Translational recoding signals between <i>gag</i> and <i>pol</i> in diverse LTR retrotransposons

Gao, Xiang; Havecker, Ericka R.; Baranov, Pavel V.; Atkins, John F.; Voytas, Daniel F.

doi:10.1261/rna.5105503

Cited by 80 publications

(79 citation statements)

References 49 publications

(46 reference statements)

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“…The splicing of CRR transcripts is unique in that at least two regions, both of which are different from the spliced regions in the three abovementioned retrotransposons, are spliced from autonomous CRR elements. CRR elements seem to encode all protein domains within a single ORF and thus cannot regulate the GAG (GAG-PRO) to GAG-PRO-POL ratio by the two common translational recoding mechanisms on the basis of stop-codon readthrough or ribosomal frameshifting (Swanstrom and Wills 1997;Vogt 1997;Gao et al 2003). However, as GAG is generally required in a higher molar amount than POL (Swanstrom and Wills 1997), CRRs must use a strategy that favors expression of GAG or GAG-PRO over GAG-PRO-POL polyproteins.…”

Section: Discussionmentioning

confidence: 99%

The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference

2007

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Retrotransposons consist of significant portions of many complex eukaryotic genomes and are often enriched in heterochromatin. The centromeric retrotransposon (CR) family in grass species is colonized in the centromeres and highly conserved among species that have been diverged for .50 MY. These unique characteristics have inspired scientists to speculate about the roles of CR elements in organization and function of centromeric chromatin. Here we report that the CRR (CR of rice) elements in rice are highly enriched in chromatin associated with H3K9me2, a hallmark for heterochromatin. CRR elements were transcribed in root, leaf, and panicle tissues, suggesting a constitutive transcription of this retrotransposon family. However, the overall transcription level was low and the CRR transcripts appeared to be derived from relatively few loci. The majority of the CRR transcripts had chimerical structures and contained only partial CRR sequences. We detected small RNAs (smRNAs) cognate to nonautonomous CRR1 (noaCRR1) and CRR1, but not CRR2 elements. This result was also confirmed by in silico analysis of rice smRNA sequences. These results suggest that different CRR subfamilies may play different roles in the RNAimediated pathway for formation and maintenance of centromeric heterochromatin.

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Section: Discussionmentioning

confidence: 99%

The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference

2007

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“…It is perhaps not surprising that a proportion of them also utilize frameshifting, which is well known in the decoding of retroviruses and, to an increasing extent, in retroelements (31,34), including in mammalian cells (35), yeast (36), and Drosophila (37).…”

Section: Discussionmentioning

confidence: 99%

A Functional –1 Ribosomal Frameshift Signal in the Human Paraneoplastic Ma3 Gene

Wills

Moore

Hammer

et al. 2006

Journal of Biological Chemistry

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A bioinformatics approach to finding new cases of ؊1 frameshifting in the expression of human genes revealed a classical retroviruslike 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 frameshifting. 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.Although nonoverlapping triplet reading of mRNA codons is the essence of genetic decoding, dynamic nonstandard events at specific sites can permit product diversity and provide regulatory options. One of these recoding events involves shifting to an alternative reading frame by a proportion of ribosomes, thereby changing the linearity of readout. Such utilized frameshifting commonly features both a "shifty site" in the mRNA and an appropriately positioned structural feature in the mRNA that acts to enhance the level of frameshifting, i.e. it is programmed. Although the shift involved can be to either alternative frame, a shift to the Ϫ1 frame often involves tRNAs in both the A and P sites detaching from their codons and re-pairing to mRNA at the two overlapping Ϫ1 frame codons (1, 2). This tandem detachment and re-pairing usually occurs on a "slippery" heptanucleotide sequence that follows the general pattern of X XXY YYZ where the A and P site tRNAs detach from the zero frame codons XXY YYZ and re-pair after shifting 1 nucleotide to XXX YYY. The spacer region between the shift site and the 3Ј structural element is commonly 6 -8 nt 2 (3). The most common 3Ј recoding signals for Ϫ1 frameshifting are pseudoknots (4, 5) with distinct features (6, 7). A less common type of pseudoknot is the kissing stem-loop found in the human coronavirus, HCV229E (8), but bioinformatic studies suggest that it may be involved for transmissible gastroenteritis virus frameshifting also (9).Examples of genes that require Ϫ1 frameshifting for expression are well known in viral genomes. There is only one demonstrated case of Ϫ1 frameshifting in a mammalian cellular gene (10, 11), but it does not display the phylogenetic breadth of the ϩ1 frameshifting utilized in decoding antizyme mRNA, conserved from mammals to yeasts (12). Frameshifting near the end of a coding sequence often allows a proportion of ribosomes to access an ORF that extends beyond the zero frame terminator so that the transframe (coupled ORF) protein is longer than that of standard decoding. The easiest class of Ϫ1 programmed frameshift events to search for is one that has conserved architecture of two ORFs that partially overlap and contains a defined shift site. In these cases conser...

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“…We previously described a phylogenetic analysis of Ty1/copia RT sequences retrieved from GenBank using the Sirevirus Opie-2 RT as an electronic probe (Gao et al, 2003). Two striking features were observed.…”

Section: Genomic Organization Of the Sirevirusesmentioning

confidence: 99%

The Sireviruses, a Plant-Specific Lineage of the Ty1/copia Retrotransposons, Interact with a Family of Proteins Related to Dynein Light Chain 8

2005

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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.

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Translational recoding signals between gag and pol in diverse LTR retrotransposons

Cited by 80 publications

References 49 publications

The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference

The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference

A Functional –1 Ribosomal Frameshift Signal in the Human Paraneoplastic Ma3 Gene

The Sireviruses, a Plant-Specific Lineage of the Ty1/copia Retrotransposons, Interact with a Family of Proteins Related to Dynein Light Chain 8

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