Translational recoding signals between gag and pol in diverse LTR retrotransposons

Identification of functional, endogenous programmed -1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae

In viruses, programmed -1 ribosomal frameshifting (-1 PRF) signals direct the translation of alternative proteins from a single mRNA. Given that many basic regulatory mechanisms were first discovered in viral systems, the current study endeavored to: (i) identify -1 PRF signals in genomic databases, (ii) apply the protocol to the yeast genome and (iii) test selected candidates at the bench. Computational analyses revealed the presence of 10 340 consensus -1 PRF signals in the yeast genome. Of the 6353 yeast ORFs, 1275 contain at least one strong and statistically significant -1 PRF signal. Eight out of nine selected sequences promoted efficient levels of PRF in vivo. These findings provide a robust platform for high throughput computational and laboratory studies and demonstrate that functional -1 PRF signals are widespread in the genome of Saccharomyces cerevisiae. The data generated by this study have been deposited into a publicly available database called the PRFdb. The presence of stable mRNA pseudoknot structures in these -1 PRF signals, and the observation that the predicted outcomes of nearly all of these genomic frameshift signals would direct ribosomes to premature termination codons, suggest two possible mRNA destabilization pathways through which -1 PRF signals could post-transcriptionally regulate mRNA abundance.

Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome

LTR (long terminal repeat) retrotransposons are the main components of higher plant genomic DNA. They have shaped their host genomes through insertional mutagenesis and by effects on genome size, gene expression and recombination. These Class I transposable elements are closely related to retroviruses such as the HIV by their structure and presumptive life cycle. However, the retrotransposon life cycle has been closely investigated in few systems. For retroviruses and retrotransposons, individual defective copies can parasitize the activity of functional ones. However, some LTR retrotransposon groups as a whole, such as large retrotransposon derivatives and terminal repeats in miniature, are non-autonomous even though their genomic insertion patterns remain polymorphic between organismal accessions. Here, we examine what is known of the retrotransposon life cycle in plants, and in that context discuss the role of parasitism and complementation between and within retrotransposon groups.

Ogre elements--a distinct group of plant Ty3/gypsy-like retrotransposons

Ogre elements are a group of LTR retrotransposons recently discovered in legume plants, where they constitute almost 40% of the genome in some species. They are exceptional in their size (reaching 25 kb) and possess several specific features, including an intron within a polyprotein-coding region, and an extra open reading frame (ORF1) encoding a protein of unknown function located upstream of the gag gene. Although these features make Ogres interesting for further research, identification of additional elements from a broader range of plant taxa has been complicated by the divergence of their sequences, preventing their detection using similarity-based searches. Here we report the results of structure-based computational searches for Ogre elements in available plant genomic sequences, which proved to be more efficient and revealed occurrences of Ogres in three families of dicot plants (Leguminosae, Solanaceae and Salicaceae). In addition, a representative set of 85 elements was retrieved from a model legume species Medicago truncatula. All identified full-length elements were used for comparative analysis, which showed that in spite of only little conservation of their nucleotide sequences, their protein domains were highly conserved, including several regions within ORF1. Further, the elements shared the same functional regions, including a primer binding site complementary to tRNA(arg), a conserved motif within a polypurine tract, and a putative intron between the pro and rt/rh coding domains. These findings, together with analysis of their phylogenetic relationship to other retrotransposons based on similarities of rt domains suggest that Ogre elements from different plant taxa have a common origin and thus constitute a distinct group of Ty3/gypsy retrotransposons.

Recoding in bacteriophages and bacterial IS elements

Dynamic shifts between open reading frames and the redefinition of codon meaning at specific sites, programmed by signals in mRNA, permits versatility of gene expression. Such alterations are characteristic of organisms in all domains of life and serve a variety of functional purposes. In this article, we concentrate on programmed ribosomal frameshifting, stop codon read-through and transcriptional slippage in the decoding of phage genes and bacterial mobile elements. Together with their eukaryotic counterparts, the genes encoding these elements are the richest known source of nonstandard decoding. Recent analyses revealed several novel sequences encoding programmed alterations in gene decoding and provide a glimpse of the emerging picture.

A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene

A bioinformatics approach to finding new cases of -1 frameshifting in the expression of human genes revealed a classical retrovirus-like heptanucleotide shift site followed by a potential structural stimulator in the paraneoplastic antigen Ma3 and Ma5 genes. Analysis of the sequence 3' of the shift site demonstrated that an RNA pseudoknot in Ma3 is important for promoting efficient -1 frame-shifting. Ma3 is a member of a family of six genes in humans whose protein products contain homology to retroviral Gag proteins. The -1 frameshift site and pseudoknot structure are conserved in other mammals, but there are some sequence differences. Although the functions of the Ma genes are unknown, the serious neurological effects of ectopic expression in tumor cells indicate their importance in the brain.

Tyl6, a novel Ty3/gypsy-like retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica

The novel LTR retrotransposon Tyl6 was detected in the genome of the dimorphic fungus Yarrowia lipolytica. Sequence analysis revealed that this element is related to the well-known Ty3 element of Saccharomyces cerevisiae and, especially, to the recently described Tse3 retrotransposon of Saccharomyces exiguus and to the del1-like plant retrotransposons. Tyl6 is 5108 bp long, is flanked by two identical long terminal repeats (LTR), each of 276 bp, and its ORFs are separated by a -1 frameshift. Both ORFs are intact and deduced translation products display a significant similarity with those of previously described Ty3/gypsy retrotransposons. Distribution of Tyl6 among Y. lipolytica strains of different origins was also analysed. A single copy of the novel retrotransposon is present in some commonly used laboratory strains, which are derivatives of the wild-type isolate YB423-12, whereas other strains of independent origin are devoid of Ty16. No solo LTR of Tyl6 was detected in the analysed strains.

The Sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, interact with a family of proteins related to dynein light chain 8

Plant genomes are rich in long terminal repeat retrotransposons, and here we describe a plant-specific lineage of Ty1/copia elements called the Sireviruses. The Sireviruses vary greatly in their genomic organization, and many have acquired additional coding information in the form of an envelope-like open reading frame and an extended gag gene. Two-hybrid screens were conducted with the novel domain of Gag (the Gag extension) encoded by a representative Sirevirus from maize (Zea mays) called Hopie. The Hopie Gag extension interacts with a protein related to dynein light chain 8 (LC8). LC8 also interacts with the Gag extension from a Hopie homolog from rice (Oryza sativa). Amino acid motifs were identified in both Hopie Gag and LC8 that are responsible for the interaction. Two amino acids critical for Gag recognition map within the predicted LC8-binding cleft. Two-hybrid screens were also conducted with the Gag extension encoded by the soybean (Glycine max) SIRE1 element, and an interaction was found with light chain 6 (LC6), a member of the LC8 protein family. LC8 and LC6 proteins are components of the dynein microtubule motor, with LC8 being a versatile adapter that can bind many unrelated cellular proteins and viruses. Plant LC8 and LC6 genes are abundant and divergent, yet flowering plants do not encode other components of the dynein motor. Although, to our knowledge, no cellular roles for plant LC8 family members have been proposed, we hypothesize that binding of LC8 proteins to Gag aids in the movement of retrotransposon virus-like particles within the plant cell or possibly induces important conformational changes in the Gag protein.

Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG_AGG and AGA_AGA in Escherichia coli

The rare codons AGG and AGA comprise 2% and 4%, respectively, of the arginine codons of Escherichia coli K-12, and their cognate tRNAs are sparse. At tandem occurrences of either rare codon, the paucity of cognate aminoacyl tRNAs for the second codon of the pair facilitates peptidyl-tRNA shifting to the +1 frame. However, AGG_AGG and AGA_AGA are not underrepresented and occur 4 and 42 times, respectively, in E. coli genes. Searches for corresponding occurrences in other bacteria provide no strong support for the functional utilization of frameshifting at these sequences. All sequences tested in their native context showed 1.5 to 11% frameshifting when expressed from multicopy plasmids. A cassette with one of these sequences singly integrated into the chromosome in stringent cells gave 0.9% frameshifting in contrast to two- to four-times-higher values obtained from multicopy plasmids in stringent cells and eight-times-higher values in relaxed cells. Thus, +1 frameshifting efficiency at AGG_AGG and AGA_AGA is influenced by the mRNA expression level. These tandem rare codons do not occur in highly expressed mRNAs.

Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae

The recent availability of the genome of Anopheles gambiae offers an extraordinary opportunity for comparative studies of the diversity of transposable elements (TEs) and their evolutionary dynamics between two related species, taking advantage of the existing information from Drosophila melanogaster. To this goal, we screened the genome of A. gambiae for elements belonging to the Ty3/gypsy group of long-terminal repeat (LTR) retrotransposons. The A. gambiae genome displays a rich diversity of LTR retrotransposons, clearly greater than D. melanogaster. We have characterized in detail 63 families, belonging to five of the nine main lineages of the Ty3/gypsy group. The Mag lineage is the most diverse and abundant, with more than 30 families. In sharp contrast with this finding, a single family belonging to this lineage has been found in D. melanogaster, here reported for the first time in the literature, most probably consisting of old inactive elements. The CsRn1 lineage is also abundant in A. gambiae but almost absent from D. melanogaster. Conversely, the Osvaldo lineage has been detected in Drosophila but not in Anopheles. Comparison of structural characteristics of different families led to the identification of several lineage-specific features such as the primer-binding site (PBS), the gag-pol translational recoding signal (TRS), which is extraordinarily diverse within the Ty3/gypsy retrotransposons of A. gambiae, or the presence/absence of specific amino acid motifs. Interestingly, some of these characteristics, although in general well conserved within lineages, may have evolved independently in particular branches of the phylogenetic tree. We also show evidence of recent activity for around 75% of the families. Nevertheless, almost all families contain a high proportion of degenerate members and solitary LTRs (solo LTRs), indicative of a lower turnover rate of retrotransposons belonging to the Ty3/gypsy group in A. gambiae than in D. melanogaster. Finally, we have detected significant overrepresentations of insertions on the X chromosome versus autosomes and of putatively active insertions on euchromatin versus heterochromatin.

The diversity of LTR retrotransposons

Although most long terminal repeat retrotransposons have common structural features and encode similar genes, there is nonetheless considerable diversity.

Eukaryotic genomes are full of long terminal repeat (LTR) retrotransposons. Although most LTR retrotransposons have common structural features and encode similar genes, there is nonetheless considerable diversity in their genomic organization, reflecting the different strategies they use to proliferate within the genomes of their hosts.

A programmed -1 ribosomal frameshift signal can function as a cis-acting mRNA destabilizing element

Nonsense-mediated mRNA decay (NMD) directs rapid degradation of premature termination codon (PTC)-containing mRNAs, e.g. those containing frameshift mutations. Many viral mRNAs encode polycistronic messages where programmed -1 ribosomal frameshift (-1 PRF) signals direct ribosomes to synthesize polyproteins. A previous study, which identified consensus -1 PRF signals in the yeast genome, found that, in contrast to viruses, the majority of predicted -1 PRF events would direct translating ribosomes to PTCs. Here we tested the hypothesis that a -1 PRF signal can function as a cis-acting mRNA destabilizing element by inserting an L-A viral -1 PRF signal into a PGK1 reporter construct in the 'genomic' orientation. The results show that even low levels of -1 PRF are sufficient to target the reporter mRNA for degradation via the NMD pathway, with half-lives similar to messages containing in-frame PTCs. The demonstration of an inverse correlation between frameshift efficiency and mRNA half-lives suggests that modulation of -1 PRF frequencies can be used to post-transcriptionally regulate gene expression. Analysis of the mRNA decay profiles of the frameshift-signal- containing reporter mRNAs also supports the notion that NMD remains active on mRNAs beyond the 'pioneer round' of translation in yeast.