans and the ability to colonize or block fleas. Our results support a model in which a genetic change in the Y. pseudotuberculosis progenitor of Y. pestis extended its pre-existing ex vivo biofilm-forming ability to the flea gut environment, thus enabling proventricular blockage and efficient flea-borne transmission.

Sato, Manami et al. (2015) International Worm Meeting "Expression pattern of C. elegans Y RNA homologs."

Ushida, Chisato, Kihara, Shinya, Sato, Manami

[International Worm Meeting, 2015]

Y RNA is a small structured ncRNA of about 100 nt in length. This RNA binds to Ro60 protein, which is a target of autoimmune disease antibody in patients with systemic lupus erythematosus and Sjogren's syndrome. Several lines of evidence suggest that the role of Y RNA and Ro60 function in the quality control of structured ncRNAs in cells under stress conditions. It is also indicated that vertebrate Y RNAs function in the initiation of DNA replication without Ro60. However, the molecular mechanisms of these functions and the contribution of Ro60/Y RNP to the autoimmune disease are still unclear. C. elegans genome encodes one Ro60 homolog (ROP-1) and 19 Y RNA homologs (1 CeY RNA and 18 sbRNAs). Other animals also have several Y RNA homologs, but C. elegans is the first example which has more than 5 Y RNA homologs encoded in the genome. Here we show the expression pattern and the cellular localization of these Y RNA homologs in C. elegans examined by the RNA fluorescent in situ hybridization (RNA-FISH). The signals of 14 homologs were detected in the intestinal cytoplasm. The signals of two other homologs were detected in the germ cytoplasm. The remaining three could not be detected, probably because they present in too low abundance to be detected by RNA-FISH. All 19 Y RNA homologs have the structural elements required for the binding of ROP-1. In other organisms, Ro60 binding stabilizes Y RNAs in cells. To know whether C. elegans Y RNA homologs also stabilized by the presence of ROP-1, we examined RNA-FISH of the Y RNA homologs against a mutant strain MQ470, which has a transposon insertion in the middle of the ROP-1 gene and lacks ROP-1 proteins in the cell. As expected, all Y RNAs examined so far decreased extensively. These were confirmed by northern hybridization. The results suggest that several C. elegans Y RNA homologs are expressed in a tissue-specific manner and most Y RNA homologs are stabilized by ROP-1 binding as well as those in other organisms.

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

De Bono M, Zarkower D, Hodgkin JA

[Worm Breeder's Gazette, 1994]

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